Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Sinéad Boyce, Richard Cammack, Ron Caspi, Minoru Kanehisa, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The entries were added on the date indicated and fully approved after four weeks.

An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.


Contents

EC 1.7.2.4 nitrous-oxide reductase (6 April 2011)
EC 1.7.99.6 transferred now EC 1.7.2.4 (6 April 2011)
EC 1.8.5.3 dimethylsulfoxide reductase (6 April 2011)
EC 1.13.12.14 transferred now EC 1.14.13.122 (6 April 2011)
EC 1.14.13.122 chlorophyllide-a oxygenase (6 April 2011)
*EC 2.3.1.93 13-hydroxylupanine O-tigloyltransferase (6 April 2011)
EC 2.4.1.130 transferred, now covered by EC 2.4.1.258, EC 2.4.1.259, EC 2.4.1.260 and EC 2.4.1.261 (6 April 2011)
*EC 2.4.1.131 GDP-Man:Man3GlcNAc2-PP-Dol α-1,2-mannosyltransferase (6 April 2011)
*EC 2.4.1.132 GDP-Man:Man1GlcNAc2-PP-dolichol α-1,3-mannosyltransferase (6 April 2011)
*EC 2.4.1.191 luteolin-7-O-diglucuronide 4'-O-glucuronosyltransferase (6 April 2011)
EC 2.4.1.256 Dol-P-Glc:Glc2Man9GlcNAc2-PP-Dol α1,2-glucosyltransferase (6 April 2011)
EC 2.4.1.257 GDP-Man:Man2GlcNAc2-PP-Dol α-1,6-mannosyltransferase (6 April 2011)
EC 2.4.1.258 Dol-P-Man:Man5GlcNAc2-PP-Dol α-1,3-mannosyltransferase (6 April 2011)
EC 2.4.1.259 Dol-P-Man:Man6GlcNAc2-PP-Dol α-1,2-mannosyltransferase (6 April 2011)
EC 2.4.1.260 Dol-P-Man:Man7GlcNAc2-PP-Dol α-1,6-mannosyltransferase (6 April 2011)
EC 2.4.1.261 Dol-P-Man:Man8GlcNAc2-PP-Dol α-1,2-mannosyltransferase (6 April 2011)
*EC 2.5.1.31 ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] (6 April 2011)
*EC 2.5.1.89 tritrans,polycis-undecaprenyl-diphosphate synthase [geranylgeranyl-diphosphate specific] (6 April 2011)
*EC 2.5.1.92 (2Z,6Z)-farnesyl diphosphate synthase (6 April 2011)
*EC 2.7.8.30 undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase (6 April 2011)
EC 2.7.8.33 UDP-GlcNAc:undecaprenyl-phosphate GlcNAc-1-phosphate transferase (6 April 2011)
EC 3.1.2.29 fluoroacetyl-CoA thioesterase (6 April 2011)
*EC 3.1.3.73 adenosylcobalamin/α-ribazole phosphatase (6 April 2011)
*EC 3.2.2.1 purine nucleosidase (6 April 2011)
*EC 3.4.13.19 membrane dipeptidase (6 April 2011)
*EC 3.4.15.1 peptidyl-dipeptidase A (6 April 2011)
*EC 3.4.16.6 carboxypeptidase D (6 April 2011)
*EC 3.5.1.4 amidase (6 April 2011)
*EC 4.1.1.52 6-methylsalicylate decarboxylase (6 April 2011)
*EC 4.1.1.77 4-oxalocrotonate decarboxylase (6 April 2011)
*EC 4.1.3.39 4-hydroxy-2-oxovalerate aldolase (6 April 2011)
EC 4.1.99.16 geosmin synthase (6 April 2011)
*EC 4.2.3.22 germacradienol synthase (6 April 2011)
EC 4.2.3.61 5-epiaristolochene synthase (6 April 2011)
EC 4.2.3.62 (–)-γ-cadinene synthase (6 April 2011)
EC 4.2.3.63 (+)-cubenene synthase (6 April 2011)
EC 4.2.3.64 (+)-epicubenol synthase (6 April 2011)
EC 4.2.3.65 zingiberene synthase (6 April 2011)
EC 4.2.3.66 β-selinene cyclase (6 April 2011)
EC 4.2.3.67 cis-muuroladiene synthase (6 April 2011)
EC 4.2.3.68 β-eudesmol synthase (6 April 2011)
EC 4.2.3.69 (+)-α-barbatene synthase (6 April 2011)
EC 4.2.3.70 patchoulol synthase (6 April 2011)
EC 4.2.3.71 (E,E)-germacrene B synthase (6 April 2011)
EC 4.2.3.72 α-gurjunene synthase (6 April 2011)
EC 4.2.3.73 valencene synthase (6 April 2011)
*EC 4.3.1.20 erythro-3-hydroxy-L-aspartate ammonia-lyase (6 April 2011)
EC 6.4.1.8 acetophenone carboxylase (6 April 2011)

EC 1.7.2.4

Accepted name: nitrous-oxide reductase

Reaction: nitrogen + H2O + 2 cytochrome c = nitrous oxide + 2 reduced cytochrome c

Other name(s): nitrous oxide reductase; N2O reductase; nitrogen:(acceptor) oxidoreductase (N2O-forming)

Systematic name: nitrogen:cytochrome c oxidoreductase (N2O-forming)

Comments: The reaction is observed only in the direction of nitrous oxide reduction. Contains the mixed-valent dinuclear CuA species at the electron entry site of the enzyme, and the tetranuclear Cu-Z centre in the active site. In Paracoccus pantotrophus, the electron donor is cytochrome c552.

References:

1. Coyle, C.L., Zumft, W.G., Kroneck, P.M.H., Körner, H. and Jakob, W. Nitrous oxide reductase from denitrifying Pseudomonas perfectomarina. Purification and properties of a novel multicopper enzyme. Eur. J. Biochem. 153 (1985) 459-467. [PMID: 3000778]

2. Zumft, W.G. and Kroneck, P.M. Respiratory transformation of nitrous oxide (N2O) to dinitrogen by bacteria and archaea. Adv. Microb. Physiol. 52 (2007) 107-227. [PMID: 17027372]

3. Dell'Acqua, S., Pauleta, S.R., Paes de Sousa, P.M., Monzani, E., Casella, L., Moura, J.J. and Moura, I. A new CuZ active form in the catalytic reduction of N2O by nitrous oxide reductase from Pseudomonas nautica. J. Biol. Inorg. Chem. 15 (2010) 967-976. [PMID: 20422435]

[EC 1.7.2.4 created 1989 as EC 1.7.99.6, modified 1999, transferred 2011 to EC 1.7.2.4]

[EC 1.7.99.6 Transferred entry: nitrous-oxide reductase. Now EC 1.7.2.4, nitrous-oxide reductase (EC 1.7.99.6 created 1989, modified 1999, deleted 2011)]

EC 1.8.5.3

Accepted name: dimethylsulfoxide reductase

Reaction: dimethyl sulfide + menaquinone + H2O = dimethyl sulfoxide + menaquinol

Other name(s): DMSO reductase

Systematic name: dimethyl sulfide: menaquinone oxidoreductase

Comments: Contains molybdopterin and [4Fe-4S] clusters. Also reduces pyridine N-oxide and trimethylamine N-oxide, with lower activity, to the corresponding amines.

References:

1. Simala-Grant, J.L. and Weiner, J.H. Kinetic analysis and substrate specificity of Escherichia coli dimethyl sulfoxide reductase. Microbiology 142 (1996) 3231-3239. [PMID: 8969520]

2. Daruwala, R. and Meganathan, R. Dimethyl sulfoxide reductase is not required for trimethylamine N-oxide reduction in Escherichia coli. FEMS Microbiol. Lett. 67 (1991) 255-259. [PMID: 1769531]

3. Miguel, L. and Meganthan, R. Electron donors and the quinone involved in dimethyl sulfoxide reduction in Escherichia coli. Curr. Microbiol. 22 (1991) 109-115.

