Enzyme Nomenclature

Continued from EC 5.3.3 to EC 5.3.99

EC 5.4

Intramolecular Transferases

Sections

EC 5.4.1 Transferring Acyl Groups
EC 5.4.2 Phosphotransferases (Phosphomutases)
EC 5.4.3 Transferring Amino Groups
EC 5.4.4 Transferring Hydroxy Groups
EC 5.4.99 Transferring Other Groups


EC 5.4.1 Transferring Acyl Groups

Contents

EC 5.4.1.1 lysolecithin acylmutase
EC 5.4.1.2 transferred now EC 5.4.99.61
EC 5.4.1.3 2-methylfumaryl-CoA isomerase
EC 5.4.1.4 D-galactarolactone isomerase

Entries

EC 5.4.1.1

Accepted name: lysolecithin acylmutase

Reaction: 2-lysolecithin = 3-lysolecithin

Other name(s): lysolecithin migratase

Systematic name: lysolecithin 2,3-acylmutase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9031-24-7

References:

1. Uziel, M. and Hanahan, D.J. An enzyme-catalyzed acyl migration: a lysolecithin migratase. J. Biol. Chem. 226 (1957) 789-798.

[EC 5.4.1.1 created 1961]

[EC 5.4.1.2 Transferred entry: precorrin-8X methylmutase. Now classified as EC 5.4.99.61, precorrin-8X methylmutase. (EC 5.4.1.2 created 1999, deleted 2014)]

EC 5.4.1.3

Accepted name: 2-methylfumaryl-CoA isomerase

Reaction: 2-methylfumaryl-CoA = 3-methylfumaryl-CoA

For diagram of reaction click here.

Glossary: 2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA
3-methylfumaryl-CoA = (E)-3-carboxybut-2-enoyl-CoA

Other name(s): mesaconyl-CoA C1-C4 CoA transferase; Mct

Systematic name: 2-methylfumaryl-CoA 1,4-CoA-mutase

Comments: The enzyme, purified from the bacterium Chloroflexus aurantiacus, acts as an intramolecular CoA transferase and does not transfer CoA to free mesaconate. It is part of the 3-hydroxypropanoate cycle for carbon assimilation.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Zarzycki, J., Brecht, V., Muller, M. and Fuchs, G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. USA 106 (2009) 21317-21322. [PMID: 19955419]

[EC 5.4.1.3 created 2014]

EC 5.4.1.4

Accepted name: D-galactarolactone isomerase

Reaction: D-galactaro-1,5-lactone = D-galactaro-1,4-lactone

Other name(s): GLI

Systematic name: D-galactaro-1,5-lactone isomerase (D-galactaro-1,4-lactone-forming)

Comments: The enzyme, characterized from the bacterium Agrobacterium fabrum strain C58, belongs to the amidohydrolase superfamily. It participates in the degradation of D-galacturonate.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Bouvier, J.T., Groninger-Poe, F.P., Vetting, M., Almo, S.C. and Gerlt, J.A. Galactaro δ-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily. Biochemistry 53 (2014) 614-616. [PMID: 24450804]

[EC 5.4.1.4 created 2015]


EC 5.4.2 Phosphotransferases (Phosphomutases)

Contents

EC 5.4.2.1 transferred now EC 5.4.2.11 and EC 5.4.2.12
EC 5.4.2.2 phosphoglucomutase (α-D-glucose-1,6-bisphosphate-dependent)
EC 5.4.2.3 phosphoacetylglucosamine mutase
EC 5.4.2.4 bisphosphoglycerate mutase
EC 5.4.2.5 phosphoglucomutase (glucose-cofactor)
EC 5.4.2.6 β-phosphoglucomutase
EC 5.4.2.7 phosphopentomutase
EC 5.4.2.8 phosphomannomutase
EC 5.4.2.9 phosphoenolpyruvate mutase
EC 5.4.2.10 phosphoglucosamine mutase

EC 5.4.2.11 phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
EC 5.4.2.12 phosphoglycerate mutase (2,3-diphosphoglycerate-independent)


Entries

[EC 5.4.2.1 Transferred entry: phosphoglycerate mutase. Now recognized as two separate enzymes EC 5.4.2.11, phosphoglycerate mutase (2,3-diphosphoglycerate-cofactor) and EC 5.4.2.12, phosphoglycerate mutase (Mn2+/Co2+ dependent) (EC 5.4.2.1 created 1961 (EC 2.7.5.3 created 1961, incorporated 1984), deleted 2013)]

EC 5.4.2.2

Accepted name: phosphoglucomutase (α-D-glucose-1,6-bisphosphate-dependent)

Reaction: α-D-glucose 1-phosphate = D-glucose 6-phosphate

For diagram click here.

Other name(s): glucose phosphomutase; phosphoglucose mutase

Systematic name: α-D-glucose 1,6-phosphomutase

Comments: Maximum activity is only obtained in the presence of α-D-glucose 1,6-bisphosphate. This bisphosphate is an intermediate in the reaction, being formed by transfer of a phosphate residue from the enzyme to the substrate, but the dissociation of bisphosphate from the enzyme complex is much slower than the overall isomerization. The enzyme also catalyses (more slowly) the interconversion of 1-phosphate and 6-phosphate isomers of many other α-D-hexoses, and the interconversion of α-D-ribose 1-phosphate and 5-phosphate. EC 5.4.2.5, phosphoglucomutase (glucose-cofactor).

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9001-81-4

References:

1. Joshi, J.G. and Handler, P. Phosphoglucomutase. I. Purification and properties of phosphoglucomutase from Escherichia coli. J. Biol. Chem. 239 (1964) 2741-2751. [PMID: 14216423]

2. Najjar, V.A. Phosphoglucomutase, in Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds.), The Enzymes, 2nd edn., vol. 6, Academic Press, New York, 1962, pp. 161-178.

3. Ray, W.J. and Roscelli, G.A. A kinetic study of the phosphoglucomutase pathway. J. Biol. Chem. 239 (1964) 1228-1236.

4. Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases, in Boyer, P.D. (Ed.), The Enzymes, 3rd edn., vol. 6, Academic Press, New York , 1972, pp. 407-477.

5. Sutherland, E.W., Cohn, M., Posternak, T. and Cori, C.F. The mechanism of the phosphoglucomutase reaction. J. Biol. Chem. 180 (1949) 1285-1295.

[EC 5.4.2.2 created 1961 as EC 2.7.5.1, transferred 1984 to EC 5.4.2.2]

EC 5.4.2.3

Accepted name: phosphoacetylglucosamine mutase

Reaction: N-acetyl-α-D-glucosamine 1-phosphate = N-acetyl-D-glucosamine 6-phosphate

For diagram click here.

Other name(s): acetylglucosamine phosphomutase; acetylglucosamine phosphomutase; acetylaminodeoxyglucose phosphomutase; phospho-N-acetylglucosamine mutase; N-acetyl-D-glucosamine 1,6-phosphomutase

Systematic name: N-acetyl-α-D-glucosamine 1,6-phosphomutase

Comments: The enzyme is activated by N-acetyl-α-D-glucosamine 1,6-bisphosphate. Formerly EC 2.7.5.2.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9027-51-4

References:

1. Carlson, D.M. Phosphoacetylglucosamine mutase from pig submaxillary gland. Methods Enzymol. 8 (1966) 179-182.

2. Leloir, L.F. and Cardini, C.E. Enzymes acting on glucosamine phosphates. Biochim. Biophys. Acta 20 (1956) 33-42.

3. Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases, in Boyer, P.D. (Ed.), The Enzymes, 3rd edn., vol. 6, Academic Press, New York , 1972, pp. 407-477.

4. Reissig, J.L. and Leloir, L.F. Phosphoacetylglucosamine mutase from Neurospora. Methods Enzymol. 8 (1966) 175-178.

[EC 5.4.2.3 created 1961 as EC 2.7.5.2, transferred 1984 to EC 5.4.2.3]

EC 5.4.2.4

Accepted name: bisphosphoglycerate mutase

Reaction: 3-phospho-D-glyceroyl phosphate = 2,3-bisphospho-D-glycerate

Other name(s): diphosphoglycerate mutase; glycerate phosphomutase; bisphosphoglycerate synthase; bisphosphoglyceromutase; biphosphoglycerate synthase; diphosphoglyceric mutase; 2,3-diphosphoglycerate mutase; phosphoglyceromutase; 2,3-diphosphoglycerate synthase; DPGM; 2,3-bisphosphoglycerate mutase; BPGM; diphosphoglyceromutase; 2,3-diphosphoglyceromutase

Systematic name: 3-phospho-D-glycerate 1,2-phosphomutase

Comments: In the direction shown, this enzyme is phosphorylated by 3-phosphoglyceroyl phosphate, to give phosphoenzyme and 3-phosphoglycerate. The latter is rephosphorylated by the enzyme to yield 2,3-bisphosphoglycerate, but this reaction is slowed by dissociation of 3-phosphoglycerate from the enzyme, which is therefore more active in the presence of added 3-phosphoglycerate. This enzyme also catalyses, slowly, the reactions of EC 3.1.3.13 (bisphosphoglycerate phosphatase) and EC 5.4.2.1 (phosphoglycerate mutase). Formerly EC 2.7.5.4.

Comments: In the direction shown, this enzyme is phosphorylated by 3-phosphoglyceroyl phosphate, to give phosphoenzyme and 3-phosphoglycerate. The latter is rephosphorylated by the enzyme to yield 2,3-bisphosphoglycerate, but this reaction is slowed by dissociation of 3-phosphoglycerate from the enzyme, which is therefore more active in the presence of added 3-phosphoglycerate. This enzyme also catalyses, slowly, the reactions of EC 3.1.3.13 (bisphosphoglycerate phosphatase), EC 5.4.2.11 [phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)] and EC 5.4.2.12 [phosphoglycerate mutase (2,3-diphosphoglycerate-independent)].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37211-69-1

References:

1. Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases, in Boyer, P.D. (Ed.), The Enzymes, 3rd edn., vol. 6, Academic Press, New York , 1972, pp. 407-477.

2. Rose, Z.B. The purification and properties of diphosphoglycerate mutase from human erythrocytes. J. Biol. Chem. 243 (1968) 4810-4820. [PMID: 5687724]

3. Rose, Z.B. The enzymology of 2,3-bisphosphoglycerate. Adv. Enzymol. Relat. Areas Mol. Biol. 51 (1980) 211-253. [PMID: 6255773]

[EC 5.4.2.4 created 1961 as EC 2.7.5.4, transferred 1984 to EC 5.4.2.4]

EC 5.4.2.5

Accepted name: phosphoglucomutase (glucose-cofactor)

Reaction: α-D-glucose 1-phosphate = D-glucose 6-phosphate

Other name(s): glucose phosphomutase; glucose-1-phosphate phosphotransferase

Systematic name: α-D-glucose 1,6-phosphomutase (glucose-cofactor)

Comments: The enzyme is activated by D-glucose, which probably acts as an acceptor for a phosphate residue from the substrate, thus being itself converted into the product. cf. EC 5.4.2.2, phosphoglucomutase (α-D-glucose-1,6-bisphosphate-dependent).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37278-22-1

References:

1. Fujimoto, A., Ingram, P. and Smith, R.A. D-Glucose-1-phosphate:D-glucose-6-phosphotransferase. Biochim. Biophys. Acta 96 (1965) 91-101. [PMID: 14285271]

2. Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases, in Boyer, P.D. (Ed.), The Enzymes, 3rd edn., vol. 6, Academic Press, New York , 1972, pp. 407-477.

[EC 5.4.2.5 created 1972 as EC 2.7.5.5, transferred 1984 to EC 5.4.2.5]

EC 5.4.2.6

Accepted name: β-phosphoglucomutase

Reaction: β-D-glucose 1-phosphate = β-D-glucose 6-phosphate

For diagram of reaction click here.

Systematic name: β-D-glucose 1,6-phosphomutase

Comments: The enzyme requires Mg2+ and phosphorylation of an aspartate residue at the active site. The enzyme is able to autophosphorylate itself with its substrate β-D-glucose 1-phosphate. Although this is a slow reaction, only a single turnover is required for activation. Once the phosphorylated enzyme is formed, it generates the reaction intermediate β-D-glucose 1,6-bisphosphate, which can be used to phosphorylate the enzyme in subsequent cycles [4]. cf. EC 5.4.2.2, phosphoglucomutase (α-D-glucose-1,6-bisphosphate-dependent).

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 68651-99-0

References:

1. Ben-Zvi, R. and Schramm, M. A phosphoglucomutase specific for β-glucose 1-phosphate. J. Biol. Chem. 236 (1961) 2186-2189.

2. Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases, in Boyer, P.D. (Ed.), The Enzymes, 3rd edn., vol. 6, Academic Press, New York , 1972, pp. 407-477.

3. Lahiri, S.D., Zhang, G., Dunaway-Mariano, D. and Allen, K.N. The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction. Science 299 (2003) 2067-2071. [PMID: 12637673]

4. Dai, J., Wang, L., Allen, K.N., Radstrom, P. and Dunaway-Mariano, D. Conformational cycling in β-phosphoglucomutase catalysis: reorientation of the β-D-glucose 1,6-(bis)phosphate intermediate. Biochemistry 45 (2006) 7818-7824. [PMID: 16784233]

[EC 5.4.2.6 created 1984]

EC 5.4.2.7

Accepted name: phosphopentomutase

Reaction: α-D-ribose 1-phosphate = D-ribose 5-phosphate

Other name(s): phosphodeoxyribomutase; deoxyribose phosphomutase; deoxyribomutase; phosphoribomutase; α-D-glucose-1,6-bisphosphate:deoxy-D-ribose-1-phosphate phosphotransferase; D-ribose 1,5-phosphomutase

Systematic name: α-D-ribose 1,5-phosphomutase

Comments: Also converts 2-deoxy-α-D-ribose 1-phosphate into 2-deoxy-D-ribose 5-phosphate. α-D-Ribose 1,5-bisphosphate, 2-deoxy-α-D-ribose 1,5-bisphosphate, or α-D-glucose 1,6-bisphosphate can act as cofactor. Formerly EC 2.7.5.6.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9026-77-1

References:

1. Hammen-Jepersen, K. and Munch-Petersen, A. Phosphodeoxyribomutase from Escherichia coli. Purification and some properties. Eur. J. Biochem. 17 (1970) 397-407. [PMID: 4992818]

2. Kammen, H.O. and Koo, R. Phosphopentomutases. I. Identification of two activities in rabbit tissues. J. Biol. Chem. 244 (1969) 4888-4893. [PMID: 5824563]

3. Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases, in Boyer, P.D. (Ed.), The Enzymes, 3rd edn., vol. 6, Academic Press, New York , 1972, pp. 407-477.

[EC 5.4.2.7 created 1972 as EC 2.7.5.6, transferred 1984 to EC 5.4.2.7]

EC 5.4.2.8

Accepted name: phosphomannomutase

Reaction: α-D-mannose 1-phosphate = D-mannose 6-phosphate

For diagram click here.

Other name(s): mannose phosphomutase; phosphomannose mutase; D-mannose 1,6-phosphomutase

Systematic name: α-D-mannose 1,6-phosphomutase

Comments: α-D-Mannose 1,6-bisphosphate or α-D-glucose 1,6-bisphosphate can act as cofactor. Formerly EC 2.7.5.7.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 59536-73-1

References:

1. Small, D.M. and Matheson, N.K. Phosphomannomutase and phosphoglucomutase in developing Cassia corymbosa seeds. Phytochemistry 18 (1979) 1147-1150.

[EC 5.4.2.8 created 1981 as EC 2.7.5.7, transferred 1984 to EC 5.4.2.8]

EC 5.4.2.9

Accepted name: phosphoenolpyruvate mutase

Reaction: phosphoenolpyruvate = 3-phosphonopyruvate

For diagram of reaction click here.

Other name(s): phosphoenolpyruvate-phosphonopyruvate phosphomutase; PEP phosphomutase; phosphoenolpyruvate phosphomutase; PEPPM; PEP phosphomutase

Systematic name: phosphoenolpyruvate 2,3-phosphonomutase

Comments: Involved in the biosynthesis of the C-P bond, although the equilibrium greatly favours phosphoenolpyruvate.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 115756-49-5

References:

1. Bowman, E., McQueney, M., Barry, R.J. and Dunaway-Mariano, D. Catalysis and thermodynamics of the phosphoenolpyruvate phosphonopyruvate rearrangement - entry into the phosphonate class of naturally-occurring organo-phosphorus compounds. J. Am. Chem. Soc. 110 (1988) 5575-5576.

2. Hikada, T., Imai, S., Hara, O., Anzai, H., Murakami, T., Nagaoka, K. and Seto, H. Carboxyphosphonoenolpyruvate phosphonomutase, a novel enzyme catalyzing C-P bond formation. J. Bacteriol. 172 (1990) 3066-3072. [PMID: 2160937]

3. Seidel, H.M., Freeman, S. and Knowles, J.R. Phosphonate biosynthesis: isolation of the enzyme responsible for the formation of a carbon-phosphorus bond. Nature 335 (1988) 457-458. [PMID: 3138545]

[EC 5.4.2.9 created 1990]

EC 5.4.2.10

Accepted name: phosphoglucosamine mutase

Reaction: α-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate

For diagram click here.

Other Name(s): D-glucosamine 1,6-phosphomutase

Systematic name: α-D-glucosamine 1,6-phosphomutase

Comments: The enzyme is involved in the pathway for bacterial cell-wall peptidoglycan and lipopolysaccharide biosyntheses, being an essential step in the pathway for UDP-N-acetylglucosamine biosynthesis. The enzyme from Escherichia coli is activated by phosphorylation and can be autophosphorylated in vitro by α-D-glucosamine 1,6-bisphosphate, which is an intermediate in the reaction, α-D-glucose 1,6-bisphosphate or ATP. It can also catalyse the interconversion of α-D-glucose 1-phosphate and glucose 6-phosphate, although at a much lower rate.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9031-92-9

References:

1. Mengin-Lecreulx, D. and van Heijenoort, J. Characterization of the essential gene glmM encoding phosphoglucosamine mutase in Escherichia coli. J. Biol. Chem. 271 (1996) 32-39. [PMID: 8550580]

2. de Reuse, H., Labigne, A. and Mengin-Lecreulx, D. The Helicobacter pylori ureC gene codes for a phosphoglucosamine mutase. J. Bacteriol. 179 (1997) 3488-3493. [PMID: 9171391]

3. Jolly, L., Wu, S., van Heijenoort, J., de Lencastre, H., Mengin-Lecreulx, D. and Tomas, A. The femR315 gene from Staphylococcus aureus, the interruption of which results in reduced methicillin resistance, encodes a phosphoglucosamine mutase. J. Bacteriol. 179 (1997) 5321-5325. [PMID: 9286983]

4. Jolly, L., Ferrari, P., Blanot, D., van Heijenoort, J., Fassy, F. and Mengin-Lecreulx, D. Reaction mechanism of phosphoglucosamine mutase from Escherichia coli. Eur. J. Biochem. 262 (1999) 202-210. [PMID: 10231382]

5. Jolly, L., Pompeo, F., van Heijenoort, J., Fassy, F. and Mengin-Lecreulx, D. Autophosphorylation of phosphoglucosamine mutase from Escherichia coli. J. Bacteriol. 182 (2000) 1280-1285. [PMID: 10671448]

[EC 5.4.2.10 created 2001]

EC 5.4.2.11

Accepted name: phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)

Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate (overall reaction)
(1a) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Nτ-phospho-L-histidine + 2/3-phospho-D-glycerate
(1b) [enzyme]-Nτ-phospho-L-histidine + 2-phospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate
(1c) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Nτ-phospho-L-histidine + 3-phospho-D-glycerate
(1d) [enzyme]-Nτ-phospho-L-histidine + 2/3-bisphospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate

For diagram of reaction click here.

Glossary: 2/3-phospho-D-glycerate = 2-phospho-D-glycerate or 3-phospho-D-glycerate

Other name(s): glycerate phosphomutase (diphosphoglycerate cofactor); 2,3-diphosphoglycerate dependent phosphoglycerate mutase; cofactor dependent phosphoglycerate mutase; phosphoglycerate phosphomutase (ambiguous); phosphoglyceromutase (ambiguous); monophosphoglycerate mutase (ambiguous); monophosphoglyceromutase (ambiguous); GriP mutase (ambiguous); PGA mutase (ambiguous); MPGM; PGAM; PGAM-d; PGM; dPGM

Systematic name: D-phosphoglycerate 2,3-phosphomutase (2,3-diphosphoglycerate-dependent)

Comments: The enzymes from vertebrates, platyhelminths, mollusks, annelids, crustaceans, insects, algae, fungi, yeast and some bacteria (particularly Gram-negative) require 2,3-bisphospho-D-glycerate as a cofactor. The enzyme is activated by 2,3-bisphospho-D-glycerate by transferring a phosphate to histidine (His10 in man and Escherichia coli, His8 in Saccharomyces cerevisiae). This phosphate can be transferred to the free OH of 2-phospho-D-glycerate, followed by transfer of the phosphate already on the phosphoglycerate back to the histidine. cf. EC 5.4.2.12 phosphoglycerate mutase. The enzyme has no requirement for metal ions. This enzyme also catalyse, slowly, the reactions of EC 5.4.2.4 bisphosphoglycerate mutase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Grisolia, S. Phosphoglyceric acid mutase. Methods Enzymol. 5 (1962) 236-242.

2. Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, 1972, pp. 407-477.

3. Rose, Z.B. The enzymology of 2,3-bisphosphoglycerate. Adv. Enzymol. Relat. Areas Mol. Biol. 51 (1980) 211-253. [PMID: 6255773]

4. Rigden, D.J., Walter, R.A., Phillips, S.E. and Fothergill-Gilmore, L.A. Sulphate ions observed in the 2.12 Å structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism. J. Mol. Biol. 286 (1999) 1507-1517. [PMID: 10064712]

5. Bond, C.S., White, M.F. and Hunter, W.N. High resolution structure of the phosphohistidine-activated form of Escherichia coli cofactor-dependent phosphoglycerate mutase. J. Biol. Chem. 276 (2001) 3247-3253. [PMID: 11038361]

6. Rigden, D.J., Mello, L.V., Setlow, P. and Jedrzejas, M.J. Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity. J. Mol. Biol. 315 (2002) 1129-1143. [PMID: 11827481]

7. Rigden, D.J., Littlejohn, J.E., Henderson, K. and Jedrzejas, M.J. Structures of phosphate and trivanadate complexes of Bacillus stearothermophilus phosphatase PhoE: structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily. J. Mol. Biol. 325 (2003) 411-420. [PMID: 12498792]

[EC 5.4.2.11 created 1961 as EC 5.4.2.1 (EC 2.7.5.3 created 1961, incorporated 1984) transferred 2013 to 5.4.2.11, modified 2014]

EC 5.4.2.12

Accepted name: phosphoglycerate mutase (2,3-diphosphoglycerate-independent)

Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate

For diagram of reaction click here.

Other name(s): cofactor independent phosphoglycerate mutase; 2,3-diphosphoglycerate-independent phosphoglycerate mutase; phosphoglycerate phosphomutase (ambiguous); phosphoglyceromutase (ambiguous); monophosphoglycerate mutase (ambiguous); monophosphoglyceromutase (ambiguous); GriP mutase (ambiguous); PGA mutase (ambiguous); iPGM; iPGAM; PGAM-i

Systematic name: D-phosphoglycerate 2,3-phosphomutase (2,3-diphosphoglycerate-independent)

Comments: The enzymes from higher plants, algae, fungi, nematodes, sponges, coelenterates, myriapods, arachnids, echinoderms, archaea and some bacteria (particularly Gram-positive) have maximum activity in the absence of 2,3-bisphospho-D-glycerate. cf. EC 5.4.2.11 phosphoglycerate mutase (2,3-diphosphoglycerate-dependent). The enzyme contains two Mn2+ (or in some species two Co2+ ions). The reaction involves a phosphotransferase reaction to serine followed by transfer back to the glycerate at the other position. Both metal ions are involved in the reaction.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Jedrzejas, M.J., Chander, M., Setlow, P. and Krishnasamy, G. Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with 2-phosphoglycerate. J. Biol. Chem. 275 (2000) 23146-23153. [PMID: 10764795]

2. Rigden, D.J., Lamani, E., Mello, L.V., Littlejohn, J.E. and Jedrzejas, M.J. Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J. Mol. Biol. 328 (2003) 909-920. [PMID: 12729763]

3. Zhang, Y., Foster, J.M., Kumar, S., Fougere, M. and Carlow, C.K. Cofactor-independent phosphoglycerate mutase has an essential role in Caenorhabditis elegans and is conserved in parasitic nematodes. J. Biol. Chem. 279 (2004) 37185-37190. [PMID: 15234973]

4. Nukui, M., Mello, L.V., Littlejohn, J.E., Setlow, B., Setlow, P., Kim, K., Leighton, T. and Jedrzejas, M.J. Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species. Biophys J 92 (2007) 977-988. [PMID: 17085493]

5. Nowicki, M.W., Kuaprasert, B., McNae, I.W., Morgan, H.P., Harding, M.M., Michels, P.A., Fothergill-Gilmore, L.A. and Walkinshaw, M.D. Crystal structures of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism and a new enzyme subclass. J. Mol. Biol. 394 (2009) 535-543. [PMID: 19781556]

6. Mercaldi, G.F., Pereira, H.M., Cordeiro, A.T., Michels, P.A. and Thiemann, O.H. Structural role of the active-site metal in the conformation of Trypanosoma brucei phosphoglycerate mutase. FEBS J. 279 (2012) 2012-2021. [PMID: 22458781]

[EC 5.4.2.12 created 2013]


EC 5.4.3 Transferring Amino Groups

Contents

EC 5.4.3.1 deleted
EC 5.4.3.2 lysine 2,3-aminomutase
EC 5.4.3.3 lysine 5,6-aminomutase
EC 5.4.3.4 transferred, now included in EC 5.4.3.3
EC 5.4.3.5 D-ornithine 4,5-aminomutase
EC 5.4.3.6 tyrosine 2,3-aminomutase
EC 5.4.3.7 leucine 2,3-aminomutase
EC 5.4.3.8 glutamate-1-semialdehyde 2,1-aminomutase
EC 5.4.3.9 glutamate 2,3-aminomutase
EC 5.4.3.10 phenylalanine aminomutase (L-β-phenylalanine forming)
EC 5.4.3.11 phenylalanine aminomutase (D-β-phenylalanine forming)


Entries

[EC 5.4.3.1 Deleted entry: ornithine 4,5-aminomutase. This reaction was due to a mixture of EC 5.1.1.12 (ornithine racemase) and EC 5.4.3.5 (D-ornithine 4,5-aminomutase) (EC 5.4.3.1 created 1972, deleted 1976)]

EC 5.4.3.2

Accepted name: lysine 2,3-aminomutase

Reaction: L-lysine = (3S)-3,6-diaminohexanoate

For diagram of reaction click here.

Systematic name: L-lysine 2,3-aminomutase

Comments: Activity is stimulated by S-adenosyl-L-methionine and pyridoxal phosphate.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9075-20-1

References:

1. Aberhart, D.J., Lim, H.-J. and Weiller, B.H. Stereochemistry of lysine 2,3-aminomutase. J. Am. Chem. Soc. 103 (1981) 6750-6752.

2. Zappia, V. and Barker, H.A. Studies on lysine-2,3-aminomutase. Subunit structure and sulfhydryl groups. Biochim. Biophys. Acta 207 (1970) 505-513. [PMID: 5452674]

[EC 5.4.3.2 created 1972]

EC 5.4.3.3

Accepted name: lysine 5,6-aminomutase

Reaction: (1) (3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate
(2) D-lysine = 2,5-diaminohexanoate

For diagram of reaction click here.

Other name(s): β-lysine 5,6-aminomutase; β-lysine mutase; L-β-lysine 5,6-aminomutase; D-lysine 5,6-aminomutase; D-α-lysine mutase; adenosylcobalamin-dependent D-lysine 5,6-aminomutase

Systematic name: (3S)-3,6-diaminohexanoate 5,6-aminomutase

Comments: This enzyme is a member of the ‘AdoMet radical’ (radical SAM) family. It requires pyridoxal phosphate and adenosylcobalamin for activity. A 5'-deoxyadenosyl radical is generated during the reaction cycle by reductive cleavage of adenosylcobalamin, which is regenerated at the end of the reaction.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9075-69-8

References:

1. Stadtman, T.C. and Tasi, L. A cobamide coenzyme dependent migration of the ε-amino group of D-lysine. Biochem. Biophys. Res. Commun. 28 (1967) 920-926. [PMID: 4229021]

2. Stadtman, T.C. and Renz, P. Anaerobic degradation of lysine. V. Some properties of the cobamide coenzyme-dependent β-lysine mutase of Clostridium sticklandii. Arch. Biochem. Biophys. 125 (1968) 226-239. [PMID: 5649516]

3. Morley, C.G.D. and Stadtman, T.C. Studies on the fermentation of D-α-lysine. Purification and properties of an adenosine triphosphate regulated B12-coenzyme-dependent D-α-lysine mutase complex from Clostridium sticklandii. Biochemistry 9 (1970) 4890-4900. [PMID: 5480154]

4. Retey, J., Kunz, F., Arigoni, D. and Stadtman, T.C. Zur Kenntnis der β-Lysin-Mutase-Reaktion: mechanismus und sterischer Verlauf. Helv. Chim. Acta 61 (1978) 2989-2998.