4. Rothery, R.A., Trieber, C.A. and Weiner, J.H. Interactions between the molybdenum cofactor and iron-sulfur clusters of Escherichia coli dimethylsulfoxide reductase. J. Biol. Chem. 274 (1999) 13002-13009. [PMID: 10224050]

[EC 1.8.5.3 created 2011]

[EC 1.13.12.14 Transferred entry: chlorophyllide-a oxygenase. Now EC 1.14.13.122, chlorophyllide-a oxygenase (EC 1.13.12.14 created 2006, deleted 2011)]

EC 1.14.13.122

Accepted name: chlorophyllide-a oxygenase

Reaction: (1) chlorophyllide a + O2 + NADPH + H+ = 71-hydroxychlorophyllide a + H2O + NADP+
(2) 71-hydroxychlorophyllide a + O2 + NADPH + H+ = chlorophyllide b + 2 H2O + NADP+

Other name(s): chlorophyllide a oxygenase; chlorophyll-b synthase; CAO

Systematic name: chlorophyllide-a:oxygen 7-oxidoreductase

Comments: Chlorophyll b is required for the assembly of stable light-harvesting complexes (LHCs) in the chloroplast of green algae, cyanobacteria and plants [2,3]. Contains a mononuclear iron centre [3]. The enzyme catalyses two successive hydroxylations at the 7-methyl group of chlorophyllide a. The second step yields the aldehyde hydrate, which loses H2O spontaneously to form chlorophyllide b [2]. Chlorophyll a and protochlorophyllide a are not substrates [2].

References:

1. Espineda, C.E., Linford, A.S., Devine, D. and Brusslan, J.A. The AtCAO gene, encoding chlorophyll a oxygenase, is required for chlorophyll b synthesis in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 96 (1999) 10507-10511. [PMID: 10468639]

2. Oster, U., Tanaka, R., Tanaka, A. and Rudiger, W. Cloning and functional expression of the gene encoding the key enzyme for chlorophyll b biosynthesis (CAO) from Arabidopsis thaliana. Plant J. 21 (2000) 305-310. [PMID: 10758481]

3. Eggink, L.L., LoBrutto, R., Brune, D.C., Brusslan, J., Yamasato, A., Tanaka, A. and Hoober, J.K. Synthesis of chlorophyll b: localization of chlorophyllide a oxygenase and discovery of a stable radical in the catalytic subunit. BMC Plant Biol. 4 (2004) 5. [PMID: 15086960]

4. Porra, R.J., Schafer, W., Cmiel, E., Katheder, I. and Scheer, H. The derivation of the formyl-group oxygen of chlorophyll b in higher plants from molecular oxygen. Achievement of high enrichment of the 7-formyl-group oxygen from 18O2 in greening maize leaves. Eur. J. Biochem. 219 (1994) 671-679. [PMID: 8307032]

[EC 1.14.13.122 created 2006 as EC 1.13.12.14, transferred 2011 to EC 1.14.13.122]

*EC 2.3.1.93

Accepted name: 13-hydroxylupanine O-tigloyltransferase

Reaction: (E)-2-methylcrotonoyl-CoA + 13-hydroxylupanine = CoA + 13-[(E)-2-methylcrotonoyl]oxylupanine

Glossary: (E)-2-methylcrotonoyl-CoA = tigloyl-CoA = (E)-2-methylbut-2-enoyl-CoA

Other name(s): tigloyl-CoA:13-hydroxylupanine O-tigloyltransferase; 13-hydroxylupanine acyltransferase

Systematic name: (E)-2-methylcrotonoyl-CoA:13-hydroxylupanine O-2-methylcrotonoyltransferase

Comments: Benzoyl-CoA and, more slowly, pentanoyl-CoA, 3-methylbutanoyl-CoA and butanoyl-CoA can act as acyl donors. Involved in the synthesis of lupanine alkaloids.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 85341-00-0

References:

1. Wink, M. and Hartmann, T. Enzymatic synthesis of quinolizidine alkaloid esters: a tigloyl-CoA:13-hydroxylupanine O-tigloyl transferase from Lupinus albus L. Planta 156 (1982) 560-565.

2. Okada, T.. Hirai, M.Y., Suzuki, H., Yamazaki, M. and Saito, K. Molecular characterization of a novel quinolizidine alkaloid O-tigloyltransferase: cDNA cloning, catalytic activity of recombinant protein and expression analysis in Lupinus plants. Plant Cell Physiol. 46 (2005) 233-244.

3. Suzuki, H., Murakoshi, I. and Saito, K. A novel O-tigloyltransferase for alkaloid biosynthesis in plants. Purification, characterization, and distribution in Lupinus plants. J. Biol. Chem. 269 (1994) 15853-15860. [PMID: 8195240]

[EC 2.3.1.93 created 1986, modified 2011]

[EC 2.4.1.130 Transferred entry: dolichyl-phosphate-mannose—glycolipid α-mannosyltransferase. Now covered by EC 2.4.1.258 (Dol-P-Man:Man5GlcNAc2-PP-Dol α-1,3-mannosyltransferase), EC 2.4.1.259 (Dol-P-Man:Man6GlcNAc2-PP-Dol α-1,2-mannosyltransferase), EC 2.4.1.260 (Dol-P-Man:Man7GlcNAc2-PP-Dol α-1,6-mannosyltransferase) and EC 2.4.1.261 (Dol-P-Man:Man8GlcNAc2-PP-Dol α-1,2-mannosyltransferase). (EC 2.4.1.130 created 1984, deleted 2011)]

*EC 2.4.1.131

Accepted name: GDP-Man:Man3GlcNAc2-PP-Dol α-1,2-mannosyltransferase

Reaction: 2 GDP-D-mannose + D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol

Other name(s): ALG11; ALG11 mannosyltransferase; LEW3 (gene name); At2G40190 (gene name); gmd3 (gene name); galactomannan deficiency protein 3; GDP-mannose:glycolipid 1,2-α-D-mannosyltransferase; glycolipid 2-α-mannosyltransferase

Systematic name: GDP-D-mannose:D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,2-mannosyltransferase

Comments: The biosynthesis of asparagine-linked glycoproteins (N-linked protein glycosylation) utilizes a dolichyl diphosphate-linked glycosyl donor, which is assembled by the series of membrane-bound glycosyltransferases that comprise the dolichol pathway. ALG11 mannosyltransferase from Saccharomyces cerevisiae carries out two sequential steps in the formation of the lipid-linked core oligosaccharide, adding two mannose residues in α(1→2) linkages to the nascent oligosaccharide.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 74506-43-7

References:

1. O'Reilly, M.K., Zhang, G. and Imperiali, B. In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis. Biochemistry 45 (2006) 9593-9603. [PMID: 16878994]

2. Absmanner, B., Schmeiser, V., Kampf, M. and Lehle, L. Biochemical characterization, membrane association and identification of amino acids essential for the function of Alg11 from Saccharomyces cerevisiae, an α1,2-mannosyltransferase catalysing two sequential glycosylation steps in the formation of the lipid-linked core oligosaccharide. Biochem. J. 426 (2010) 205-217. [PMID: 19929855]

3. Schutzbach, J.S., Springfield, J.D. and Jensen, J.W. The biosynthesis of oligosaccharide-lipids. Formation of an α-1,2-mannosyl-mannose linkage. J. Biol. Chem. 255 (1980) 4170-4175. [PMID: 6154707]

[EC 2.4.1.131 created 1984, modified 2011]

*EC 2.4.1.132

Accepted name: GDP-Man:Man1GlcNAc2-PP-dolichol α-1,3-mannosyltransferase

Reaction: GDP-D-mannose + D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = GDP + D-Man-α-(1→3)-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol

Other name(s): Alg2 mannosyltransferase (ambiguous); ALG2 (gene name, ambiguous); glycolipid 3-α-mannosyltransferase; GDP-mannose:glycolipid 1,3-α-D-mannosyltransferase

Systematic name: GDP-D-mannose:D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol 3-α-mannosyltransferase

Comments: The biosynthesis of asparagine-linked glycoproteins utilizes a dolichyl diphosphate-linked glycosyl donor, which is assembled by the series of membrane-bound glycosyltransferases that comprise the dolichol pathway. Alg2 mannosyltransferase from Saccharomyces cerevisiae carries out an α1,3-mannosylation of D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol, followed by an α1,6-mannosylation (cf. EC 2.4.1.257), to form the first branched pentasaccharide intermediate of the dolichol pathway [1,2].