5. Chang, C.H. and Frey, P.A. Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-lysine 5, 6-aminomutase from Clostridium sticklandii. J. Biol. Chem. 275 (2000) 106-114. [PMID: 10617592]

6. Tang, K.H., Harms, A. and Frey, P.A. Identification of a novel pyridoxal 5'-phosphate binding site in adenosylcobalamin-dependent lysine 5,6-aminomutase from Porphyromonas gingivalis. Biochemistry 41 (2002) 8767-8776. [PMID: 12093296]

7. Tang, K.H., Mansoorabadi, S.O., Reed, G.H. and Frey, P.A. Radical triplets and suicide inhibition in reactions of 4-thia-D- and 4-thia-L-lysine with lysine 5,6-aminomutase. Biochemistry 48 (2009) 8151-8160. [PMID: 19634897]

8. Berkovitch, F., Behshad, E., Tang, K.H., Enns, E.A., Frey, P.A. and Drennan, C.L. A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase. Proc. Natl Acad. Sci. USA 101 (2004) 15870-15875. [PMID: 15514022]

[EC 5.4.3.3 created 1972 (EC 5.4.3.4 created 1972, incorporated 2017), modified 2017]

[EC 5.4.3.4 Transferred entry: D-lysine 5,6-aminomutase. Now included in EC 5.4.3.3, lysine 5,6-aminomutase (EC 5.4.3.4 created 1972, modified 2003, deleted 2017)]

EC 5.4.3.5

Accepted name: D-ornithine 4,5-aminomutase

Reaction: D-ornithine = (2R,4S)-2,4-diaminopentanoate

Other name(s): D-α-ornithine 5,4-aminomutase; D-ornithine aminomutase

Systematic name: D-ornithine 4,5-aminomutase

Comments: A pyridoxal-phosphate protein that requires a cobamide coenzyme for activity.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 62213-30-3

References:

1. Somack, R. and Costilow, R.N. Purification and properties of a pyridoxal phosphate and coenzyme B12 dependent D-α-ornithine 5,4-aminomutase. Biochemistry 12 (1973) 2597-2604. [PMID: 4711468]

[EC 5.4.3.5 created 1972 as EC 5.4.3.1, transferred 1976 to EC 5.4.3.5, modified 2003]

EC 5.4.3.6

Accepted name: tyrosine 2,3-aminomutase

Reaction: L-tyrosine = 3-amino-3-(4-hydroxyphenyl)propanoate

Other name(s): tyrosine αβ-mutase

Systematic name: L-tyrosine 2,3-aminomutase

Comments: Requires ATP.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9073-38-5

References:

1. Kurylo-Borowska, Z. and Abramsky, T. Biosynthesis of β-tyrosine. Biochim. Biophys. Acta 264 (1972) 1-10. [PMID: 5021987]

[EC 5.4.3.6 created 1976]

EC 5.4.3.7

Accepted name: leucine 2,3-aminomutase

Reaction: (2S)-α-leucine = (3R)-β-leucine

Systematic name: (2S)-α-leucine 2,3-aminomutase

Comments: Requires a cobamide coenzyme.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 59125-53-0

References:

1. Freer, I., Pedrocchi-Fantoni, G., Picken, D.J. and Overton, K.H. Stereochemistry of the leucine 2,3-aminomutase from tissue-cultures of Andrographis paniculata. J. Chem. Soc. Chem. Commun. (1981) 80-82.

2. Poston, J.M. Leucine 2,3-aminomutase, an enzyme of leucine catabolism. J. Biol. Chem. 251 (1976) 1859-1863. [PMID: 1270414]

3. Poston, J.M. Coenzyme B12-dependent enzymes in potatoes: leucine 2,3-aminomutase and methylmalonyl-CoA mutase. Phytochemistry 17 (1976) 401-402.

[EC 5.4.3.7 created 1982]

EC 5.4.3.8

Accepted name: glutamate-1-semialdehyde 2,1-aminomutase

Reaction: L-glutamate 1-semialdehyde = 5-aminolevulinate

For diagram click here and mechanism here.

Glossary: L-glutamate 1-semialdehyde = (S)-4-amino-5-oxopentanoate

Other name(s): glutamate-1-semialdehyde aminotransferase

Systematic name: (S)-4-amino-5-oxopentanoate 4,5-aminomutase

Comments: Requires pyridoxal phosphate.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 68518-07-0

References:

1. Gough, S.P. and Kannangara, C.G. Biosynthesis of Δ-aminolevulinate in greening barley leaves: glutamate 1-semialdehyde aminotransferase. Carlsberg Res. Commun. 43 (1978) 185-194.

[EC 5.4.3.8 created 1983]

EC 5.4.3.9

Accepted name: glutamate 2,3-aminomutase

Reaction: L-glutamate = 3-aminopentanedioate

Glossary: 3-aminopentanedioate = isoglutamate

Systematic name: L-glutamate 2,3-aminomutase

Comments: This enzyme is a member of the 'AdoMet radical' (radical SAM) family. It contains pyridoxal phosphate and a [4Fe-4S] cluster, which is coordinated by 3 cysteines and binds an exchangeable S-adenosyl-L-methionine molecule. During the reaction cycle, the AdoMet forms a 5'-deoxyadenosyl radical, which is regenerated at the end of the reaction.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Ruzicka, F.J. and Frey, P.A. Glutamate 2,3-aminomutase: a new member of the radical SAM superfamily of enzymes. Biochim. Biophys. Acta 1774 (2007) 286-296. [PMID: 17222594]

[EC 5.4.3.9 created 2012]

EC 5.4.3.10

Accepted name: phenylalanine aminomutase (L-β-phenylalanine forming)

Reaction: L-phenylalanine = L-β-phenylalanine

Glossary: L-β-phenylalanine = (R)-3-amino-3-phenylpropanoate

Systematic name: L-phenylalanine 2,3-aminomutase [(R)-3-amino-3-phenylpropanoate forming]

Comments: The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO). This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine. cf. EC 5.4.3.11, phenylalanine aminomutase (D-β-phenylalanine forming).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Feng, L., Wanninayake, U., Strom, S., Geiger, J. and Walker, K.D. Mechanistic, mutational, and structural evaluation of a Taxus phenylalanine aminomutase. Biochemistry 50 (2011) 2919-2930. [PMID: 21361343]

[EC 5.4.3.10 created 2013]

EC 5.4.3.11

Accepted name: phenylalanine aminomutase (D-β-phenylalanine forming)

Reaction: L-phenylalanine = D-β-phenylalanine

Glossary: D-β-phenylalanine = (S)-3-amino-3-phenylpropanoate

Other name(s): admH (gene name); L-phenylalanine 2,3-aminomutase [(S)-3-amino-3-phenylpropanoate]

Systematic name: L-phenylalanine 2,3-aminomutase [(S)-3-amino-3-phenylpropanoate forming]

Comments: The enzyme from the bacterium Pantoea agglomerans produces D-β-phenylalanine, an intermediate in the biosynthesis of the polyketide non-ribosomal antibiotic andrimid. The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine. cf. EC 5.4.3.10, phenylalanine aminomutase (L-β-phenylalanine forming).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Ratnayake, N.D., Wanninayake, U., Geiger, J.H. and Walker, K.D. Stereochemistry and mechanism of a microbial phenylalanine aminomutase. J. Am. Chem. Soc. 133 (2011) 8531-8533. [PMID: 21561099]

[EC 5.4.3.11 created 2013]


EC 5.4.4 Transferring Hydroxy Groups

Contents

EC 5.4.4.1 (hydroxyamino)benzene mutase
EC 5.4.4.2 isochorismate synthase
EC 5.4.4.3 3-(hydroxyamino)phenol mutase
EC 5.4.4.4 geraniol isomerase
EC 5.4.4.5 9,12-octadecadienoate 8-hydroperoxide 8R-isomerase
EC 5.4.4.6 9,12-octadecadienoate 8-hydroperoxide 8S-isomerase
EC 5.4.4.7 hydroperoxy icosatetraenoate isomerase
EC 5.4.4.8 linalool isomerase


EC 5.4.4.1

Accepted name: (hydroxyamino)benzene mutase

Reaction: (hydroxyamino)benzene = 2-aminophenol

Other name(s): HAB mutase; hydroxylaminobenzene hydroxymutase; hydroxylaminobenzene mutase

Systematic name: (hydroxyamino)benzene hydroxymutase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number: 261765-91-7

References:

1. He, Z., Nadeau, L.J. and Spain, J.C. Characterization of hydroxylaminobenzene mutase from pNBZ139 cloned from Pseudomonas pseudoalcaligenes JS45: a highly-associated sodium-dodecyl-sulfate-stable enzyme catalyzing an intramolecular transfer of hydroxyl group. Eur. J. Biochem. 267 (2000) 1110-1116. [PMID: 10672020]

2. Davis, J.K., Paoli, G.C., He, Z., Nadeau, L.J., Somerville, C.C. and Spain, J.C. Sequence analysis and initial characterization of two isozymes of hydroxylaminobenzene mutase from Pseudomonas pseudoalcaligenes JS45. Appl. Environ. Microbiol. 66 (2000) 2965-2971. [PMID: 10877793]

[EC 5.4.4.1 created 2003]

EC 5.4.4.2

Accepted name: isochorismate synthase

Reaction: chorismate = isochorismate

For diagram click here.

Other name(s): MenF

Systematic name: isochorismate hydroxymutase

Comments: Requires Mg2+. The reaction is reversible.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37318-53-9

References:

1. Young, I.G. and Gibson, F. Regulation of the enzymes involved in the biosynthesis of 2,3-dihydroxybenzoic acid in Aerobacter aerogenes and Escherichia coli. Biochim. Biophys. Acta 177 (1969) 401-411. [PMID: 4306838]

2. van Tegelen, L.J., Moreno, P.R., Croes, A.F., Verpoorte, R. and Wullems, G.J. Purification and cDNA cloning of isochorismate synthase from elicited cell cultures of Catharanthus roseus. Plant Physiol. 119 (1999) 705-712. [PMID: 9952467]

3. Dahm, C., Müller, R., Schulte, G., Schmidt, K. and Leistner, E. The role of isochorismate hydroxymutase genes entC and menF in enterobactin and menaquinone biosynthesis in Escherichia coli. Biochim. Biophys. Acta 1425 (1998) 377-386. [PMID: 9795253]

4. Daruwala, R., Kwon, O., Meganathan, R. and Hudspeth, M.E. A new isochorismate synthase specifically involved in menaquinone (vitamin K2) biosynthesis encoded by the menF gene. FEMS Microbiol. Lett. 140 (1996) 159-163. [PMID: 8764478]

[EC 5.4.4.2 created 1972 as EC 5.4.99.6, transferred 2003 to EC 5.4.4.2]

EC 5.4.4.3

Accepted name: 3-(hydroxyamino)phenol mutase

Reaction: 3-hydroxyaminophenol = aminohydroquinone

Other name(s): 3-hydroxylaminophenol mutase; 3HAP mutase

Systematic name: 3-(hydroxyamino)phenol hydroxymutase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number: 224427-05-8

References:

1. Schenzle, A., Lenke, H., Spain, J.C. and Knackmuss, H.J. 3-Hydroxylaminophenol mutase from Ralstonia eutropha JMP134 catalyzes a Bamberger rearrangement. J. Bacteriol. 181 (1999) 1444-1450. [PMID: 10049374]

[EC 5.4.4.3 created 2003]

EC 5.4.4.4

Accepted name: geraniol isomerase

Reaction: geraniol = (3S)-linalool

For diagram of reaction click here.

Systematic name: geraniol hydroxymutase

Comments: In absence of oxygen the bifunctional linalool dehydratase-isomerase can catalyse in vitro two reactions, the isomerization of (3S)-linalool to geraniol and the hydration of myrcene to (3S)-linalool, the latter activity being classified as EC 4.2.1.127, linalool dehydratase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Brodkorb, D., Gottschall, M., Marmulla, R., Lüddeke, F. and Harder, J. Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes. J. Biol. Chem. 285 (2010) 30436-30442. [PMID: 20663876]

2. Lüddeke, F. and Harder, J. Enantiospecific (S)-(+)-linalool formation from β-myrcene by linalool dehydratase-isomerase. Z. Naturforsch. C 66 (2011) 409-412. [PMID: 21950166]

[EC 5.4.4.4 created 2011, modified 2012]

EC 5.4.4.5

Accepted name: 9,12-octadecadienoate 8-hydroperoxide 8R-isomerase

Reaction: (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate = (5S,8R,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate

Other name(s): 5,8-LDS (bifunctional enzyme); 5,8-linoleate diol synthase (bifunctional enzyme); 8-hydroperoxide isomerase; (8R,9Z,12Z)-8-hydroperoxy-9,12-octadecadienoate mutase ((5S,8R,9Z,12Z)-5,8-dihydroxy-9,12-octadecadienoate-forming); PpoA

Systematic name: (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate hydroxymutase [(5S,8R,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate-forming]

Comments: The enzyme contains heme [3]. The bifunctional enzyme from Aspergillus nidulans uses different heme domains to catalyse two separate reactions. Linoleic acid is oxidized within the N-terminal heme peroxidase domain to (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate (cf. EC 1.13.11.60, linoleate 8R-lipoxygenase), which is subsequently isomerized to (5S,8R,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate within the C-terminal P-450 heme thiolate domain [3].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Hoffmann, I., Jerneren, F., Garscha, U. and Oliw, E.H. Expression of 5,8-LDS of Aspergillus fumigatus and its dioxygenase domain. A comparison with 7,8-LDS, 10-dioxygenase, and cyclooxygenase. Arch. Biochem. Biophys. 506 (2011) 216-222. [PMID: 21130068]

2. Jerneren, F., Garscha, U., Hoffmann, I., Hamberg, M. and Oliw, E.H. Reaction mechanism of 5,8-linoleate diol synthase, 10R-dioxygenase, and 8,11-hydroperoxide isomerase of Aspergillus clavatus. Biochim. Biophys. Acta 1801 (2010) 503-507. [PMID: 20045744]

3. Brodhun, F., Gobel, C., Hornung, E. and Feussner, I. Identification of PpoA from Aspergillus nidulans as a fusion protein of a fatty acid heme dioxygenase/peroxidase and a cytochrome P450. J. Biol. Chem. 284 (2009) 11792-11805. [PMID: 19286665]

[EC 5.4.4.5 created 2011]

EC 5.4.4.6

Accepted name: 9,12-octadecadienoate 8-hydroperoxide 8S-isomerase

Reaction: (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate = (7S,8S,9Z,12Z)-7,8-dihydroxyoctadeca-9,12-dienoate

Other name(s): 8-hydroperoxide isomerase (ambiguous); (8R,9Z,12Z)-8-hydroperoxy-9,12-octadecadienoate mutase ((7S,8S,9Z,12Z)-5,8-dihydroxy-9,12-octadecadienoate-forming)

Systematic name: (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate hydroxymutase [(7S,8S,9Z,12Z)-7,8-dihydroxyoctadeca-9,12-dienoate-forming]

Comments: The enzyme contains heme. The bifunctional enzyme from Gaeumannomyces graminis catalyses the oxidation of linoleic acid to (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate (cf. EC 1.13.11.60, linoleate 8R-lipoxygenase), which is then isomerized to (7S,8S,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate [3].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Hamberg, M., Zhang, L.-Y., Brodowsky, I.D. and Oliw, E.H. Sequential oxygenation of linoleic acid in the fungus Gaeumannomyces graminis: stereochemistry of dioxygenase and hydroperoxide isomerase reactions. Arch. Biochem. Biophys. 309 (1994) 77-80. [PMID: 8117115]

2. Su, C., Sahlin, M. and Oliw, E.H. A protein radical and ferryl intermediates are generated by linoleate diol synthase, a ferric hemeprotein with dioxygenase and hydroperoxide isomerase activities. J. Biol. Chem. 273 (1998) 20744-20751. [PMID: 9694817]

3. Su, C. and Oliw, E.H. Purification and characterization of linoleate 8-dioxygenase from the fungus Gaeumannomyces graminis as a novel hemoprotein. J. Biol. Chem. 271 (1996) 14112-14118. [PMID: 8662736]

[EC 5.4.4.6 created 2011]

EC 5.4.4.7

Accepted name: hydroperoxy icosatetraenoate isomerase

Reaction: a hydroperoxyicosatetraenoate = a hydroxyepoxyicosatrienoate

Glossary: (12R)-HPETE = (5Z,8Z,10E,12R,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate
(8S)-HPETE = (5Z,8S,9E,11Z,14Z)-8-hydroperoxyicosa-5,9,11,14-tetraenoate

Other name(s): epidermal lipoxygenase-3 (ambiguous); eLOX3 (ambiguous)

Systematic name: hydroperoxyicosatetraenoate hydroxymutase

Comments: Binds Fe2+. The enzyme from mammals accepts a range of hydroperoxyicosatetraenoates producing one or several different hydroxyepoxyicosatrienoates. The human enzyme has highest activity with (12R)-HPETE producing (5Z,8R,9E,11R,12R,14Z)-8-hydroxy-11,12-epoxyicosa-5,9,14-trienoate, followed by (12S)-HPETE producing (5Z,8Z,10R,11S,12S,14Z)-10-hydroxy-11,12-epoxyicosa-5,8,14-trienoate and (5Z,8R,9E,11S,12S,14Z)-8-hydroxy-11,12-epoxyicosa-5,9,14-trienoate [1]. The mouse enzyme has highest activity with (8S)-HPETE, producing (5Z,8S,9S,10R,11Z,14Z)-10-hydroxy-8,9-epoxyicosa-5,11,14-trienoate [2]. The enzymes also have the activity of EC 4.2.1.152, hydroperoxy icosatetraenoate dehydratase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Yu, Z., Schneider, C., Boeglin, W.E., Marnett, L.J. and Brash, A.R. The lipoxygenase gene ALOXE3 implicated in skin differentiation encodes a hydroperoxide isomerase. Proc. Natl. Acad. Sci. USA 100 (2003) 9162-9167. [PMID: 12881489]

2. Yu, Z., Schneider, C., Boeglin, W.E. and Brash, A.R. Human and mouse eLOX3 have distinct substrate specificities: implications for their linkage with lipoxygenases in skin. Arch. Biochem. Biophys. 455 (2006) 188-196. [PMID: 17045234]

3. Zheng, Y. and Brash, A.R. Dioxygenase activity of epidermal lipoxygenase-3 unveiled: typical and atypical features of its catalytic activity with natural and synthetic polyunsaturated fatty acids. J. Biol. Chem. 285 (2010) 39866-39875. [PMID: 20921226]

[EC 5.4.4.7 created 2014]

EC 5.4.4.8

Accepted name: linalool isomerase

Reaction: (RS)-linalool = geraniol

For diagram of reaction click here

Other name(s): 3,1-hydroxyl-Δ12-mutase (linalool isomerase)

Systematic name: (RS)-linalool hydroxymutase

Comments: Isolated from the bacterium Thauera linaloolentis grown on (RS)-linalool as the sole source of carbon. Unlike EC 5.4.4.4, geraniol isomerase, which only acts on (S)-linalool, this enzyme acts equally well on both enantiomers.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Marmulla, R., Šafarić, B., Markert, S., Schweder, T. and Harder, J. Linalool isomerase, a membrane-anchored enzyme in the anaerobic monoterpene degradation in Thauera linaloolentis 47Lol. BMC Biochem. 17 (2016) 6. [PMID: 26979141]

[EC 5.4.4.8 created 2017]


EC 5.4.99 Transferring Other Groups

Contents

EC 5.4.99.1 methylaspartate mutase
EC 5.4.99.2 methylmalonyl-CoA mutase
EC 5.4.99.3 2-acetolactate mutase
EC 5.4.99.4 2-methyleneglutarate mutase
EC 5.4.99.5 chorismate mutase
EC 5.4.99.6 now EC 5.4.4.2
EC 5.4.99.7 lanosterol synthase
EC 5.4.99.8 cycloartenol synthase
EC 5.4.99.9 UDP-galactopyranose mutase
EC 5.4.99.10 deleted, included in EC 5.4.99.11
EC 5.4.99.11 isomaltulose synthase
EC 5.4.99.12 tRNA pseudouridine38-40 synthase
EC 5.4.99.13 isobutyryl-CoA mutase
EC 5.4.99.14 4-carboxymethyl-4-methylbutenolide mutase
EC 5.4.99.15 (1→4)-α-D-glucan 1-α-D-glucosylmutase
EC 5.4.99.16 maltose α-D-glucosyltransferase
EC 5.4.99.17 squalene—hopene cyclase
EC 5.4.99.18 5-(carboxyamino)imidazole ribonucleotide mutase
EC 5.4.99.19 16S rRNA pseudouridine516 synthase
EC 5.4.99.20 23S rRNA pseudouridine2457 synthase
EC 5.4.99.21 23S rRNA pseudouridine2604 synthase
EC 5.4.99.22 23S rRNA pseudouridine2605 synthase
EC 5.4.99.23 23S rRNA pseudouridine1911/1915/1917 synthase
EC 5.4.99.24 23S rRNA pseudouridine955/2504/2580 synthase
EC 5.4.99.25 tRNA pseudouridine55 synthase
EC 5.4.99.26 tRNA pseudouridine65 synthase
EC 5.4.99.27 tRNA pseudouridine13 synthase
EC 5.4.99.28 tRNA pseudouridine32 synthase
EC 5.4.99.29 23S rRNA pseudouridine746 synthase
EC 5.4.99.30 UDP-arabinopyranose mutase
EC 5.4.99.31 thalianol synthase
EC 5.4.99.32 protostadienol synthase
EC 5.4.99.33 cucurbitadienol synthase
EC 5.4.99.34 germanicol synthase
EC 5.4.99.35 taraxerol synthase
EC 5.4.99.36 isomultiflorenol synthase
EC 5.4.99.37 dammaradiene synthase
EC 5.4.99.38 camelliol C synthase
EC 5.4.99.39 β-amyrin synthase
EC 5.4.99.40 α-amyrin synthase
EC 5.4.99.41 lupeol synthase
EC 5.4.99.42 tRNA pseudouridine31 synthase
EC 5.4.99.43 21S rRNA pseudouridine2819 synthase
EC 5.4.99.44 mitochondrial tRNA pseudouridine27/28 synthase
EC 5.4.99.45 tRNA pseudouridine38/39 synthase
EC 5.4.99.46 shionone synthase
EC 5.4.99.47 parkeol synthase
EC 5.4.99.48 achilleol B synthase
EC 5.4.99.49 glutinol synthase
EC 5.4.99.50 friedelin synthase
EC 5.4.99.51 baccharis oxide synthase
EC 5.4.99.52 α-seco-amyrin synthase
EC 5.4.99.53 marneral synthase
EC 5.4.99.54 β-seco-amyrin synthase
EC 5.4.99.55 δ-amyrin synthase
EC 5.4.99.56 tirucalladienol synthase
EC 5.4.99.57 baruol synthase
EC 5.4.99.58 methylornithine synthase
EC 5.4.99.59 dTDP-fucopyranose mutase
EC 5.4.99.60 cobalt-precorrin-8 methylmutase
EC 5.4.99.61 precorrin-8X methylmutase
EC 5.4.99.62 D-ribose pyranase
EC 5.4.99.63 ethylmalonyl-CoA mutase
EC 5.4.99.64 2-hydroxyisobutanoyl-CoA mutase
EC 5.4.99.65 pre-α-onocerin synthase
EC 5.4.99.66 α-onocerin synthase

Entries

EC 5.4.99.1

Accepted name: methylaspartate mutase

Reaction: L-threo-3-methylaspartate = L-glutamate

Other name(s): glutamate mutase; glutamic mutase; glutamic isomerase; glutamic acid mutase; glutamic acid isomerase; methylaspartic acid mutase; β-methylaspartate-glutamate mutase; glutamate isomerase

Systematic name: L-threo-3-methylaspartate carboxy-aminomethylmutase

Comments: Requires a cobamide coenzyme.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9032-97-7

References:

1. Barker, H.A., Rooze, V., Suzuki, F. and Iodice, A.A. The glutamate mutase system. Assays and properties. J. Biol. Chem. 239 (1964) 3260-3266.

2. Weissbach, H., Toohey, J. and Barker, H.A. Isolation and properties of B12 coenzymes containing benzimidazole or dimethylbenzimidazole. Proc. Natl. Acad. Sci. USA 45 (1959) 521-528.

[EC 5.4.99.1 created 1961]

EC 5.4.99.2

Accepted name: methylmalonyl-CoA mutase

Reaction: (R)-methylmalonyl-CoA = succinyl-CoA

For diagram of reaction click here (another example).

Other name(s): methylmalonyl-CoA CoA-carbonyl mutase; methylmalonyl coenzyme A mutase; methylmalonyl coenzyme A carbonylmutase; (S)-methylmalonyl-CoA mutase; (R)-2-methyl-3-oxopropanoyl-CoA CoA-carbonylmutase [incorrect]

Systematic name: (R)-methylmalonyl-CoA CoA-carbonylmutase

Comments: Requires a cobamide coenzyme.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 9023-90-9

References:

1. Barker, H.A. Coenzyme B12-dependent mutases causing carbon chain rearrangements, in Boyer, P.D. (Ed.), The Enzymes, 3rd edn., vol. 6, Academic Press, New York, 1972, pp. 509-537.

[EC 5.4.99.2 created 1961, modified 1983]

EC 5.4.99.3

Accepted name: 2-acetolactate mutase

Reaction: 2-acetolactate = 3-hydroxy-3-methyl-2-oxobutanoate

Other name(s): acetolactate mutase; acetohydroxy acid isomerase

Systematic name: 2-acetolactate methylmutase

Comments: Requires ascorbic acid; also converts 2-aceto-2-hydroxybutanoate to 3-hydroxy-3-methyl-2-oxopentanoate.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37318-52-8

References:

1. Allaudeen, H.S. and Ramakrishnan, T. Biosynthesis of isoleucine and valine in Mycobacterium tuberculosis H37 Rv. Arch. Biochem. Biophys. 125 (1968) 199-209. [PMID: 4384955]

[EC 5.4.99.3 created 1972]

EC 5.4.99.4

Accepted name: 2-methyleneglutarate mutase

Reaction: 2-methyleneglutarate = 2-methylene-3-methylsuccinate

For diagram click here.

Other name(s): α-methyleneglutarate mutase

Systematic name: 2-methyleneglutarate carboxy-methylenemethylmutase

Comments: Requires a cobamide coenzyme.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 9059-10-3

References:

1. Kung, H.-F., Cederbaum, S., Tsai, L. and Stadtman, T.C. Nicotinic acid metabolism. V. A cobamide coenzyme-dependent conversion of α-methyleneglutaric acid to dimethylmaleic acid. Proc. Natl. Acad. Sci. USA 65 (1970) 978-984. [PMID: 5266166]

2. Kung, H.-F. and Stadtman, T.C. Nicotinic acid metabolism. VI. Purification and properties of α-methyleneglutarate mutase (B12-dependent) and methylitaconate isomerase. J. Biol. Chem. 246 (1971) 3378-3388. [PMID: 5574401]

[EC 5.4.99.4 created 1972]

EC 5.4.99.5

Accepted name: chorismate mutase

Reaction: chorismate = prephenate

For diagram click here and mechanism here.

Other name(s): hydroxyphenylpyruvate synthase

Systematic name: chorismate pyruvatemutase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9068-30-8

References:

1. Cotton, R.G.H. and Gibson, F. The biosynthesis of phenylalanine and tyrosine; enzymes converting chorismic acid into prephenic acid and their relationships to prephenate dehydratase and prephenate dehydrogenase. Biochim. Biophys. Acta 100 (1965) 76-88.

2. Lorence, J.H. and Nester, E.W. Multiple molecular forms of chorismate mutase in Bacillus subtillis. Biochemistry 6 (1967) 1541-1543. [PMID: 4962500]

3. Sprössler, B. and Lingens, F. Chorismat-Mutase aus Claviceps. I. Eigenschaften der Chorismat-Mutase aus verschiedenen Claviceps-Stämmen. Hoppe-Seyler's Z. Physiol. Chem. 351 (1970) 448-458. [PMID: 5443801]

4. Woodin, T.S. and Nishioka, L. Evidence for three isozymes of chorismate mutase in alfalfa. Biochim. Biophys. Acta 309 (1973) 211-223. [PMID: 4708674]

[EC 5.4.99.5 created 1972]

[EC 5.4.99.6 Transferred entry: now EC 5.4.4.2 isochorismate synthase. (EC 5.4.99.6 created 1972, deleted 2003)]

EC 5.4.99.7

Accepted name: lanosterol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = lanosterol

For reaction pathway click here.

Other name(s): 2,3-epoxysqualene lanosterol cyclase; squalene-2,3-oxide-lanosterol cyclase; lanosterol 2,3-oxidosqualene cyclase; squalene 2,3-epoxide:lanosterol cyclase; 2,3-oxidosqualene sterol cyclase; oxidosqualene cyclase; 2,3-oxidosqualene cyclase; 2,3-oxidosqualene-lanosterol cyclase; oxidosqualene-lanosterol cyclase; squalene epoxidase-cyclase; (S)-2,3-epoxysqualene mutase (cyclizing, lanosterol-forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, lanosterol-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9032-71-7

References:

1. Dean, P.D.G., Oritz de Montellano, P.R., Bloch, K. and Corey, E.J. A soluble 2,3-oxidosqualene sterol cyclase. J. Biol. Chem. 242 (1967) 3014-3015. [PMID: 6027261]

[EC 5.4.99.7 created 1961 as EC 1.99.1.13, transferred 1965 to EC 1.14.1.3, part transferred 1972 to EC 5.4.99.7 rest to EC 1.14.99.7]

EC 5.4.99.8

Accepted name: cycloartenol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = cycloartenol

For reaction pathway click here.

Other name(s): 2,3-epoxysqualene cycloartenol-cyclase; squalene-2,3-epoxide-cycloartenol cyclase; 2,3-epoxysqualene cycloartenol-cyclase; 2,3-epoxysqualene-cycloartenol cyclase; 2,3-oxidosqualene-cycloartenol cyclase; (S)-2,3-epoxysqualene mutase (cyclizing, cycloartenol-forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, cycloartenol-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9075-25-6

References:

1. Rees, H.H., Goad, L.J. and Goodwin, T.W. 2,3-Oxidosqualene cycloartenol cyclase from Ochromonas malhamensis. Biochim. Biophys. Acta 176 (1969) 892-894. [PMID: 5797101]

[EC 5.4.99.8 created 1972]

EC 5.4.99.9

Accepted name: UDP-galactopyranose mutase

Reaction: UDP-α-D-galactopyranose = UDP-α-D-galactofuranose

For diagram of reaction click here and (mechanism here).

Other name(s): UGM; UDP-D-galactopyranose furanomutase

Systematic name: UDP-α-D-galactopyranose furanomutase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 174632-18-9

References:

1. Trejo, A.G., Chittenden, G.J.F., Buchanan, J.G. and Baddiley, J. Uridine diphosphate α-D-galactofuranose, an intermediate in the biosynthesis of galactofuranosyl residues. Biochem. J. 117 (1970) 637-639. [PMID: 5419754]

2. Karunan Partha, S., Bonderoff, S.A., van Straaten, K.E. and Sanders, D.A. Expression, purification and preliminary X-ray crystallographic analysis of UDP-galactopyranose mutase from Deinococcus radiodurans. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 843-845. [PMID: 19652355]

3. Dhatwalia, R., Singh, H., Oppenheimer, M., Karr, D.B., Nix, J.C., Sobrado, P. and Tanner, J.J. Crystal structures and small-angle x-ray scattering analysis of UDP-galactopyranose mutase from the pathogenic fungus Aspergillus fumigatus. J. Biol. Chem. 287 (2012) 9041-9051. [PMID: 22294687]

4. van Straaten, K.E., Routier, F.H. and Sanders, D.A. Towards the crystal structure elucidation of eukaryotic UDP-galactopyranose mutase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 (2012) 455-459. [PMID: 22505419]

[EC 5.4.99.9 created 1984]

[EC 5.4.99.10 Deleted entry: Now included with EC 5.4.99.11 isomaltulose synthase (EC 5.4.99.10 created 1984, deleted 1992)]

EC 5.4.99.11

Accepted name: isomaltulose synthase

Reaction: sucrose = 6-O-α-D-glucopyranosyl-D-fructofuranose

Other name(s): isomaltulose synthetase; sucrose α-glucosyltransferase; trehalulose synthase

Systematic name: sucrose glucosylmutase

Comments: The enzyme simultaneously produces isomaltulose (6-O-α-D-glucopyranosyl-D-fructose) and smaller amounts of trehalulose (1-O-α-D-glucopyranosyl-β-D-fructose) from sucrose.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 159940-49-5

References:

1. Cheetham, P.S.J. The extraction and mechanism of a novel isomaltulose-synthesizing enzyme from Erwinia rhapontici. Biochem. J. 220 (1984) 213-220. [PMID: 6743261]

2. Cheetham, P.S.J., Imber, C.E. and Isherwood, J. The formation of isomaltulose by immobilized Erwinia rhapontici. Nature 299 (1982) 628-631.