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 81181-76-2

References:

1. Kampf, M., Absmanner, B., Schwarz, M. and Lehle, L. Biochemical characterization and membrane topology of Alg2 from Saccharomyces cerevisiae as a bifunctional α1,3- and 1,6-mannosyltransferase involved in lipid-linked oligosaccharide biosynthesis. J. Biol. Chem. 284 (2009) 11900-11912. [PMID: 19282279]

2. O'Reilly, M.K., Zhang, G. and Imperiali, B. In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis. Biochemistry 45 (2006) 9593-9603. [PMID: 16878994]

[EC 2.4.1.132 created 1984, modified 2011]

*EC 2.4.1.191

Accepted name: luteolin-7-O-diglucuronide 4'-O-glucuronosyltransferase

Reaction: UDP-glucuronate + luteolin 7-O-[β-D-glucuronosyl-(1→2)-β-D-glucuronide] = UDP + luteolin 7-O-[β-D-glucuronosyl-(1→2)-β-D-glucuronide]-4'-O-β-D-glucuronide

For diagram of reaction click here

Other name(s): uridine diphosphoglucuronate-luteolin 7-O-diglucuronide glucuronosyltransferase; UDP-glucuronate:luteolin 7-O-diglucuronide-glucuronosyltransferase; UDPglucuronate:luteolin 7-O-diglucuronide-4'-O-glucuronosyl-transferase; LDT

Systematic name: UDP-glucuronate:luteolin-7-O-β-D-diglucuronide 4'-O-glucuronosyltransferase

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 115490-50-1

References:

1. Schulz, M. and Weissenböck, G. 3 specific UDP-glucuronate-flavone-glucuronosyl-transferases from primary leaves of Secale cereale. Phytochemistry 27 (1988) 1261-1267.

[EC 2.4.1.191 created 1992, modified 2011]

EC 2.4.1.256

Accepted name: Dol-P-Glc:Glc2Man9GlcNAc2-PP-Dol α1,2-glucosyltransferase

Reaction: dolichyl β-D-glucosyl phosphate + D-Glc-α-(1→3)-D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = D-Glc-α-(1→2)-D-Glc-α-(1→3)-D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate

Other name(s): ALG10

Systematic name: dolichyl β-D-glucosyl phosphate:D-Glc-α-(1→3)-D-Glc-α-(1→3)-D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,2-glucosyltransferase

Comments: This enzyme performs the final step in the synthesis of the lipid-linked oligosaccharide attaching D-glucose in an α-1,2-linkage to the outermost D-glucose in the long branch.

References:

1. Burda, P. and Aebi, M. The ALG10 locus of Saccharomyces cerevisiae encodes the α-1,2 glucosyltransferase of the endoplasmic reticulum: the terminal glucose of the lipid-linked oligosaccharide is required for efficient N-linked glycosylation. Glycobiology 8 (1998) 455-462. [PMID: 9597543]

[EC 2.4.1.256 created 2011]

EC 2.4.1.257

Accepted name: GDP-Man:Man2GlcNAc2-PP-Dol α-1,6-mannosyltransferase

Reaction: GDP-D-mannose + D-Man-α-(1→3)-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = GDP + D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol

Other name(s): Alg2 mannosyltransferase (ambiguous); ALG2 (gene name, ambiguous); GDP-Man:Man1GlcNAc2-PP-dolichol mannosyltransferase (ambiguous)

Systematic name: GDP-D-mannose:D-Man-α-(1→3)-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-6-mannosyltransferase

Comments: The biosynthesis of asparagine-linked glycoproteins utilizes a dolichyl diphosphate-linked glycosyl donor, which is assembled by the series of membrane-bound glycosyltransferases that comprise the dolichol pathway. Alg2 mannosyltransferase from Saccharomyces cerevisiae carries out an α1,3-mannosylation (cf. EC 2.4.1.132) of D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-GlcNAc-diphosphodolichol, followed by an α1,6-mannosylation, to form the first branched pentasaccharide intermediate of the dolichol pathway [1,2].

References:

1. Kampf, M., Absmanner, B., Schwarz, M. and Lehle, L. Biochemical characterization and membrane topology of Alg2 from Saccharomyces cerevisiae as a bifunctional α1,3- and 1,6-mannosyltransferase involved in lipid-linked oligosaccharide biosynthesis. J. Biol. Chem. 284 (2009) 11900-11912. [PMID: 19282279]

2. O'Reilly, M.K., Zhang, G. and Imperiali, B. In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis. Biochemistry 45 (2006) 9593-9603. [PMID: 16878994]

[EC 2.4.1.257 created 2011]

EC 2.4.1.258

Accepted name: Dol-P-Man:Man5GlcNAc2-PP-Dol α-1,3-mannosyltransferase

Reaction: dolichyl β-D-mannosyl phosphate + D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→3)-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate

Other name(s): Man5GlcNAc2-PP-Dol mannosyltransferase; ALG3; dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase; Not56-like protein; Alg3 α-1,3-mannosyl transferase

Systematic name: dolichyl β-D-mannosyl phosphate:D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,3-mannosyltransferase

Comments: The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl diphosphate. Early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9Glc-NAc2-PP-Dol on the lumenal side use dolichyl β-D-mannosyl phosphate. The first step of this assembly pathway on the luminal side of the endoplasmic reticulum is catalysed by ALG3.

References:

1. Sharma, C.B., Knauer, R. and Lehle, L. Biosynthesis of lipid-linked oligosaccharides in yeast: the ALG3 gene encodes the Dol-P-Man:Man5GlcNAc2-PP-Dol mannosyltransferase. Biol. Chem. 382 (2001) 321-328. [PMID: 11308030]

2. Cipollo, J.F. and Trimble, R.B. The accumulation of Man(6)GlcNAc(2)-PP-dolichol in the Saccharomyces cerevisiae Δalg9 mutant reveals a regulatory role for the Alg3p α1,3-Man middle-arm addition in downstream oligosaccharide-lipid and glycoprotein glycan processing. J. Biol. Chem. 275 (2000) 4267-4277. [PMID: 10660594]

[EC 2.4.1.258 created 1976 as EC 2.4.1.130, part-transferred 2011 to EC 2.4.1.258]

EC 2.4.1.259

Accepted name: Dol-P-Man:Man6GlcNAc2-PP-Dol α-1,2-mannosyltransferase

Reaction: dolichyl β-D-mannosyl phosphate + D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→3)-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate

Other name(s): ALG9; ALG9 α1,2 mannosyltransferase; dolichylphosphomannose-dependent ALG9 mannosyltransferase; ALG9 mannosyltransferase

Systematic name: dolichyl β-D-mannosyl phosphate: D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→3)-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,2-mannosyltransferase

Comments: The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl diphosphate. Early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9Glc-NAc2-PP-Dol on the lumenal side use dolichyl β-D-mannosyl phosphate. ALG9 mannosyltransferase catalyses the addition of two different α-1,2-mannose residues the addition of α-1,2-mannose to Man6GlcNAc2-PP-Dol (EC 2.4.1.259) and the addition of α-1,2-mannose to Man8GlcNAc2-PP-Dol (EC 2.4.1.261).

References:

1. Vleugels, W., Keldermans, L., Jaeken, J., Butters, T.D., Michalski, J.C., Matthijs, G., Foulquier, F. Quality control of glycoproteins bearing truncated glycans in an ALG9-defective (CDG-IL) patient. Glycobiology 19 (2009) 910-917. [PMID: 19451548]

2. Cipollo, J.F. and Trimble, R.B. The accumulation of Man(6)GlcNAc(2)-PP-dolichol in the Saccharomyces cerevisiae Δalg9 mutant reveals a regulatory role for the Alg3p α1,3-Man middle-arm addition in downstream oligosaccharide-lipid and glycoprotein glycan processing. J. Biol. Chem. 275 (2000) 4267-4277. [PMID: 10660594]

3. Frank, C.G. and Aebi, M. ALG9 mannosyltransferase is involved in two different steps of lipid-linked oligosaccharide biosynthesis. Glycobiology 15 (2005) 1156-1163. [PMID: 15987956]

[EC 2.4.1.259 created 1976 as EC 2.4.1.130, part-transferred 2011 to EC 2.4.1.259]

EC 2.4.1.260

Accepted name: Dol-P-Man:Man7GlcNAc2-PP-Dol α-1,6-mannosyltransferase

Reaction: dolichyl β-D-mannosyl phosphate + D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate

Other name(s): ALG12; ALG12 mannosyltransferase; ALG12 α1,6mannosyltransferase; dolichyl-P-mannose:Man7GlcNAc2-PP-dolichyl mannosyltransferase; dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl α6-mannosyltransferase; EBS4

Systematic name: dolichyl β-D-mannosyl phosphate:D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,6-mannosyltransferase

Comments: The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl diphosphate. Early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9Glc-NAc2-PP-Dol on the lumenal side use dolichyl β-D-mannosyl phosphate.