[EC 5.4.99.11 created 1989 (EC 5.4.99.10 created 1984, incorporated 1992)]

EC 5.4.99.12

Accepted name: tRNA pseudouridine38-40 synthase

Reaction: tRNA uridine38-40 = tRNA pseudouridine38-40

For diagram of mechanism click here.

Other name(s): TruA; tRNA pseudouridine synthase I; PSUI; hisT (gene name)

Systematic name: tRNA-uridine38-40 uracil mutase

Comments: The uridylate residues at positions 38, 39 and 40 of nearly all tRNAs are isomerized to pseudouridine. TruA specifically modifies uridines at positions 38, 39, and/or 40 in the anticodon stem loop of tRNAs with highly divergent sequences and structures [1].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 61506-89-6

References:

1. Hur, S. and Stroud, R.M. How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA. Mol. Cell 26 (2007) 189-203. [PMID: 17466622]

2. Huang, L., Pookanjanatavip, M., Gu, X. and Santi, D.V. A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst. Biochemistry 37 (1998) 344-351. [PMID: 9425056]

3. Kammen, H.O., Marvel, C.C., Hardy, L. and Penhoet, E.E. Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. J. Biol. Chem. 263 (1988) 2255-2263. [PMID: 3276686]

4. Turnbough, C.L., Jr., Neill, R.J., Landsberg, R. and Ames, B.N. Pseudouridylation of tRNAs and its role in regulation in Salmonella typhimurium. J. Biol. Chem. 254 (1979) 5111-5119. [PMID: 376505]

5. Zhao, X. and Horne, D.A. The role of cysteine residues in the rearrangement of uridine to pseudouridine catalyzed by pseudouridine synthase I. J. Biol. Chem. 272 (1997) 1950-1955. [PMID: 8999885]

6. Foster, P.G., Huang, L., Santi, D.V. and Stroud, R.M. The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I. Nat. Struct. Biol. 7 (2000) 23-27. [PMID: 10625422]

7. Dong, X., Bessho, Y., Shibata, R., Nishimoto, M., Shirouzu, M., Kuramitsu, S. and Yokoyama, S. Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8. RNA Biol 3 (2006) 115-122. [PMID: 17114947]

8. Arena, F., Ciliberto, G., Ciampi, S. and Cortese, R. Purification of pseudouridylate synthetase I from Salmonella typhimurium. Nucleic Acids Res. 5 (1978) 4523-4536. [PMID: 370771]

[EC 5.4.99.12 created 1990, modified 2011]

EC 5.4.99.13

Accepted name: isobutyryl-CoA mutase

Reaction: 2-methylpropanoyl-CoA = butanoyl-CoA

Other name(s): isobutyryl coenzyme A mutase; butyryl-CoA:isobutyryl-CoA mutase

Systematic name: 2-methylpropanoyl-CoA CoA-carbonylmutase

Comments: Requires a cobamide coenzyme.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 116405-23-3

References:

1. Brendelberger, G., Rétey, J., Ashworth, D.M., Reynolds, K., Willenbrock, F. and Robinson, J.A. The enzymic interconversion of isobutyryl and N-butyrylcarba(dethia)-coenzyme-A - a coenzyme-B12-dependent carbon skeleton rearrangement. Angew. Chem. Int. Ed. Engl. 27 (1988) 1089-1091.

[EC 5.4.99.13 created 1992]

EC 5.4.99.14

Accepted name: 4-carboxymethyl-4-methylbutenolide mutase

Reaction: 4-carboxymethyl-4-methylbut-2-en-1,4-olide = 4-carboxymethyl-3-methylbut-2-en-1,4-olide

Other name(s): 4-methyl-2-enelactone isomerase; 4-methylmuconolactone methylisomerase; 4-methyl-3-enelactone methyl isomerase

Systematic name: 4-carboxymethyl-4-methylbut-2-en-1,4-olide methylmutase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 115300-03-3

References:

1. Bruce, N.C. and Cain, R.B. β-Methylmuconolactone, a key intermediate in the dissimilation of methylaromatic compounds by a modified 3-oxoadipate pathway evolved in nocardioform actinomycetes. FEMS Microbiol. Lett. 50 (1988) 233-239.

[EC 5.4.99.14 created 1992]

EC 5.4.99.15

Accepted name: (1→4)-α-D-glucan 1-α-D-glucosylmutase

Reaction: 4-[(1→4)-α-D-glucosyl]n-1-D-glucose = 1-α-D-[(1→4)-α-D-glucosyl]n-1-α-D-glucopyranoside

Other name(s): malto-oligosyltrehalose synthase; maltodextrin α-D-glucosyltransferase

Systematic name: (1→4)-α-D-glucan 1-α-D-glucosylmutase

Comments: The enzyme from Arthrobacter sp., Sulfolobus acidocaldarius acts on (1→4)-α-D-glucans containing three or more (1→4)-α-linked D-glucose units. Not active towards maltose.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 170780-49-1

References:

1. Maruta, K., Nakada, T., Kubota, M., Chaen, H., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Formation of trehalose from maltooligosaccharides by a novel enzymatic system. Biosci. Biotechnol. Biochem. 59 (1995) 1829-1834. [PMID: 8534970]

2. Nakada, T., Maruta, K., Tsusaki, K., Kubota, M., Chaen, H., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Purification and properties of a novel enzyme, maltooligosyl trehalose synthase, from Arthrobacter sp. Q36. Biosci. Biotechnol. Biochem. 59 (1995) 2210-2214. [PMID: 8611744]

3. Nakada, T., Ikegami, S., Chaen, H., Kubota, M., Fukuda, S., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Purification and characterization of thermostable maltooligosyl trehalose synthase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. Biosci. Biotechnol. Biochem. 60 (1996) 263-266. [PMID: 9063973]

[EC 5.4.99.15 created 1999]

EC 5.4.99.16

Accepted name: maltose α-D-glucosyltransferase

Reaction: maltose = α,α-trehalose

Other name(s): trehalose synthase; maltose glucosylmutase

Systematic name: maltose α-D-glucosylmutase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 395644-91-4

References:

1. Nishimoto, T., Nakano, M., Ikegami, S., Chaen, H., Fukuda, S., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Existence of a novel enzyme converting maltose to trehalose. Biosci. Biotechnol. Biochem. 59 (1995) 2189-2190.

2. Nishimoto, T., Nakano, M., Nakada, T., Chaen, H., Fukuda, S., Sugimoto, T., Kurimoto, M., Tsujisaka, Y. Purification and properties of a novel enzyme, trehalose synthase, from Pimelobacter sp. R48. Biosci. Biotechnol. Biochem. 60 (1996) 640-644. [PMID: 8829531]

[EC 5.4.99.16 created 1999]

EC 5.4.99.17

Accepted name: squalene—hopene cyclase

Reaction: squalene = hop-22(29)-ene

For diagram of reaction click here

Systematic name: squalene mutase (cyclizing, hop-22(29)-ene-forming)

Comments: The enzyme also produces the cyclization product hopan-22-ol by addition of water (cf. EC 4.2.1.129, squalene—hopanol cyclase). Hopene and hopanol are formed at a constant ratio of 5:1.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 76600-69-6

References:

1. Hoshino, T. and Sato, T. Squalene-hopene cyclase: catalytic mechanism and substrate recognition. Chem. Commun. (2002) 291-301. [PMID: 12120044]

2. Hoshino, T., Nakano, S., Kondo, T., Sato, T. and Miyoshi, A. Squalene-hopene cyclase: final deprotonation reaction, conformational analysis for the cyclization of (3R,S)-2,3-oxidosqualene and further evidence for the requirement of an isopropylidene moiety both for initiation of the polycyclization cascade and for the formation of the 5-membered E-ring. Org Biomol Chem 2 (2004) 1456-1470. [PMID: 15136801]

3. Sato, T., Kouda, M. and Hoshino, T. Site-directed mutagenesis experiments on the putative deprotonation site of squalene-hopene cyclase from Alicyclobacillus acidocaldarius. Biosci. Biotechnol. Biochem. 68 (2004) 728-738. [PMID: 15056909]

4. Reinert, D.J., Balliano, G. and Schulz, G.E. Conversion of squalene to the pentacarbocyclic hopene. Chem. Biol. 11 (2004) 121-126. [PMID: 15113001]

[EC 5.4.99.17 created 2002, modified 2011]

EC 5.4.99.18

Accepted name: 5-(carboxyamino)imidazole ribonucleotide mutase

Reaction: 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate

For diagram, click here

Other name(s): N5-CAIR mutase; PurE; N5-carboxyaminoimidazole ribonucleotide mutase; class I PurE

Systematic name: 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole carboxymutase

Comments: In eubacteria, fungi and plants, this enzyme, along with EC 6.3.4.18, 5-(carboxyamino)imidazole ribonucleotide synthase, is required to carry out the single reaction catalysed by EC 4.1.1.21, phosphoribosylaminoimidazole carboxylase, in vertebrates [6]. In the absence of EC 6.3.2.6, phosphoribosylaminoimidazolesuccinocarboxamide synthase, the reaction is reversible [3]. The substrate is readily converted into 5-amino-1-(5-phospho-D-ribosyl)imidazole by non-enzymic decarboxylation [3].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 255379-40-9

References:

1. Meyer, E., Leonard, N.J., Bhat, B., Stubbe, J. and Smith, J.M. Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway. Biochemistry 31 (1992) 5022-5032. [PMID: 1534690]

2. Mueller, E.J., Meyer, E., Rudolph, J., Davisson, V.J. and Stubbe, J. N5-Carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. Biochemistry 33 (1994) 2269-2278. [PMID: 8117684]

3. Meyer, E., Kappock, T.J., Osuji, C. and Stubbe, J. Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase. Biochemistry 38 (1999) 3012-3018. [PMID: 10074353]

4. Mathews, I.I., Kappock, T.J., Stubbe, J. and Ealick, S.E. Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway. Structure 7 (1999) 1395-1406. [PMID: 10574791]

5.  Firestine, S.M., Poon, S.W., Mueller, E.J., Stubbe, J. and Davisson, V.J. Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: a case for divergent catalytic mechanisms. Biochemistry 33 (1994) 11927–11934. [PMID: 7918411]

6.  Firestine, S.M., Misialek, S., Toffaletti, D.L., Klem, T.J., Perfect, J.R. and Davisson, V.J. Biochemical role of the Cryptococcus neoformans ADE2 protein in fungal de novo purine biosynthesis. Arch. Biochem. Biophys. 351 (1998) 123–134. [PMID: 9500840]

[EC 5.4.99.18 created 2006]

EC 5.4.99.19

Accepted name: 16S rRNA pseudouridine516 synthase

Reaction: 16S rRNA uridine516 = 16S rRNA pseudouridine516

For diagram of mechanism click here.

Other name(s): 16S RNA pseudouridine516 synthase; 16S PsiI516 synthase; 16S RNA Ψ516 synthase; RNA pseudouridine synthase RsuA; RsuA; 16S RNA pseudouridine 516 synthase

Systematic name: 16S rRNA-uridine516 uracil mutase

Comments: The enzyme is specific for uridine516 in 16S rRNA. In vitro, the enzyme does not modify free 16S rRNA. The preferred substrate is a 5'-terminal fragment of 16S rRNA complexed with 30S ribosomal proteins [1].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Wrzesinski, J., Bakin, A., Nurse, K., Lane, B.G. and Ofengand, J. Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli. Biochemistry 34 (1995) 8904-8913. [PMID: 7612632]

2. Conrad, J., Niu, L., Rudd, K., Lane, B.G. and Ofengand, J. 16S ribosomal RNA pseudouridine synthase RsuA of Escherichia coli: deletion, mutation of the conserved Asp102 residue, and sequence comparison among all other pseudouridine synthases. RNA 5 (1999) 751-763. [PMID: 10376875]

3. Sivaraman, J., Sauve, V., Larocque, R., Stura, E.A., Schrag, J.D., Cygler, M. and Matte, A. Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Nat. Struct. Biol. 9 (2002) 353-358. [PMID: 11953756]

[EC 5.4.99.19 created 2011]

EC 5.4.99.20

Accepted name: 23S rRNA pseudouridine2457 synthase

Reaction: 23S rRNA uridine2457 = 23S rRNA pseudouridine2457

For diagram of mechanism click here.

Other name(s): RluE; YmfC

Systematic name: 23S rRNA-uridine2457 uracil mutase

Comments: The enzyme modifies uridine2457 in a stem of 23S RNA in Escherichia coli.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615. [PMID: 11720289]

2. Pan, H., Ho, J.D., Stroud, R.M. and Finer-Moore, J. The crystal structure of E. coli rRNA pseudouridine synthase RluE. J. Mol. Biol. 367 (2007) 1459-1470. [PMID: 17320904]

[EC 5.4.99.20 created 2011]

EC 5.4.99.21

Accepted name: 23S rRNA pseudouridine2604 synthase

Reaction: 23S rRNA uridine2604 = 23S rRNA pseudouridine2604

For diagram of mechanism click here.

Other name(s): RluF; YjbC

Systematic name: 23S rRNA-uridine2604 uracil mutase

Comments: The enzyme is not completely specific for uridine2604 and can, to a small extent, also react with uridine2605 [1].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615. [PMID: 11720289]

2. Alian, A., DeGiovanni, A., Griner, S.L., Finer-Moore, J.S. and Stroud, R.M. Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome. J. Mol. Biol. 388 (2009) 785-800. [PMID: 19298824]

3. Sunita, S., Zhenxing, H., Swaathi, J., Cygler, M., Matte, A. and Sivaraman, J. Domain organization and crystal structure of the catalytic domain of E. coli RluF, a pseudouridine synthase that acts on 23S rRNA. J. Mol. Biol. 359 (2006) 998-1009. [PMID: 16712869]

[EC 5.4.99.21 created 2011]

EC 5.4.99.22

Accepted name: 23S rRNA pseudouridine2605 synthase

Reaction: 23S rRNA uridine2605 = 23S rRNA pseudouridine2605

For diagram of mechanism click here.

Other name(s): RluB; YciL

Systematic name: 23S rRNA-uridine2605 uracil mutase

Comments: Pseudouridine synthase RluB converts uridine2605 of 23S rRNA to pseudouridine.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615. [PMID: 11720289]

2. Jiang, M., Sullivan, S.M., Walker, A.K., Strahler, J.R., Andrews, P.C. and Maddock, J.R. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J. Bacteriol. 189 (2007) 3434-3444. [PMID: 17337586]

[EC 5.4.99.22 created 2011]

EC 5.4.99.23

Accepted name: 23S rRNA pseudouridine1911/1915/1917 synthase

Reaction: 23S rRNA uridine1911/uridine1915/uridine1917 = 23S rRNA pseudouridine1911/pseudouridine1915/pseudouridine1917

For diagram of mechanism click here.

Other name(s): RluD; pseudouridine synthase RluD

Systematic name: 23S rRNA-uridine1911/1915/1917 uracil mutase

Comments: Pseudouridine synthase RluD converts uridines at positions 1911, 1915, and 1917 of 23S rRNA to pseudouridines. These nucleotides are located in the functionally important helix-loop 69 of 23S rRNA [1].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Leppik, M., Peil, L., Kipper, K., Liiv, A. and Remme, J. Substrate specificity of the pseudouridine synthase RluD in Escherichia coli. FEBS J. 274 (2007) 5759-5766. [PMID: 17937767]

2. Ejby, M., Sorensen, M.A. and Pedersen, S. Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination. Proc. Natl. Acad. Sci. USA 104 (2007) 19410-19415. [PMID: 18032607]

3. Sivaraman, J., Iannuzzi, P., Cygler, M. and Matte, A. Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. J. Mol. Biol. 335 (2004) 87-101. [PMID: 14659742]

4. Wrzesinski, J., Bakin, A., Ofengand, J. and Lane, B.G. Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD). IUBMB Life 50 (2000) 33-37. [PMID: 11087118]

[EC 5.4.99.23 created 2011]

EC 5.4.99.24

Accepted name: 23S rRNA pseudouridine955/2504/2580 synthase

Reaction: 23S rRNA uridine955/uridine2504/uridine2580 = 23S rRNA pseudouridine955/pseudouridine2504/pseudouridine2580

For diagram of mechanism click here.

Other name(s): RluC; pseudouridine synthase RluC

Systematic name: 23S rRNA-uridine955/2504/2580 uracil mutase

Comments: The enzyme converts uridines at position 955, 2504 and 2580 of 23S rRNA to pseudouridines.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Jiang, M., Sullivan, S.M., Walker, A.K., Strahler, J.R., Andrews, P.C. and Maddock, J.R. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J. Bacteriol. 189 (2007) 3434-3444. [PMID: 17337586]

2. Conrad, J., Sun, D., Englund, N. and Ofengand, J. The rluC gene of Escherichia coli codes for a pseudouridine synthase that is solely responsible for synthesis of pseudouridine at positions 955, 2504, and 2580 in 23 S ribosomal RNA. J. Biol. Chem. 273 (1998) 18562-18566. [PMID: 9660827]

3. Corollo, D., Blair-Johnson, M., Conrad, J., Fiedler, T., Sun, D., Wang, L., Ofengand, J. and Fenna, R. Crystallization and characterization of a fragment of pseudouridine synthase RluC from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 302-304. [PMID: 10089432]

4. Toh, S.M. and Mankin, A.S. An indigenous posttranscriptional modification in the ribosomal peptidyl transferase center confers resistance to an array of protein synthesis inhibitors. J. Mol. Biol. 380 (2008) 593-597. [PMID: 18554609]

[EC 5.4.99.24 created 2011]

EC 5.4.99.25

Accepted name: tRNA pseudouridine55 synthase

Reaction: tRNA uridine55 = tRNA pseudouridine55

For diagram of mechanism click here.

Other name(s): TruB; aCbf5; Pus4; YNL292w (gene name); Ψ55 tRNA pseudouridine synthase; tRNA:Ψ55-synthase; tRNA pseudouridine 55 synthase; tRNA:pseudouridine-55 synthase; Ψ55 synthase; tRNA Ψ55 synthase; tRNA:Ψ55 synthase; tRNA-uridine55 uracil mutase; Pus10; tRNA-uridine54/55 uracil mutase

Systematic name: tRNA-uridine55 uracil mutase

Comments: Pseudouridine synthase TruB from Escherichia coli specifically modifies uridine55 in tRNA molecules [1]. The bifunctional archaeal enzyme also catalyses the pseudouridylation of uridine54 [6]. It is not known whether the enzyme from Escherichia coli can also act on position 54 in vitro, since this position is occupied in Escherichia coli tRNAs by thymine.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 430429-15-5

References:

1. Nurse, K., Wrzesinski, J., Bakin, A., Lane, B.G. and Ofengand, J. Purification, cloning, and properties of the tRNA Ψ55 synthase from Escherichia coli. RNA 1 (1995) 102-112. [PMID: 7489483]

2. Becker, H.F., Motorin, Y., Planta, R.J. and Grosjean, H. The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of Ψ55 in both mitochondrial and cytoplasmic tRNAs. Nucleic Acids Res. 25 (1997) 4493-4499. [PMID: 9358157]

3. Pienkowska, J., Wrzesinski, J. and Szweykowska-Kulinska, Z. A cell-free yellow lupin extract containing activities of pseudouridine 35 and 55 synthases. Acta Biochim. Pol. 45 (1998) 745-754. [PMID: 9918501]

4. Chaudhuri, B.N., Chan, S., Perry, L.J. and Yeates, T.O. Crystal structure of the apo forms of Ψ55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft. J. Biol. Chem. 279 (2004) 24585-24591. [PMID: 15028724]

5. Hoang, C., Hamilton, C.S., Mueller, E.G. and Ferre-D'Amare, A.R. Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain. Protein Sci. 14 (2005) 2201-2206. [PMID: 15987897]

6. Gurha, P. and Gupta, R. Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA. RNA 14 (2008) 2521-2527. [PMID: 18952823]

[EC 5.4.99.25 created 2011, modified 2011]

EC 5.4.99.26

Accepted name: tRNA pseudouridine65 synthase

Reaction: tRNA uridine65 = tRNA pseudouridine65

For diagram of mechanism click here.

Other name(s): TruC; YqcB

Systematic name: tRNA-uridine65 uracil mutase

Comments: TruC specifically modifies uridines at positions 65 in tRNA.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Del Campo, M., Kaya, Y. and Ofengand, J. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7 (2001) 1603-1615. [PMID: 11720289]

[EC 5.4.99.26 created 2011]

EC 5.4.99.27

Accepted name: tRNA pseudouridine13 synthase

Reaction: tRNA uridine13 = tRNA pseudouridine13

For diagram of mechanism click here.

Other name(s): TruD; YgbO; tRNA PSI13 synthase; RNA:PSI-synthase Pus7p; Pus7p; RNA:pseudouridine-synthase Pus7p; Pus7 protein

Systematic name: tRNA-uridine13 uracil mutase

Comments: Pseudouridine synthase TruD from Escherichia coli specifically acts on uridine13 in tRNA [2,3]. The Pus7 protein from Saccharomyces cerevisiae is a multisite-multisubstrate pseudouridine synthase that is able to modify uridine13 in several yeast tRNAs, uridine35 in the pre-tRNATyr, uridine35 in U2 small nuclear RNA, and uridine50 in 5S rRNA [5].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Ericsson, U.B., Nordlund, P. and Hallberg, B.M. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. FEBS Lett. 565 (2004) 59-64. [PMID: 15135053]

2. Chan, C.M. and Huang, R.H. Enzymatic characterization and mutational studies of TruD—the fifth family of pseudouridine synthases. Arch. Biochem. Biophys. 489 (2009) 15-19. [PMID: 19664587]

3. Kaya, Y. and Ofengand, J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA 9 (2003) 711-721. [PMID: 12756329]

4. Behm-Ansmant, I., Urban, A., Ma, X., Yu, Y.T., Motorin, Y. and Branlant, C. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Ψ-synthase also acting on tRNAs. RNA 9 (2003) 1371-1382. [PMID: 14561887]

5. Urban, A., Behm-Ansmant, I., Branlant, C. and Motorin, Y. RNA sequence and two-dimensional structure features required for efficient substrate modification by the Saccharomyces cerevisiae RNA:Ψ-synthase Pus7p. J. Biol. Chem. 284 (2009) 5845-5858. [PMID: 19114708]

[EC 5.4.99.27 created 2011]

EC 5.4.99.28

Accepted name: tRNA pseudouridine32 synthase

Reaction: tRNA uridine32 = tRNA pseudouridine32

For diagram of mechanism click here.

Other name(s): RluA (ambiguous); pseudouridine synthase RluA (ambiguous)

Systematic name: tRNA-uridine32 uracil mutase

Comments: The dual-specificity enzyme also catalyses the formation of pseudouridine746 in 23S rRNA [5]. cf. EC 5.4.99.29 (23S rRNA pseudouridine746 synthase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S., Mueller, E.G. and Ferre-D'Amare, A.R. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol. Cell 24 (2006) 535-545. [PMID: 17188032]

2. Spedaliere, C.J., Hamilton, C.S. and Mueller, E.G. Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues. Biochemistry 39 (2000) 9459-9465. [PMID: 10924141]

3. Raychaudhuri, S., Niu, L., Conrad, J., Lane, B.G. and Ofengand, J. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J. Biol. Chem. 274 (1999) 18880-18886. [PMID: 10383384]

4. Ramamurthy, V., Swann, S.L., Spedaliere, C.J. and Mueller, E.G. Role of cysteine residues in pseudouridine synthases of different families. Biochemistry 38 (1999) 13106-13111. [PMID: 10529181]

5. Wrzesinski, J., Nurse, K., Bakin, A., Lane, B.G. and Ofengand, J. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi746 in 23S RNA is also specific for Ψ32 in tRNA(phe). RNA 1 (1995) 437-448. [PMID: 7493321]

[EC 5.4.99.28 created 2011]

EC 5.4.99.29

Accepted name: 23S rRNA pseudouridine746 synthase

Reaction: 23S rRNA uridine746 = 23S rRNA pseudouridine746

For diagram of mechanism click here.

Other name(s): RluA (ambiguous); 23S RNA PSI746 synthase; 23S rRNA pseudouridine synthase; pseudouridine synthase RluA (ambiguous)

Systematic name: 23S rRNA-uridine746 uracil mutase

Comments: RluA is the sole protein responsible for the in vivo formation of 23S RNA pseudouridine746 [2]. The dual-specificity enzyme also catalyses the formation of uridine32 in tRNA [3]. cf. EC 5.4.99.28 (tRNA pseudouridine32 synthase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S., Mueller, E.G. and Ferre-D'Amare, A.R. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol. Cell 24 (2006) 535-545. [PMID: 17188032]

2. Raychaudhuri, S., Niu, L., Conrad, J., Lane, B.G. and Ofengand, J. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J. Biol. Chem. 274 (1999) 18880-18886. [PMID: 10383384]

3. Wrzesinski, J., Nurse, K., Bakin, A., Lane, B.G. and Ofengand, J. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi746 in 23S RNA is also specific for Ψ32 in tRNA(phe). RNA 1 (1995) 437-448. [PMID: 7493321]

[EC 5.4.99.29 created 2011]

EC 5.4.99.30

Accepted name: UDP-arabinopyranose mutase

Reaction: UDP-β-L-arabinofuranose = UDP-β-L-arabinopyranose

Other name(s): Os03g40270 protein; UAM1; UAM3; RGP1; RGP3; OsUAM1; OsUAM2; Os03g0599800 protein; Os07g41360 protein

Systematic name: UDP-arabinopyranose pyranomutase

Comments: The reaction is reversible and at thermodynamic equilibrium the pyranose form is favored over the furanose form (90:10) [1].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Konishi, T., Takeda, T., Miyazaki, Y., Ohnishi-Kameyama, M., Hayashi, T., O'Neill, M.A. and Ishii, T. A plant mutase that interconverts UDP-arabinofuranose and UDP-arabinopyranose. Glycobiology 17 (2007) 345-354. [PMID: 17182701]

2. Konishi, T., Ohnishi-Kameyama, M., Funane, K., Miyazaki, Y., Konishi, T. and Ishii, T. An arginyl residue in rice UDP-arabinopyranose mutase is required for catalytic activity and autoglycosylation. Carbohydr. Res. 345 (2010) 787-791. [PMID: 20149347]

3. Konishi, T., Miyazaki, Y., Yamakawa, S., Iwai, H., Satoh, S. and Ishii, T. Purification and biochemical characterization of recombinant rice UDP-arabinopyranose mutase generated in insect cells. Biosci. Biotechnol. Biochem. 74 (2010) 191-194. [PMID: 20057139]

[EC 5.4.99.30 created 2011]

EC 5.4.99.31

Accepted name: thalianol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = thalianol

For diagram of reaction click here.

Other name(s): (S)-2,3-epoxysqualene mutase (cyclizing, thalianol-forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, thalianol-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Fazio, G.C., Xu, R. and Matsuda, S.P.T. Genome mining to identify new plant triterpenoids. J. Am. Chem. Soc. 126 (2004) 5678-5679. [PMID: 15125655]

[EC 5.4.99.31 created 2011]

EC 5.4.99.32

Accepted name: protostadienol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = (17Z)-protosta-17(20),24-dien-3β-ol

For reaction pathway click here.

Other name(s): PdsA; (S)-2,3-epoxysqualene mutase [cyclizing, (17Z)-protosta-17(20),24-dien-3β-ol-forming]

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase [cyclizing, (17Z)-protosta-17(20),24-dien-3β-ol-forming]

Comments: (17Z)-Protosta-17(20),24-dien-3β-ol is a precursor of the steroidal antibiotic helvolic acid.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Lodeiro, S., Xiong, Q., Wilson, W.K., Ivanova, Y., Smith, M.L., May, G.S. and Matsuda, S.P. Protostadienol biosynthesis and metabolism in the pathogenic fungus Aspergillus fumigatus. Org Lett 11 (2009) 1241-1244. [PMID: 19216560]

[EC 5.4.99.32 created 2011]

EC 5.4.99.33

Accepted name: cucurbitadienol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = cucurbitadienol

For reaction pathway click here.

Other name(s): CPQ (gene name); (S)-2,3-epoxysqualene mutase (cyclizing, cucurbitadienol-forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, cucurbitadienol-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Shibuya, M., Adachi, S., and Ebizuka, Y. Cucurbitadienol synthase, the first committed enzyme for cucurbitacin biosynthesis, is a distinct enzyme from cycloartenol synthase for phytosterol biosynthesis. Tetrahedron 60 (2004) 6995-7003.

[EC 5.4.99.33 created 2011]

EC 5.4.99.34

Accepted name: germanicol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = germanicol

For diagram of reaction click here.

Other name(s): RsM1; (S)-2,3-epoxysqualene mutase (cyclizing, germanicol-forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, germanicol-forming)

Comments: The enzyme produces germanicol, β-amyrin and lupeol in the ratio 63:33:4.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Basyuni, M., Oku, H., Tsujimoto, E., Kinjo, K., Baba, S. and Takara, K. Triterpene synthases from the Okinawan mangrove tribe, Rhizophoraceae. FEBS J. 274 (2007) 5028-5042. [PMID: 17803686]

[EC 5.4.99.34 created 2011]

EC 5.4.99.35

Accepted name: taraxerol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = taraxerol

For diagram of reaction click here.

Other name(s): RsM2; (S)-2,3-epoxysqualene mutase (cyclizing, taraxerol-forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, taraxerol-forming)

Comments: The enzyme gives taraxerol, β-amyrin and lupeol in the ratio 70:17:13.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Basyuni, M., Oku, H., Tsujimoto, E., Kinjo, K., Baba, S. and Takara, K. Triterpene synthases from the Okinawan mangrove tribe, Rhizophoraceae. FEBS J. 274 (2007) 5028-5042. [PMID: 17803686]

[EC 5.4.99.35 created 2011]

EC 5.4.99.36

Accepted name: isomultiflorenol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = isomultiflorenol

For diagram of reaction click here.