References:

1. Frank, C.G. and Aebi, M. ALG9 mannosyltransferase is involved in two different steps of lipid-linked oligosaccharide biosynthesis. Glycobiology 15 (2005) 1156-1163. [PMID: 15987956]

2. Hong, Z., Jin, H., Fitchette, A.C., Xia, Y., Monk, A.M., Faye, L. and Li, J. Mutations of an α1,6 mannosyltransferase inhibit endoplasmic reticulum-associated degradation of defective brassinosteroid receptors in Arabidopsis. Plant Cell 21 (2009) 3792-3802. [PMID: 20023196]

3. Cipollo, J.F. and Trimble, R.B. The Saccharomyces cerevisiae alg12δ mutant reveals a role for the middle-arm α1,2Man- and upper-arm α1,2Manα1,6Man- residues of Glc3Man9GlcNAc2-PP-Dol in regulating glycoprotein glycan processing in the endoplasmic reticulum and Golgi apparatus. Glycobiology 12 (2002) 749-762. [PMID: 12460943]

4. Grubenmann, C.E., Frank, C.G., Kjaergaard, S., Berger, E.G., Aebi, M. and Hennet, T. ALG12 mannosyltransferase defect in congenital disorder of glycosylation type lg. Hum. Mol. Genet. 11 (2002) 2331-2339. [PMID: 12217961]

[EC 2.4.1.260 created 1976 as EC 2.4.1.130, part-transferred 2011 to EC 2.4.1.160]

EC 2.4.1.261

Accepted name: Dol-P-Man:Man8GlcNAc2-PP-Dol α-1,2-mannosyltransferase

Reaction: dolichyl β-D-mannosyl phosphate + D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol = D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate

Other name(s): ALG9; ALG9 α1,2 mannosyltransferase; dolichylphosphomannose-dependent ALG9 mannosyltransferase; ALG9 mannosyltransferase

Systematic name: dolichyl β-D-mannosyl phosphate:D-Man-α-(1→2)-D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→2)-D-Man-α-(1→3)-[D-Man-α-(1→6)]-D-Man-α-(1→6)]-D-Man-β-(1→4)-D-GlcNAc-β-(1→4)-D-GlcNAc-diphosphodolichol α-1,2-mannosyltransferase

Comments: The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl diphosphate. Early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9Glc-NAc2-PP-Dol on the lumenal side use dolichyl β-D-mannosyl phosphate. ALG9 mannosyltransferase catalyses the addition of two different α-1,2-mannose residues: the addition of α-1,2-mannose to Man6GlcNAc2-PP-Dol (EC 2.4.1.259) and the addition of α-1,2-mannose to Man8GlcNAc2-PP-Dol (EC 2.4.1.261).

References:

1. Vleugels, W., Keldermans, L., Jaeken, J., Butters, T.D., Michalski, J.C., Matthijs, G., Foulquier, F. Quality control of glycoproteins bearing truncated glycans in an ALG9-defective (CDG-IL) patient. Glycobiology 19 (0) 910-917. [PMID: 19451548]

2. Frank, C.G. and Aebi, M. ALG9 mannosyltransferase is involved in two different steps of lipid-linked oligosaccharide biosynthesis. Glycobiology 15 (2005) 1156-1163. [PMID: 15987956]

[EC 2.4.1.261 created 1976 as EC 2.4.1.130, part-transferred 2011 to EC 2.4.1.261]

*EC 2.5.1.31

Accepted name: ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]

Reaction: (2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + ditrans,octacis-undecaprenyl diphosphate

For diagram of reaction click here

Other name(s): di-trans,poly-cis-undecaprenyl-diphosphate synthase; undecaprenyl-diphosphate synthase; bactoprenyl-diphosphate synthase; UPP synthetase; undecaprenyl diphosphate synthetase; undecaprenyl pyrophosphate; synthetase; di-trans,poly-cis-decaprenylcistransferase

Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 8 isopentenyl units)

Comments: Undecaprenyl pyrophosphate synthase catalyses the consecutive condensation reactions of a farnesyl diphosphate with eight isopentenyl diphosphates, in which new cis-double bonds are formed, to generate undecaprenyl diphosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall [3].

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 52350-87-5

References:

1. Muth, J.D. and Allen, C.M. Undecaprenyl pyrophosphate synthetase from Lactobacillus plantarum: a dimeric protein. Arch. Biochem. Biophys. 230 (1984) 49-60. [PMID: 6712246]

2. Takahashi, I. and Ogura, K. Prenyltransferases of Bacillus subtilis: undecaprenyl pyrophosphate synthetase and geranylgeranyl pyrophosphate synthetase. J. Biochem. (Tokyo) 92 (1982) 1527-1537. [PMID: 6818223]

3. Guo, R.T., Ko, T.P., Chen, A.P., Kuo, C.J., Wang, A.H. and Liang, P.H. Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis. J. Biol. Chem. 280 (2005) 20762-20774. [PMID: 15788389]

4. Ko, T.P., Chen, Y.K., Robinson, H., Tsai, P.C., Gao, Y.G., Chen, A.P., Wang, A.H. and Liang, P.H. Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis. J. Biol. Chem. 276 (2001) 47474-47482. [PMID: 11581264]

5. Fujikura, K., Zhang, Y.W., Fujihashi, M., Miki, K. and Koyama, T. Mutational analysis of allylic substrate binding site of Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase. Biochemistry 42 (2003) 4035-4041. [PMID: 12680756]

6. Fujihashi, M., Zhang, Y.W., Higuchi, Y., Li, X.Y., Koyama, T. and Miki, K. Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase. Proc. Natl. Acad. Sci. USA 98 (2001) 4337-4342. [PMID: 11287651]

7. Pan, J.J., Chiou, S.T. and Liang, P.H. Product distribution and pre-steady-state kinetic analysis of Escherichia coli undecaprenyl pyrophosphate synthase reaction. Biochemistry 39 (2000) 10936-10942. [PMID: 10978182]

8. Kharel, Y., Zhang, Y.W., Fujihashi, M., Miki, K. and Koyama, T. Significance of highly conserved aromatic residues in Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase. J. Biochem. 134 (2003) 819-826. [PMID: 14769870]

[EC 2.5.1.31 created 1984, modified 2011]

*EC 2.5.1.89

Accepted name: tritrans,polycis-undecaprenyl-diphosphate synthase [geranylgeranyl-diphosphate specific]

Reaction: geranylgeranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + tritrans,heptacis-undecaprenyl diphosphate

Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 7 isopentenyl units)

Comments: This enzyme is involved in the biosynthesis of the glycosyl carrier lipid in some archaebacteria. Unlike EC 2.5.1.31, its counterpart in most bacteria, it prefers geranylgeranyl diphosphate to farnesyl diphosphate as the allylic substrate, resulting in production of a tritrans,polycis variant of undecaprenyl diphosphate [1].

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

References:

1. Hemmi, H., Yamashita, S., Shimoyama, T., Nakayama, T. and Nishino, T. Cloning, expression, and characterization of cis-polyprenyl diphosphate synthase from the thermoacidophilic archaeon Sulfolobus acidocaldarius. J. Bacteriol. 183 (2001) 401-404. [PMID: 11114943]

[EC 2.5.1.89 created 2010, modified 2011]

*EC 2.5.1.92

Accepted name: (2Z,6Z)-farnesyl diphosphate synthase

Reaction: dimethylallyl diphosphate + 2 isopentenyl diphosphate = 2 diphosphate + (2Z,6Z)-farnesyl diphosphate

Other name(s): cis,cis-farnesyl diphosphate synthase; Z,Z-FPP synthase; zFPS; Z,Z-farnesyl pyrophosphate synthase

Systematic name: dimethylallyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 2 isopentenyl units)

Comments: This enzyme, originally characterized from wild tomato, specifically forms (2Z,6Z)-farnesyl diphosphate via neryl diphosphate and isopentenyl diphosphate. In wild tomato it is involved in the biosynthesis of several sesquiterpenes. See also EC 2.5.1.68 [(2Z,6E)-farnesyl diphosphate synthase] and EC 2.5.1.10 [(2E,6E)-farnesyl diphosphate synthase].