Other name(s): LcIMS1; (S)-2,3-epoxysqualene mutase (cyclizing, isomultiflorenol-forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, isomultiflorenol-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Hayashi, H., Huang, P., Inoue, K., Hiraoka, N., Ikeshiro, Y., Yazaki, K., Tanaka, S., Kushiro, T., Shibuya, M. and Ebizuka, Y. Molecular cloning and characterization of isomultiflorenol synthase, a new triterpene synthase from Luffa cylindrica, involved in biosynthesis of bryonolic acid. Eur. J. Biochem. 268 (2001) 6311-6317. [PMID: 11733028]

[EC 5.4.99.36 created 2011]

EC 5.4.99.37

Accepted name: dammaradiene synthase

Reaction: squalene = dammara-20,24-diene

For diagram of reaction click here.

Systematic name: squalene mutase (cyclizing, dammara-20,24-diene-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Shinozaki, J., Shibuya, M., Masuda, K. and Ebizuka, Y. Dammaradiene synthase, a squalene cyclase, from Dryopteris crassirhizoma Nakai. Phytochemistry 69 (2008) 2559-2564. [PMID: 18790509]

[EC 5.4.99.37 created 2011]

EC 5.4.99.38

Accepted name: camelliol C synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = camelliol C

For diagram of reaction click here.

Other name(s): CAMS1; LUP3 (gene name)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, camelliol-C-forming)

Comments: The product is 97% camelliol, 2% achilleol A and 0.2% β-amyrin. Achilleol is an isomer of camelliol C with a 4-methylenecyclohexanol ring system. This enzyme probably evolved from EC 5.4.99.39, β-amyrin synthase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Kolesnikova, M.D., Wilson, W.K., Lynch, D.A., Obermeyer, A.C. and Matsuda, S.P. Arabidopsis camelliol C synthase evolved from enzymes that make pentacycles. Org. Lett. 9 (2007) 5223-5226. [PMID: 17985917]

[EC 5.4.99.38 created 2011]

EC 5.4.99.39

Accepted name: β-amyrin synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = β-amyrin

For diagram of reaction click here.

Other name(s): 2,3-oxidosqualene β-amyrin cyclase; AsbAS1; BPY; EtAS; GgbAS1; LjAMY1; MtAMY1; PNY; BgbAS

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, β-amyrin-forming)

Comments: Some organism possess a monofunctional β-amyrin synthase [3,4,6-11], other have a multifunctional enzyme that also catalyses the synthesis of α amyrin (EC 5.4.99.40) [5] or lupeol (EC 5.4.99.41) [6].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Abe, I, Ebizuka, Y., Seo, S. and Sankawa, U. Purification of squalene-2,3-epoxide cyclases from cell suspension cultures of Rabdosia japonica Hara. FEBS Lett. 249 (1989) 100-104.

2. Abe, I., Sankawa, U. and Ebizuka, Y. Purification of 2,3-oxdosqualene:β-amyrin cyclase from pea seedlings. Chem. Pharm. Bull. 37 (1989) 536.

3. Kushiro, T., Shibuya, M. and Ebizuka, Y. β-Amyrin synthase-cloning of oxidosqualene cyclase that catalyzes the formation of the most popular triterpene among higher plants. Eur. J. Biochem. 256 (1998) 238-244. [PMID: 9746369]

4. Hayashi, H., Huang, P., Kirakosyan, A., Inoue, K., Hiraoka, N., Ikeshiro, Y., Kushiro, T., Shibuya, M. and Ebizuka, Y. Cloning and characterization of a cDNA encoding β-amyrin synthase involved in glycyrrhizin and soyasaponin biosyntheses in licorice. Biol. Pharm. Bull. 24 (2001) 912-916. [PMID: 11510484]

5. Husselstein-Muller, T., Schaller, H. and Benveniste, P. Molecular cloning and expression in yeast of 2,3-oxidosqualene-triterpenoid cyclases from Arabidopsis thaliana. Plant Mol. Biol. 45 (2001) 75-92. [PMID: 11247608]

6. Iturbe-Ormaetxe, I., Haralampidis, K., Papadopoulou, K. and Osbourn, A.E. Molecular cloning and characterization of triterpene synthases from Medicago truncatula and Lotus japonicus. Plant Mol. Biol. 51 (2003) 731-743. [PMID: 12683345]

7. Zhang, H., Shibuya, M., Yokota, S. and Ebizuka, Y. Oxidosqualene cyclases from cell suspension cultures of Betula platyphylla var. japonica: molecular evolution of oxidosqualene cyclases in higher plants. Biol. Pharm. Bull. 26 (2003) 642-650. [PMID: 12736505]

8. Hayashi, H., Huang, P., Takada, S., Obinata, M., Inoue, K., Shibuya, M. and Ebizuka, Y. Differential expression of three oxidosqualene cyclase mRNAs in Glycyrrhiza glabra. Biol. Pharm. Bull. 27 (2004) 1086-1092. [PMID: 15256745]

9. Kajikawa, M., Yamato, K.T., Fukuzawa, H., Sakai, Y., Uchida, H. and Ohyama, K. Cloning and characterization of a cDNA encoding β-amyrin synthase from petroleum plant Euphorbia tirucalli L. Phytochemistry 66 (2005) 1759-1766. [PMID: 16005035]

10. Basyuni, M., Oku, H., Tsujimoto, E., Kinjo, K., Baba, S. and Takara, K. Triterpene synthases from the Okinawan mangrove tribe, Rhizophoraceae. FEBS J. 274 (2007) 5028-5042. [PMID: 17803686]

11. Liu, Y., Cai, Y., Zhao, Z., Wang, J., Li, J., Xin, W., Xia, G. and Xiang, F. Cloning and functional analysis of a β-amyrin synthase gene associated with oleanolic acid biosynthesis in Gentiana straminea MAXIM. Biol. Pharm. Bull. 32 (2009) 818-824. [PMID: 19420748]

[EC 5.4.99.39 created 2011]

EC 5.4.99.40

Accepted name: α-amyrin synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = α-amyrin

For diagram of reaction click here.

Other name(s): 2,3-oxidosqualene α-amyrin cyclase; mixed amyrin synthase

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, α-amyrin-forming)

Comments: A multifunctional enzyme which produces both α- and β-amyrin. (see EC 5.4.99.39, β-amyrin synthase)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Morita, M., Shibuya, M., Kushiro, T., Masuda, K. and Ebizuka, Y. Molecular cloning and functional expression of triterpene synthases from pea (Pisum sativum) new α-amyrin-producing enzyme is a multifunctional triterpene synthase. Eur. J. Biochem. 267 (2000) 3453-3460. [PMID: 10848960]

[EC 5.4.99.40 created 2011]

EC 5.4.99.41

Accepted name: lupeol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = lupeol

For diagram of reaction click here.

Other name(s): LUPI; BPW; RcLUS

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, lupeol-forming)

Comments: Also forms some β-amyrin. The recombinant enzyme from Arabidopsis thaliana [3] gives a 1:1 mixture of lupeol and lupan-3β,20-diol with small amounts of β-amyrin, germanicol, taraxasterol and ψ-taraxasterol. See EC 4.2.1.128 (lupan-3β,20-diol synthase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Herrera, J.B., Bartel, B., Wilson, W.K. and Matsuda, S.P. Cloning and characterization of the Arabidopsis thaliana lupeol synthase gene. Phytochemistry 49 (1998) 1905-1911. [PMID: 9883589]

2. Shibuya, M., Zhang, H., Endo, A., Shishikura, K., Kushiro, T. and Ebizuka, Y. Two branches of the lupeol synthase gene in the molecular evolution of plant oxidosqualene cyclases. Eur. J. Biochem. 266 (1999) 302-307. [PMID: 10542078]

3. Segura, M.J., Meyer, M.M. and Matsuda, S.P. Arabidopsis thaliana LUP1 converts oxidosqualene to multiple triterpene alcohols and a triterpene diol. Org. Lett. 2 (2000) 2257-2259. [PMID: 10930257]

4. Zhang, H., Shibuya, M., Yokota, S. and Ebizuka, Y. Oxidosqualene cyclases from cell suspension cultures of Betula platyphylla var. japonica: molecular evolution of oxidosqualene cyclases in higher plants. Biol. Pharm. Bull. 26 (2003) 642-650. [PMID: 12736505]

5. Hayashi, H., Huang, P., Takada, S., Obinata, M., Inoue, K., Shibuya, M. and Ebizuka, Y. Differential expression of three oxidosqualene cyclase mRNAs in Glycyrrhiza glabra. Biol. Pharm. Bull. 27 (2004) 1086-1092. [PMID: 15256745]

6. Guhling, O., Hobl, B., Yeats, T. and Jetter, R. Cloning and characterization of a lupeol synthase involved in the synthesis of epicuticular wax crystals on stem and hypocotyl surfaces of Ricinus communis. Arch. Biochem. Biophys. 448 (2006) 60-72. [PMID: 16445885]

7. Basyuni, M., Oku, H., Tsujimoto, E., Kinjo, K., Baba, S. and Takara, K. Triterpene synthases from the Okinawan mangrove tribe, Rhizophoraceae. FEBS J. 274 (2007) 5028-5042. [PMID: 17803686]

[EC 5.4.99.41 created 2011]

EC 5.4.99.42

Accepted name: tRNA pseudouridine31 synthase

Reaction: tRNA uridine31 = tRNA pseudouridine31

For diagram of mechanism click here.

Other name(s): Pus6p

Systematic name: tRNA-uridine31 uracil mutase

Comments: The enzyme specifically acts on uridine31 in tRNA.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Ansmant, I., Motorin, Y., Massenet, S., Grosjean, H. and Branlant, C. Identification and characterization of the tRNA:Ψ 31-synthase (Pus6p) of Saccharomyces cerevisiae. J. Biol. Chem. 276 (2001) 34934-34940. [PMID: 11406626]

[EC 5.4.99.42 created 2011]

EC 5.4.99.43

Accepted name: 21S rRNA pseudouridine2819 synthase

Reaction: 21S rRNA uridine2819 = 21S rRNA pseudouridine2819

For diagram of mechanism click here.

Other name(s): Pus5p

Systematic name: 21S rRNA-uridine2819 uracil mutase

Comments: The enzyme specifically acts on uridine2819 in 21S rRNA.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Ansmant, I., Massenet, S., Grosjean, H., Motorin, Y. and Branlant, C. Identification of the Saccharomyces cerevisiae RNA:pseudouridine synthase responsible for formation of psi(2819) in 21S mitochondrial ribosomal RNA. Nucleic Acids Res. 28 (2000) 1941-1946. [PMID: 10756195]

[EC 5.4.99.43 created 2011]

EC 5.4.99.44

Accepted name: mitochondrial tRNA pseudouridine27/28 synthase

Reaction: mitochondrial tRNA uridine27/28 = mitochondrial tRNA pseudouridine27/28

For diagram of mechanism click here.

Other name(s): Pus2; Pus2p; RNA:pseudouridine synthases 2

Systematic name: mitochondrial tRNA-uridine27/28 uracil mutase

Comments: The mitochondrial enzyme Pus2p is specific for position 27 or 28 in mitochondrial tRNA [1].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Behm-Ansmant, I., Branlant, C. and Motorin, Y. The Saccharomyces cerevisiae Pus2 protein encoded by YGL063w ORF is a mitochondrial tRNA:Ψ27/28-synthase. RNA 13 (2007) 1641-1647. [PMID: 17684231]

[EC 5.4.99.44 created 2011]

EC 5.4.99.45

Accepted name: tRNA pseudouridine38/39 synthase

Reaction: tRNA uridine38/39 = tRNA pseudouridine38/39

For diagram of mechanism click here.

Other name(s): Deg1; Pus3p; pseudouridine synthase 3

Systematic name: tRNA-uridine38/39 uracil mutase

Comments: The enzyme from Saccharomyces cerevisiae is active only towards uridine38 and uridine39, and shows no activity with uridine40 (cf. EC 5.4.99.12, tRNA pseudouridine38-40 synthase) [1]. In vitro the enzyme from mouse is active on uridine39 and very slightly on uridine38 (human tRNALeu) [2].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Lecointe, F., Simos, G., Sauer, A., Hurt, E.C., Motorin, Y. and Grosjean, H. Characterization of yeast protein Deg1 as pseudouridine synthase (Pus3) catalyzing the formation of Ψ38 and Ψ39 in tRNA anticodon loop. J. Biol. Chem. 273 (1998) 1316-1323. [PMID: 9430663]

2. Chen, J. and Patton, J.R. Pseudouridine synthase 3 from mouse modifies the anticodon loop of tRNA. Biochemistry 39 (2000) 12723-12730. [PMID: 11027153]

[EC 5.4.99.45 created 2011]

EC 5.4.99.46

Accepted name: shionone synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = shionone

For diagram of reaction click here.

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, shionone-forming)

Comments: The enzyme gives traces of four other triterpenoids

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Sawai, S., Uchiyama, H., Mizuno, S., Aoki, T., Akashi, T., Ayabe, S. and Takahashi, T. Molecular characterization of an oxidosqualene cyclase that yields shionone, a unique tetracyclic triterpene ketone of Aster tataricus. FEBS Lett. 585 (2011) 1031-1036. [PMID: 21377465]

[EC 5.4.99.46 created 2011]

EC 5.4.99.47

Accepted name: parkeol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = parkeol

For diagram of reaction click here.

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, parkeol-forming)

Comments: The enzyme from rice (Oryza sativa) produces parkeol as a single product [1].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Ito, R., Mori, K., Hashimoto, I., Nakano, C., Sato, T. and Hoshino, T. Triterpene cyclases from Oryza sativa L.: cycloartenol, parkeol and achilleol B synthases. Org. Lett. 13 (2011) 2678-2681. [PMID: 21526825]

[EC 5.4.99.47 created 2011]

EC 5.4.99.48

Accepted name: achilleol B synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = achilleol B

For diagram of reaction click here.

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, achilleol-B-forming)

Comments: Achilleol B is probably formed by cleavage of the 8-14 and 9-10 bonds of (3S)-2,3-epoxy-2,3-dihydrosqualene as part of the cyclization reaction, after formation of the oleanane skeleton.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Ito, R., Mori, K., Hashimoto, I., Nakano, C., Sato, T. and Hoshino, T. Triterpene cyclases from Oryza sativa L.: cycloartenol, parkeol and achilleol B synthases. Org. Lett. 13 (2011) 2678-2681. [PMID: 21526825]

[EC 5.4.99.48 created 2011]

EC 5.4.99.49

Accepted name: glutinol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = glutinol

For diagram of reaction click here.

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, glutinol-forming)

Comments: The enzyme from Kalanchoe daigremontiana also gives traces of other triterpenoids.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Wang, Z., Yeats, T., Han, H. and Jetter, R. Cloning and characterization of oxidosqualene cyclases from Kalanchoe daigremontiana: enzymes catalyzing up to 10 rearrangement steps yielding friedelin and other triterpenoids. J. Biol. Chem. 285 (2010) 29703-29712. [PMID: 20610397]

[EC 5.4.99.49 created 2011]

EC 5.4.99.50

Accepted name: friedelin synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = friedelin

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, friedelin-forming)

For diagram of reaction click here.