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

References:

1. Sallaud, C., Rontein, D., Onillon, S., Jabes, F., Duffe, P., Giacalone, C., Thoraval, S., Escoffier, C., Herbette, G., Leonhardt, N., Causse, M. and Tissier, A. A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell 21 (2009) 301-317. [PMID: 19155349]

[EC 2.5.1.92 created 2010, modified 2011]

*EC 2.7.8.30

Accepted name: undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase

Reaction: UDP-4-deoxy-4-formamido-β-L-arabinopyranose + ditrans,octacis-undecaprenyl phosphate = UDP + 4-deoxy-4-formamido-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate

Other name(s): undecaprenyl-phosphate Ara4FN transferase; Ara4FN transferase; polymyxin resistance protein PmrF; UDP-4-amino-4-deoxy-α-L-arabinose:ditrans,polycis-undecaprenyl phosphate 4-amino-4-deoxy-α-L-arabinosyltransferase

Systematic name: UDP-4-amino-4-deoxy-α-L-arabinose:ditrans,octacis-undecaprenyl phosphate 4-amino-4-deoxy-α-L-arabinosyltransferase

Comments: The enzyme shows no activity with UDP-4-amino-4-deoxy-β-L-arabinose.

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

References:

1. Breazeale, S.D., Ribeiro, A.A. and Raetz, C.R. Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid a species modified with 4-amino-4-deoxy-L-arabinose. J. Biol. Chem. 277 (2002) 2886-2896. [PMID: 11706007]

2. Breazeale, S.D., Ribeiro, A.A., McClerren, A.L. and Raetz, C.R.H. A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-amino-4-deoxy-L-arabinose. Identification and function of UDP-4-deoxy-4-formamido-L-arabinose. J. Biol. Chem. 280 (2005) 14154-14167. [PMID: 15695810]

[EC 2.7.8.30 created 2010, modified 2011]

EC 2.7.8.33

Accepted name: UDP-GlcNAc:undecaprenyl-phosphate GlcNAc-1-phosphate transferase

Reaction: UDP-N-acetyl-D-glucosamine + ditrans,octacis-undecaprenyl phosphate = UMP + N-acetyl-D-glucosaminyldiphospho-ditrans,octacis-undecaprenol

Glossary: N-acetyl-D-glucosaminyldiphospho-ditrans,octacis-undecaprenol = lipid I = GlcNAc-pyrophosphorylundecaprenol = ditrans,octacis-undecaprenyl-N-acetyl-D-glucosaminyl diphosphate

Other name(s): UDP-N-acetylglucosamine:undecaprenyl-phosphate GlcNAc-1-phosphate transferase; WecA; WecA transferase; UDP-GIcNAc:undecaprenyl phosphate N-acetylglucosaminyl 1-P transferase; GlcNAc-P-P-Und synthase; GPT, TagO

Systematic name: UDP-N-acetyl-D-glucosamine:ditrans,octacis-undecaprenyl phosphate N-acetyl-D-glucosaminephosphotransferase

Comments: This enzyme catalyses the synthesis of ditrans,octacis-undecaprenyl-N-acetyl-D-glucosaminyl diphosphate (i.e. lipid I), an essential lipid intermediate for the biosynthesis of various bacterial cell envelope components. The enzyme also initiates the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide in certain E. coli strains, including K-12 [2] and of teichoic acid in certain Gram-positive bacteria [4].

References:

1. Al-Dabbagh, B., Mengin-Lecreulx, D. and Bouhss, A. Purification and characterization of the bacterial UDP-GlcNAc:undecaprenyl-phosphate GlcNAc-1-phosphate transferase WecA. J. Bacteriol. 190 (2008) 7141-7146. [PMID: 18723618]

2. Lehrer, J., Vigeant, K.A., Tatar, L.D. and Valvano, M.A. Functional characterization and membrane topology of Escherichia coli WecA, a sugar-phosphate transferase initiating the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide. J. Bacteriol. 189 (2007) 2618-2628. [PMID: 17237164]

4. Soldo, B., Lazarevic, V. and Karamata, D. tagO is involved in the synthesis of all anionic cell-wall polymers in Bacillus subtilis 168. Microbiology 148 (2002) 2079-2087. [PMID: 12101296]

[EC 2.7.8.33 created 2011]

EC 3.1.2.29

Accepted name: fluoroacetyl-CoA thioesterase

Reaction: fluoroacetyl-CoA + H2O = fluoroacetate + CoA

Systematic name: fluoroacetyl-CoA hydrolase

Comments: Fluoroacetate is extremely toxic. It reacts with CoA to form fluoroacetyl-CoA, which substitutes for acetyl CoA and reacts with EC 2.3.3.1 (citrate synthase) to produce fluorocitrate, a metabolite of which binds very tightly to EC 4.2.1.3 (aconitase) and halts the TCA cycle. This enzyme hydrolyses fluoroacetyl-CoA before it can react with citrate synthase, and thus confers fluoroacetate resistance on the organisms that produce it. It has been described in the poisonous plant Dichapetalum cymosum and the bacterium Streptomyces cattleya, both of which are fluoroacetate producers.

References:

1. Meyer, J.J.M., Grobbelaar, N., Vleggaar, R. and Louw, A.I. Fluoroacetyl-coenzyme-A hydrolase-like activity in Dichapetalum cymosum. J. Plant Physiol. 139 (1992) 369-372.

2. Huang, F., Haydock, S.F., Spiteller, D., Mironenko, T., Li, T.L., O'Hagan, D., Leadlay, P.F. and Spencer, J.B. The gene cluster for fluorometabolite biosynthesis in Streptomyces cattleya: a thioesterase confers resistance to fluoroacetyl-coenzyme A. Chem. Biol. 13 (2006) 475-484. [PMID: 16720268]

3. Dias, M.V., Huang, F., Chirgadze, D.Y., Tosin, M., Spiteller, D., Dry, E.F., Leadlay, P.F., Spencer, J.B. and Blundell, T.L. Structural basis for the activity and substrate specificity of fluoroacetyl-CoA thioesterase FlK. J. Biol. Chem. 285 (2010) 22495-22504. [PMID: 20430898]

[EC 3.1.2.29 created 2011]

*EC 3.1.3.73

Accepted name: adenosylcobalamin/α-ribazole phosphatase

Reaction: (1) adenosylcobalamin 5'-phosphate + H2O = coenzyme B12 + phosphate
(2) α-ribazole 5'-phosphate + H2O = α-ribazole + phosphate

For diagram of the reaction click here

Other name(s): CobC; adenosylcobalamin phosphatase; α-ribazole phosphatase

Systematic name: adenosylcobalamin/α-ribazole-5'-phosphate phosphohydrolase

Comments: This enzyme catalyses the last step in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis, characterized in Salmonella enterica [3]. It also participates in a salvage pathway that recycles cobinamide into adenosylcobalamin [1].

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 251991-06-7

References:

1. O'Toole, G.A., Trzebiatowski, J.R. and Escalante-Semerena, J.C. The cobC gene of Salmonella typhimurium codes for a novel phosphatase involved in the assembly of the nucleotide loop of cobalamin. J. Biol. Chem. 269 (1994) 26503-26511. [PMID: 7929373]

2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]

3. Zayas, C.L. and Escalante-Semerena, J.C. Reassessment of the late steps of coenzyme B12 synthesis in Salmonella enterica: evidence that dephosphorylation of adenosylcobalamin-5'-phosphate by the CobC phosphatase is the last step of the pathway. J. Bacteriol. 189 (2007) 2210-2218. [PMID: 17209023]

[EC 3.1.3.73 created 2004, modified 2011]

*EC 3.2.2.1

Accepted name: purine nucleosidase

Reaction: a purine nucleoside + H2O = D-ribose + a purine base

Other name(s): nucleosidase (misleading); purine β-ribosidase; purine nucleoside hydrolase; purine ribonucleosidase; ribonucleoside hydrolase (misleading); nucleoside hydrolase (misleading); N-ribosyl purine ribohydrolase; nucleosidase g; N-D-ribosylpurine ribohydrolase; inosine-adenosine-guanosine preferring nucleoside hydrolase; purine-specific nucleoside N-ribohydrolase; IAG-nucleoside hydrolase; IAG-NH

Systematic name: purine-nucleoside ribohydrolase

Comments: The enzyme from the bacterium Ochrobactrum anthropi specifically catalyses the irreversible N-riboside hydrolysis of purine nucleosides. Pyrimidine nucleosides, purine and pyrimidine nucleotides, NAD+, NADP+ and nicotinaminde mononucleotide are not substrates [6].

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9025-44-9

References:

1. Heppel, L.A. and Hilmoe, R.J. Phosphorolysis and hydrolysis of purine ribosides from yeast. J. Biol. Chem. 198 (1952) 683-694. [PMID: 12999785]

2. Kalckar, H.M. Biosynthetic aspects of nucleosides and nucleic acids. Pubbl. Staz. Zool. (Napoli) 23 (1951) 87-103.

3. Takagi, Y. and Horecker, B.L. Purification and properties of a bacterial riboside hydrolyase. J. Biol. Chem. 225 (1956) 77-86. [PMID: 13416219]

4. Tarr, H.L.A. Fish muscle riboside hydrolases. Biochem. J. 59 (1955) 386-391. [PMID: 14363106]

5. Parkin, D.W. Purine-specific nucleoside N-ribohydrolase from Trypanosoma brucei brucei. Purification, specificity, and kinetic mechanism. J. Biol. Chem. 271 (1996) 21713-21719. [PMID: 8702965]

6. Ogawa, J., Takeda, S., Xie, S.X., Hatanaka, H., Ashikari, T., Amachi, T. and Shimizu, S. Purification, characterization, and gene cloning of purine nucleosidase from Ochrobactrum anthropi. Appl. Environ. Microbiol. 67 (2001) 1783-1787. [PMID: 11282633]

7. Versées, W., Decanniere, K., Van Holsbeke, E., Devroede, N. and Steyaert, J. Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax. J. Biol. Chem. 277 (2002) 15938-15946. [PMID: 11854281]

8. Mazumder-Shivakumar, D. and Bruice, T.C. Computational study of IAG-nucleoside hydrolase: determination of the preferred ground state conformation and the role of active site residues. Biochemistry 44 (2005) 7805-7817. [PMID: 15909995]

[EC 3.2.2.1 created 1961, modified 2006, modified 2011]

*EC 3.4.13.19

Accepted name: membrane dipeptidase

Reaction: Hydrolysis of dipeptides

Other name(s): renal dipeptidase; dehydropeptidase I (DPH I); dipeptidase (ambiguous); aminodipeptidase; dipeptide hydrolase (ambiguous); dipeptidyl hydrolase (ambiguous); nonspecific dipeptidase; glycosyl-phosphatidylinositol-anchored renal dipeptidase; MDP

Comments: A membrane-bound, zinc enzyme with broad specificity. Abundant in the kidney cortex. Inhibited by bestatin and cilastatin. Type example of peptidase family M19.

Links to other databases: BRENDA, EXPASY, KEGG, MEROPS, PDB, CAS registry number: 9031-99-6

References:

1. Campbell, B., Lin, H., Davis, R. and Ballew, E. The purification and properties of a particulate renal dipeptidase. Biochim. Biophys. Acta 118 (1966) 371-386. [PMID: 5961612]

2. Campbell, B.J. Renal dipeptidase. Methods Enzymol. 19 (1970) 722-729.

3. Kropp, H., Sundelof, J.G., Hajdu, R. and Kahan, F.M. Metabolism of thienamycin and related carbapenem antibiotics by renal dipeptidase, dehydropeptidase-I. Antimicrob. Agents Chemother. 22 (1982) 62-70. [PMID: 7125632]

4. Hooper, N.M., Keen, J.N. and Turner, A.J. Characterization of the glycosyl-phosphatidylinositol-anchored human renal dipeptidase reveals that it is more extensively glycosylated than the pig enzyme. Biochem. J. 265 (1990) 429-433. [PMID: 2137335]

[EC 3.4.13.19 created 1961 as EC 3.4.3.1 and EC 3.4.3.2, transferred 1972 to EC 3.4.13.1 and EC 3.4.13.2, transferred 1978 to EC 3.4.13.11, part transferred 1992 to EC 3.4.13.19, modified 2011]

*EC 3.4.15.1

Accepted name: peptidyl-dipeptidase A

Reaction: Release of a C-terminal dipeptide, oligopeptide┼Xaa-Yaa, when Xaa is not Pro, and Yaa is neither Asp nor Glu. Thus, conversion of angiotensin I to angiotensin II, with increase in vasoconstrictor activity, but no action on angiotensin II

Glossary: captopril = (2S)-1-(3-mercapto-2-methylpropanoyl)-L-proline

Other name(s): dipeptidyl carboxypeptidase I; peptidase P; dipeptide hydrolase (ambiguous); peptidyl dipeptidase; angiotensin converting enzyme; kininase II; angiotensin I-converting enzyme; carboxycathepsin; dipeptidyl carboxypeptidase; peptidyl dipeptidase I; peptidyl-dipeptide hydrolase; peptidyldipeptide hydrolase; endothelial cell peptidyl dipeptidase; ACE; peptidyl dipeptidase-4; PDH; peptidyl dipeptide hydrolase; DCP

Comments: A Cl-dependent, zinc glycoprotein that is generally membrane-bound. A potent inhibitor is captopril. Important in elevation of blood pressure, through formation of angiotensin II (vasoconstrictor) and destruction of bradykinin (vasodilator). Two molecular forms exist in mammalian tissues, a widely-distributed somatic form of 150- to 180-kDa that contains two non-identical catalytic sites, and a testicular form of 90- to 100-kDa that contains only a single catalytic site. Type example of peptidase family M2

Links to other databases: BRENDA, EXPASY, KEGG, MEROPS, PDB, CAS registry number: 9015-82-1

References:

1. Soubrier, F., Alhenc-Gelas, F., Hubert, C., Allegrini, J., John, M., Tregear, G. and Corvol, P. Two putative active centers in human angiotensin I-converting enzyme revealed by molecular cloning. Proc. Natl. Acad. Sci. USA 85 (1988) 9386-9390. [PMID: 2849100]

2. Ehlers, M.R.W., Fox, E.A., Strydom, D.J. and Riordan, J.F. Molecular cloning of human testicular angiotensin-converting enzyme: the testis enzyme is identical to the C-terminal half of endothelial angiotensin-converting enzyme. Proc. Natl. Acad. Sci. USA 86 (1989) 7741-7745. [PMID: 2554286]

3. Wei, L., Clauser, E., Alhenc-Gelas, F. and Corvol, P. The two homologous domains of human angiotensin I-converting enzyme interact differently with competitive inhibitors. J. Biol. Chem. 267 (1992) 13398-13405. [PMID: 1320019]

4. Corvol, P., Williams, T.A. and Soubrier, F. Peptidyl dipeptidase A: angiotensin I-converting enzyme. Methods Enzymol. 248 (1995) 283-305. [PMID: 7674927]

[EC 3.4.15.1 created 1972, modified 1981, modified 1989, modified 1996, modified 2011]

*EC 3.4.16.6

Accepted name: carboxypeptidase D

Reaction: Preferential release of a C-terminal arginine or lysine residue

Other name(s): cereal serine carboxypeptidase II; Saccharomyces cerevisiae KEX1 gene product; carboxypeptidase Kex1; gene KEX1 serine carboxypeptidase; KEX1 carboxypeptidase; KEX1 proteinase; KEX1DELTAp; CPDW-II; serine carboxypeptidase (misleading); Phaseolus proteinase

Comments: A carboxypeptidase with optimum pH 4.5-6.0, inhibited by diisopropyl fluorophosphate, and sensitive to thiol-blocking reagents (reviewed in [1]). In peptidase family S10 (carboxypeptidase C family).