Comments: The enzyme from Kalanchoe daigremontiana also gives traces of other triterpenoids.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Wang, Z., Yeats, T., Han, H. and Jetter, R. Cloning and characterization of oxidosqualene cyclases from Kalanchoe daigremontiana: enzymes catalyzing up to 10 rearrangement steps yielding friedelin and other triterpenoids. J. Biol. Chem. 285 (2010) 29703-29712. [PMID: 20610397]

[EC 5.4.99.50 created 2011]

EC 5.4.99.51

Accepted name: baccharis oxide synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = baccharis oxide

For diagram of reaction click here.

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, baccharis-oxide-forming)

Comments: The enzyme from Stevia rebaudiana also gives traces of other triterpenoids.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Shibuya, M., Sagara, A., Saitoh, A., Kushiro, T. and Ebizuka, Y. Biosynthesis of baccharis oxide, a triterpene with a 3,10-oxide bridge in the A-ring. Org. Lett. 10 (2008) 5071-5074. [PMID: 18850716]

[EC 5.4.99.51 created 2011]

EC 5.4.99.52

Accepted name: α-seco-amyrin synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = α-seco-amyrin

For diagram of reaction click here.

Glossary: α-seco-amyrin = 8,14-secoursa-7,13-diene-3β-ol

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, α-seco-amyrin-forming)

Comments: The enzyme from Arabidopsis thaliana is multifunctional and produces about equal amounts of α- and β-seco-amyrin. See EC 5.4.99.54, β-seco-amyrin synthase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Shibuya, M., Xiang, T., Katsube, Y., Otsuka, M., Zhang, H. and Ebizuka, Y. Origin of structural diversity in natural triterpenes: direct synthesis of seco-triterpene skeletons by oxidosqualene cyclase. J. Am. Chem. Soc. 129 (2007) 1450-1455. [PMID: 17263431]

[EC 5.4.99.52 created 2011]

EC 5.4.99.53

Accepted name: marneral synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = marneral

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, marneral-forming)

For diagram of reaction click here.

Comments: Marneral is a triterpenoid formed by Grob fragmentation of the A ring of 2,3-epoxy-2,3-dihydrosqualene during cyclization.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Xiong, Q., Wilson, W. K. and Matsuda, S. P. T. An Arabidopsis oxidosqualene cyclase catalyzes iridal skeleton formation by Grob fragmentation. Angew. Chem., Int. Ed. 45 (2006) 1285-1288. [PMID: 16425307]

[EC 5.4.99.53 created 2011]

EC 5.4.99.54

Accepted name: β-seco-amyrin synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = β-seco-amyrin

For diagram of reaction click here.

Glossary: β-seco-amyrin = 8,14-secooleana-7,13-diene-3β-ol

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, β-seco-amyrin-forming)

Comments: The enzyme from Arabidopsis thaliana is multifunctional and produces about equal amounts of α- and β-seco-amyrin. See EC 5.4.99.52, α-seco-amyrin synthase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Shibuya, M., Xiang, T., Katsube, Y., Otsuka, M., Zhang, H. and Ebizuka, Y. Origin of structural diversity in natural triterpenes: direct synthesis of seco-triterpene skeletons by oxidosqualene cyclase. J. Am. Chem. Soc. 129 (2007) 1450-1455. [PMID: 17263431]

[EC 5.4.99.54 created 2011]

EC 5.4.99.55

Accepted name: δ-amyrin synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = δ-amyrin

For diagram of reaction click here.

Other name(s): SlTTS2 (gene name)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, δ-amyrin-forming)

Comments: The enzyme from tomato (Solanum lycopersicum) gives 48% δ-amyrin, 18% α-amyrin, 13% β-amyrin and traces of three or four other triterpenoid alcohols [1]. See also EC 5.4.99.40, α-amyrin synthase and EC 5.4.99.39, β-amyrin synthase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Wang, Z., Guhling, O., Yao, R., Li, F., Yeats, T.H., Rose, J.K. and Jetter, R. Two oxidosqualene cyclases responsible for biosynthesis of tomato fruit cuticular triterpenoids. Plant Physiol. 155 (2011) 540-552. [PMID: 21059824]

[EC 5.4.99.55 created 2011]

EC 5.4.99.56

Accepted name: tirucalladienol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = tirucalla-7,24-dien-3β-ol

For diagram of reaction click here.

Other name(s): PEN3

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, tirucalla-7,24-dien-3β-ol-forming)

Comments: The product from Arabidopsis thaliana is 85% tirucalla-7,24-dien-3β-ol with trace amounts of other triterpenoids.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Morlacchi, P., Wilson, W.K., Xiong, Q., Bhaduri, A., Sttivend, D., Kolesnikova, M.D. and Matsuda, S.P. Product profile of PEN3: the last unexamined oxidosqualene cyclase in Arabidopsis thaliana. Org. Lett. 11 (2009) 2627-2630. [PMID: 19445469]

[EC 5.4.99.56 created 2011]

EC 5.4.99.57

Accepted name: baruol synthase

Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = baruol

For diagram of reaction click here.

Other name(s): BARS1

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, baruol-forming)

Comments: The enzyme from Arabidopsis thaliana also produces traces of 22 other triterpenoids.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Lodeiro, S., Xiong, Q., Wilson, W.K., Kolesnikova, M.D., Onak, C.S. and Matsuda, S.P. An oxidosqualene cyclase makes numerous products by diverse mechanisms: a challenge to prevailing concepts of triterpene biosynthesis. J. Am. Chem. Soc. 129 (2007) 11213-11222. [PMID: 17705488]

[EC 5.4.99.57 created 2012]

EC 5.4.99.58

Accepted name: methylornithine synthase

Reaction: L-lysine = (3R)-3-methyl-D-ornithine

Glossary: (3R)-3-methyl-D-ornithine = (2R,3R)-2,5-diamino-3-methylpentanoate

Other name(s): PylB

Systematic name: L-lysine carboxy-aminomethylmutase

Comments: The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes. Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The reaction is part of the biosynthesis pathway of pyrrolysine, a naturally occurring amino acid found in some archaeal methyltransferases.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Gaston, M.A., Zhang, L., Green-Church, K.B. and Krzycki, J.A. The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature 471 (2011) 647-650. [PMID: 21455182]

2. Quitterer, F., List, A., Eisenreich, W., Bacher, A. and Groll, M. Crystal structure of methylornithine synthase (PylB): insights into the pyrrolysine biosynthesis. Angew. Chem. Int. Ed. Engl. 51 (2012) 1339-1342. [PMID: 22095926]

[EC 5.4.99.58 created 2012]

EC 5.4.99.59

Accepted name: dTDP-fucopyranose mutase

Reaction: dTDP-α-D-fucopyranose = dTDP-β-D-fucofuranose

For diagram of reaction click here.

Other name(s): Fcf2

Systematic name: dTDP-α-D-fucopyranose furanomutase

Comments: The enzyme is involved in the biosynthesis of the Escherichia coli O52 O antigen.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Wang, Q., Ding, P., Perepelov, A.V., Xu, Y., Wang, Y., Knirel, Y.A., Wang, L. and Feng, L. Characterization of the dTDP-D-fucofuranose biosynthetic pathway in Escherichia coli O52. Mol. Microbiol. 70 (2008) 1358-1367. [PMID: 19019146]

[EC 5.4.99.59 created 2013]

EC 5.4.99.60

Accepted name: cobalt-precorrin-8 methylmutase

Reaction: cobalt-precorrin-8 = cobyrinate

For diagram of reaction click here.

Other name(s): cbiC (gene name)

Systematic name: precorrin-8 11,12-methylmutase

Comments: The enzyme catalyses the the conversion of cobalt-precorrin-8 to cobyrinate by methyl rearrangement, a step in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis. The equivalent enzyme in the aerobic pathway is EC 5.4.99.61, precorrin-8X methylmutase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Xue, Y., Wei, Z., Li, X. and Gong, W. The crystal structure of putative precorrin isomerase CbiC in cobalamin biosynthesis. J. Struct. Biol. 153 (2006) 307-311. [PMID: 16427313]

2. Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12). Proc. Natl. Acad. Sci. USA 110 (2013) 14906-14911. [PMID: 23922391]

[EC 5.4.99.60 created 2014]

EC 5.4.99.61

Accepted name: precorrin-8X methylmutase

Reaction: precorrin-8X = hydrogenobyrinate

For diagram of reaction click here.

Other name(s): precorrin isomerase; hydrogenobyrinic acid-binding protein; cobH (gene name)

Systematic name: precorrin-8X 11,12-methylmutase

Comments: The enzyme catalyses the the conversion of precorrin-8X to hydrogenobyrinate by methyl rearrangement, a step in the aerobic (late cobalt insertion) pathway of adenosylcobalamin biosynthesis. The equivalent enzyme in the anaerobic pathway is EC 5.4.99.60, precorrin-8X methylmutase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Thibaut, D., Couder, M., Famechon, A., Debussche, L., Cameron, B., Crouzet, J., Blanche, F. The final step in the biosynthesis of hydrogenobyrinic acid is catalyzed by the cobH gene product with precorrin-8X as the substrate. J. Bacteriol. 174 (1992) 1043-1049. [PMID: 1732194]

2. Roth, J.R., Lawrence, J.G., Rubenfield, M., Kieffer-Higgins, S., Church, G.M. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. J. Bacteriol. 175 (1993) 3303-3316. [PMID: 8501034]

3. Roessner, C.A., Warren, M.J., Santander, P.J., Atshaves, B.P., Ozaki, S., Stolowich, N.J., Iida, K., Scott, A.I. Expression of Salmonella typhimurium enzymes for cobinamide synthesis. Identification of the 11-methyl and 20-methyl transferases of corrin biosynthesis. FEBS Lett. 301 (1992) 73-78. [PMID: 1451790]

4. Crouzet, J., Cameron, B., Cauchois, L., Rigault, S., Rouyez, M.C., Blanche, F. , Thibaut D., Debussche, L. Genetic and sequence analysis of an 8.7-kilobase Pseudomonas denitrificans fragment carrying eight genes involved in transformation of precorrin-2 to cobyrinic acid. J. Bacteriol. 172 (1990) 5980-5990. [PMID: 2211521]

5. Shipman, L.W., Li, D., Roessner, C.A., Scott, A.I. and Sacchettini, J.C. Crystal structure of precorrin-8x methyl mutase. Structure 9 (2001) 587-596. [PMID: 11470433]

[EC 5.4.99.61 created 1999 as EC 5.4.1.2, transferred 2014 to EC 5.4.99.61]

EC 5.4.99.62

Accepted name: D-ribose pyranase

Reaction: β-D-ribopyranose = β-D-ribofuranose

Other name(s): RbsD

Systematic name: D-ribopyranose furanomutase

Comments: The enzyme also catalyses the conversion between β-allopyranose and β-allofuranose.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Kim, M.S., Shin, J., Lee, W., Lee, H.S. and Oh, B.H. Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture. J. Biol. Chem. 278 (2003) 28173-28180. [PMID: 12738765]

2. Ryu, K.S., Kim, C., Kim, I., Yoo, S., Choi, B.S. and Park, C. NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration. J. Biol. Chem. 279 (2004) 25544-25548. [PMID: 15060078]

[EC 5.4.99.62 created 2014]

EC 5.4.99.63

Accepted name: ethylmalonyl-CoA mutase

Reaction: (2R)-ethylmalonyl-CoA = (2S)-methylsuccinyl-CoA

Other name(s): Ecm

Systematic name: (2R)-ethylmalonyl-CoA CoA-carbonylmutase

Comments: The enzyme, characterized from the bacterium Rhodobacter sphaeroides, is involved in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. Requires coenzyme B12 for activity.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Erb, T.J., Retey, J., Fuchs, G. and Alber, B.E. Ethylmalonyl-CoA mutase from Rhodobacter sphaeroides defines a new subclade of coenzyme B12-dependent acyl-CoA mutases. J. Biol. Chem. 283 (2008) 32283-32293. [PMID: 18819910]

[EC 5.4.99.63 created 2015]

EC 5.4.99.64

Accepted name: 2-hydroxyisobutanoyl-CoA mutase

Reaction: 2-hydroxy-2-methylpropanoyl-CoA = (S)-3-hydroxybutanoyl-CoA

Glossary: 2-hydroxy-2-methylpropanoyl-CoA = 2-hydroxyisobutanoyl-CoA

Other name(s): hcmAB (gene names)

Systematic name: 2-hydroxy-2-methylpropanoyl-CoA mutase

Comments: The enzyme, characterized from the bacterium Aquincola tertiaricarbonis, uses radical chemistry to rearrange the positions of both a methyl group and a hydroxyl group. It consists of two subunits, the smaller one containing a cobalamin cofactor. It plays a central role in the degradation of assorted substrates containing a tert-butyl moiety.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Yaneva, N., Schuster, J., Schafer, F., Lede, V., Przybylski, D., Paproth, T., Harms, H., Muller, R.H. and Rohwerder, T. Bacterial acyl-CoA mutase specifically catalyzes coenzyme B12-dependent isomerization of 2-hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA. J. Biol. Chem. 287 (2012) 15502-15511. [PMID: 22433853]

2. Kurteva-Yaneva, N., Zahn, M., Weichler, M.T., Starke, R., Harms, H., Muller, R.H., Strater, N. and Rohwerder, T. Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase. J. Biol. Chem. 290 (2015) 9727-9737. [PMID: 25720495]

[EC 5.4.99.64 created 2016 as EC 5.3.3.20, transferred 2017 to EC 5.4.99.64]

EC 5.4.99.65

Accepted name: pre-α-onocerin synthase

Reaction: (3S,22S)-2,3:22,23-diepoxy-2,3,22,23-tetrahydrosqualene = pre-α-onocerin

For diagram of reaction click here

Glossary: pre-α-onocerin = (21S)-21,22-epoxypolypoda-8(26)-13,17-trien-3β-ol

Other name(s): LCC

Systematic name: (3S,22S)-2,3:22,23-diepoxy-2,3,22,23-tetrahydrosqualene mutase (cyclizing, pre-α-onocerin-forming)

Comments: Isolated from the plant Lycopodium clavatum. The enzyme does not act on (3S)-2,3-epoxy-2,3-dihydrosqualene and does not form any α-onocerin.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Araki, T., Saga, Y., Marugami, M., Otaka, J., Araya, H., Saito, K., Yamazaki, M., Suzuki, H. and Kushiro, T. Onocerin biosynthesis requires two highly dedicated triterpene cyclases in a fern Lycopodium clavatum. Chembiochem 17 (2016) 288-290. [PMID: 26663356]

[EC 5.4.99.65 created 2017]

EC 5.4.99.66

Accepted name: α-onocerin synthase

Reaction: pre-α-onocerin = α-onocerin

For diagram of reaction click here

Glossary: α-onocerin = 8,14-secogammacera-8(26),14(27)-diene-3β,21α-diol
pre-α-onocerin = (21S)-21,22-epoxypolypoda-8(26)-13,17-trien-3β-ol

Other name(s): LCD

Systematic name: pre-α-onocerin mutase (cyclizing, α-onocerin-forming)

Comments: Isolated from the plant Lycopodium clavatum.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Araki, T., Saga, Y., Marugami, M., Otaka, J., Araya, H., Saito, K., Yamazaki, M., Suzuki, H. and Kushiro, T. Onocerin biosynthesis requires two highly dedicated triterpene cyclases in a fern Lycopodium clavatum. Chembiochem 17 (2016) 288-290. [PMID: 26663356]

[EC 5.4.99.66 created 2017]


Continued with EC 5.5 to EC 5.99
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