Links to other databases: BRENDA, EXPASY, KEGG, MEROPS, PDB, CAS registry number: 153967-26-1

References:

1. Breddam, K. Serine carboxypeptidases. A review. Carlsberg Res. Commun. 51 (1986) 83-128.

2. Breddam, K., Sørensen, S.B. and Svendsen, I. Primary structure and enzymatic properties of carboxypeptidase II from wheat bran. Carlsberg Res. Commun. 52 (1987) 297-311.

3. Dmochowska, A., Dignard, D., Henning, D., Thomas, D.Y. and Bussey, H. Yeast KEX1 gene encodes a putative protease with a carboxypeptidase B-like function involved in killer toxin and α-factor precursor processing. Cell 50 (1987) 573-584. [PMID: 3301004]

4. Liao, D.-I., Breddam, K., Sweet, R.M., Bullock, T. and Remington, S.J. Refined atomic model of wheat serine carboxypeptidase II at 2.2-Å resolution. Biochemistry 31 (1992) 9796-9812. [PMID: 1390755]

[EC 3.4.16.6 created 1972 as EC 3.4.12.1, transferred 1978 to EC 3.4.16.1, part transferred 1993 to EC 3.4.16.6 (EC 3.4.16.3 created 1972 as EC 3.4.12.12, transferred 1978 to EC 3.4.16.3, transferred 1992 to EC 3.4.16.1), (EC 3.4.21.13 created 1972, transferred 1978 to EC 3.4.16.1), modified 2011]

*EC 3.5.1.4

Accepted name: amidase

Reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3

Other name(s): acylamidase; acylase (misleading); amidohydrolase (ambiguous); deaminase (ambiguous); fatty acylamidase; N-acetylaminohydrolase (ambiguous)

Systematic name: acylamide amidohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, PDB, UM-BBD, CAS registry number: 9012-56-0

References:

1. Bray, H.G., James, S.P., Raffan, I.M., Ryman, B.E. and Thorpe, W.V. The fate of certain organic acids and amides in the rabbit. 7. An amidase of rabbit liver. Biochem. J. 44 (1949) 618-625. [PMID: 16748573]

2. Bray, H.G., James, S.P., Thorpe, W.V. and Wasdell, M.R. The fate of certain organic acids and amides in the rabbit. 11. Further observations on the hydrolysis of amides by tissue extracts. Biochem. J. 47 (1950) 294-299. [PMID: 14800883]

[EC 3.5.1.4 created 1961, modified 2011]

*EC 4.1.1.52

Accepted name: 6-methylsalicylate decarboxylase

Reaction: 6-methylsalicylate = 3-methylphenol + CO2

Glossary: 3-methylphenol = 3-cresol = m-cresol

Other name(s): 6-methylsalicylic acid (2,6-cresotic acid) decarboxylase; 6-MSA decarboxylase; 6-methylsalicylate carboxy-lyase

Systematic name: 6-methylsalicylate carboxy-lyase (3-methylphenol-forming)

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 37289-50-2

References:

1. Light, R.J. 6-Methylsalicylic acid decarboxylase from Penicillium patulum. Biochim. Biophys. Acta 191 (1969) 430-438. [PMID: 5354271]

2. Vogel, G. and Lynen, F. 6-Methylsalicylsäure-Decarboxylase. Naturwissenschaften 57 (1970) 664.

[EC 4.1.1.52 created 1972, modified 2011]

*EC 4.1.1.77

Accepted name: 4-oxalocrotonate decarboxylase

Reaction: 4-oxalocrotonate = 2-oxopent-4-enoate + CO2

Glossary: 4-oxalocrotonate = (2E)-5-oxohex-2-enedioate

Other name(s): 4-oxalocrotonate carboxy-lyase

Systematic name: 4-oxalocrotonate carboxy-lyase (2-oxopent-4-enoate-forming)

Comments: Involved in the meta-cleavage pathway for the degradation of phenols, methylphenols and catechols

Links to other databases: BRENDA, EXPASY, KEGG, UM-BBD, CAS registry number: 37325-55-6

References:

1. Shingler, V., Marklund, U., Powlowski, J. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J. Bacteriol. 174 (1992) 711-724. [PMID: 1732207]

[EC 4.1.1.77 created 1999, modified 2011]

*EC 4.1.3.39

Accepted name: 4-hydroxy-2-oxovalerate aldolase

Reaction: 4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate

Glossary: valerate = pentanoate

Other name(s): 4-hydroxy-2-ketovalerate aldolase; HOA; DmpG; 4-hydroxy-2-oxovalerate pyruvate-lyase; 4-hydroxy-2-oxopentanoate pyruvate-lyase

Systematic name: 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)

Comments: Requires Mn2+ for maximal activity [1]. The enzyme from Pseudomonas putida is also stimulated by the presence of NADH [1]. In Pseudomonas species, this enzyme forms part of a bifunctional enzyme with EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). It catalyses the penultimate step in the meta-cleavage pathway for the degradation of phenols, methylphenols and catechol [1].

Links to other databases: BRENDA, EXPASY, KEGG, UM-BBD, CAS registry number: 37325-52-3

References:

1. Manjasetty, B.A., Powlowski, J. and Vrielink, A. Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Proc. Natl. Acad. Sci. USA 100 (2003) 6992-6997. [PMID: 12764229]

2. Powlowski, J., Sahlman, L. and Shingler, V. Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. J. Bacteriol. 175 (1993) 377-385. [PMID: 8419288]

3. Manjasetty, B.A., Croteau, N., Powlowski, J. and Vrielink, A. Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase—aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 582-585. [PMID: 11264589]

[EC 4.1.3.39 created 2006, modified 2011]

EC 4.1.99.16

Accepted name: geosmin synthase

Reaction: (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O = (–)-geosmin + acetone

Systematic name: germacradienol geosmin-lyase (acetone forming)

Comments: Requires Mg2+. Geosmin is the cause of the characteristic smell of moist soil. It is a bifunctional enzyme. The N-terminal part of the enzyme is EC 4.2.3.22, germacradienol synthase, and forms germacradienol from farnesyl diphosphate. The C-terminal part of the enzyme catalyses the conversion of germacradienol to geosmin via (1S,4aS,8aS)-8,10-dimethyl-1,2,3,4,4a,5,6,8a-octahydronaphthalene.

References:

1. Jiang, J., He, X. and Cane, D.E. Geosmin biosynthesis. Streptomyces coelicolor germacradienol/germacrene D synthase converts farnesyl diphosphate to geosmin. J. Am. Chem. Soc. 128 (2006) 8128-8129. [PMID: 16787064]

2. Cane, D.E., He, X., Kobayashi, S., Omura, S. and Ikeda, H. Geosmin biosynthesis in Streptomyces avermitilis. Molecular cloning, expression, and mechanistic study of the germacradienol/geosmin synthase. J. Antibiot. (Tokyo) 59 (2006) 471-479. [PMID: 17080683]

3. Jiang, J., He, X. and Cane, D.E. Biosynthesis of the earthy odorant geosmin by a bifunctional Streptomyces coelicolor enzyme. Nat. Chem. Biol. 3 (2007) 711-715. [PMID: 17873868]

[EC 4.1.99.16 created 2011]

*EC 4.2.3.22 Accepted name: germacradienol synthase

Reaction: (1) (2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
(2) (2E,6E)-farnesyl diphosphate = (–)-(7S)-germacrene D + diphosphate

Other name(s): germacradienol/germacrene-D synthase; 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase [(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol-forming]

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol-forming]

Comments: Requires Mg2+ for activity. H-1si of farnesyl diphosphate is lost in the formation of (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol. Formation of (–)-germacrene D involves a stereospecific 1,3-hydride shift of H-1si of farnesyl diphosphate. Both products are formed from a common intermediate [2]. Other enzymes produce germacrene D as the sole product using a different mechanism. The enzyme mediates a key step in the biosynthesis of geosmin (see EC 4.1.99.16 geosmin synthase), a widely occurring metabolite of many streptomycetes, bacteria and fungi [2].

Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 211049-88-6

References:

1. Cane, D.E. and Watt, R.M. Expression and mechanistic analysis of a germacradienol synthase from Streptomyces coelicolor implicated in geosmin biosynthesis. Proc. Natl. Acad. Sci. USA 100 (2003) 1547-1551. [PMID: 12556563]

2. He, X. and Cane, D.E. Mechanism and stereochemistry of the germacradienol/germacrene D synthase of Streptomyces coelicolor A3(2). J. Am. Chem. Soc. 126 (2004) 2678-2679. [PMID: 14995166]

3. Gust, B., Challis, G.L., Fowler, K., Kieser, T. and Chater, K.F. PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc. Natl. Acad. Sci. USA 100 (2003) 1541-1546. [PMID: 12563033]

[EC 4.2.3.22 created 2006, modified 2011]

EC 4.2.3.61

Accepted name: 5-epiaristolochene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (+)-5-epiaristolochene + diphosphate

Other name(s): 5-epi-aristolochene synthase; tobacco epiaristolochene synthase; farnesyl pyrophosphate cyclase (ambiguous); EAS; TEAS

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-5-epiaristolochene-forming]

Comments: Initial cyclization gives (+)-germacrene A in an enzyme bound form which is not released to the medium.

References:

1. Back, K., Yin, S. and Chappell, J. Expression of a plant sesquiterpene cyclase gene in Escherichia coli. Arch. Biochem. Biophys. 315 (1994) 527-532. [PMID: 7986100]

2. Starks, C.M., Back, K., Chappell, J. and Noel, J.P. Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase. Science 277 (1997) 1815-1820. [PMID: 9295271]

3. Back, K., He, S., Kim, K.U. and Shin, D.H. Cloning and bacterial expression of sesquiterpene cyclase, a key branch point enzyme for the synthesis of sesquiterpenoid phytoalexin capsidiol in UV-challenged leaves of Capsicum annuum. Plant Cell Physiol. 39 (1998) 899-904. [PMID: 9816674]

4. Rising, K.A., Starks, C.M., Noel, J.P. and Chappell, J. Demonstration of germacrene A as an intermediate in 5-epi-aristolochene synthase catalysis. J. Am. Chem. Soc. 122 (2000) 1861-1866.

5. Bohlmann, J., Stauber, E.J., Krock, B., Oldham, N.J., Gershenzon, J. and Baldwin, I.T. Gene expression of 5-epi-aristolochene synthase and formation of capsidiol in roots of Nicotiana attenuata and N. sylvestris. Phytochemistry 60 (2002) 109-116. [PMID: 12009313]

6. O'Maille, P.E., Chappell, J. and Noel, J.P. Biosynthetic potential of sesquiterpene synthases: alternative products of tobacco 5-epi-aristolochene synthase. Arch. Biochem. Biophys. 448 (2006) 73-82. [PMID: 16375847]

[EC 4.2.3.61 created 2011]

EC 4.2.3.62

Accepted name: (–)-γ-cadinene synthase

Reaction: (2Z,6E)-farnesyl diphosphate = (–)-γ-cadinene + diphosphate

Other name(s): (–)-γ-cadinene cyclase

Systematic name: (2Z,6E)-farnesyl-diphosphate diphosphate-lyase [(–)-γ-cadinene-forming]

References:

1. Nabeta, K., Fujita, M., Komuro, K., Katayama, K., and Takasawa, T. In vitro biosynthesis of cadinanes by cell-free extracts of cultured cells of Heteroscyphus planus. J. Chem. Soc., Perkin Trans. 1 (1997) 2065-2070.

[EC 4.2.3.62 created 2011]

EC 4.2.3.63

Accepted name: (+)-cubenene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (+)-cubenene + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-cubenene-forming]

Comments: Requires Mg2+.

References:

1. Nabeta, K., Kigure, K., Fujita, M., Nagoya, T., Ishikawa, T., Okuyama, H. and Takasawa, T. Bioynthesis of (+)-cubenene and (+)-epicubenol by cell-free extracts of cultured cells of Heteroscyphus planus and cyclization of [2H]farnesyl diphosphates. J. Chem. Soc., Perkin Trans. 1 (1995) 1935-1939.

2. Nabeta, K., Fujita, M., Komuro, K., Katayama, K., and Takasawa, T. In vitro biosynthesis of cadinanes by cell-free extracts of cultured cells of Heteroscyphus planus. J. Chem. Soc., Perkin Trans. 1 (1997) 2065-2070.

[EC 4.2.3.63 created 2011]

EC 4.2.3.64

Accepted name: (+)-epicubenol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H2O = (+)-epicubenol + diphosphate

Other name(s): farnesyl pyrophosphate cyclase (ambiguous)

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-epicubenol-forming]

Comments: Requires Mg2+. In the bacteria Streptomyces and the liverwort Heteroscyphus the (+)-isomer is formed in contrast to higher plants where the (–)-isomer is formed.

References:

1. Cane, D.E., Tandon, M., and Prabhakaran, P.C. Epicubenol synthase and the enzymatic cyclization of farnesyl diphosphate. J. Am. Chem. Soc. 115 (1993) 8103-8106.

2. Cane, D.E. and Tandon, M. Biosynthesis of (+)-epicubenol. Tetrahedron Lett. 35 (1994) 5355-5358.

3. Cane, D.E. and Tandon, M. Epicubenol synthase and the stereochemistry of the enzymatic cyclization of farnesyl and nerolidyl diphosphate. J. Am. Chem. Soc. 117 (1995) 5602-5603.

4. Nabeta, K., Kigure, K., Fujita, M., Nagoya, T., Ishikawa, T., Okuyama, H. and Takasawa, T. Bioynthesis of (+)-cubenene and (+)-epicubenol by cell-free extracts of cultured cells of Heteroscyphus planus and cyclization of [2H]farnesyl diphosphates. J. Chem. Soc., Perkin Trans. 1 (1995) 1935-1939.

5. Nabeta, K., Fujita, M., Komuro, K., Katayama, K., and Takasawa, T. In vitro biosynthesis of cadinanes by cell-free extracts of cultured cells of Heteroscyphus planus. J. Chem. Soc., Perkin Trans. 1 (1997) 2065-2070.

[EC 4.2.3.64 created 2011]

EC 4.2.3.65

Accepted name: zingiberene synthase

Reaction: (2E,6E)-farnesyl diphosphate = zingiberene + diphosphate

Other name(s): α-zingiberene synthase; ZIS

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (zingiberene-forming)

References:

1. Davidovich-Rikanati, R., Lewinsohn, E., Bar, E., Iijima, Y., Pichersky, E. and Sitrit, Y. Overexpression of the lemon basil α-zingiberene synthase gene increases both mono- and sesquiterpene contents in tomato fruit. Plant J. 56 (2008) 228-238. [PMID: 18643974]

[EC 4.2.3.65 created 2011]

EC 4.2.3.66

Accepted name: β-selinene cyclase

Reaction: (2E,6E)-farnesyl diphosphate = β-selinene + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (β-selinene-forming)

Comments: Initial cyclization gives (+)-germacrene A in an enzyme bound form which is not released to the medium.

References:

1. Belingher, L., Cartayrade, A., Pauly, G. and Gleizes, M. Partial purification and properties of the sesquiterpene β-selinene cyclase from Citrofortunella mitis. Plant Sci. 84 (1992) 129-136.

[EC 4.2.3.66 created 2011]

EC 4.2.3.67

Accepted name: cis-muuroladiene synthase

Reaction: (1) (2E,6E)-farnesyl diphosphate = cis-muurola-3,5-diene + diphosphate
(2) (2E,6E)-farnesyl diphosphate = cis-muurola-4(14),5-diene + diphosphate

Other name(s): MxpSS1

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cis-muuroladiene-forming)

Comments: The recombinant enzyme from black peppermint (Mentha x piperita) gave a mixture of cis-muurola-3,5-diene (45%) and cis-muurola-4(14),5-diene (43%).

References:

1. Prosser, I.M., Adams, R.J., Beale, M.H., Hawkins, N.D., Phillips, A.L., Pickett, J.A. and Field, L.M. Cloning and functional characterisation of a cis-muuroladiene synthase from black peppermint (Mentha × piperita) and direct evidence for a chemotype unable to synthesise farnesene. Phytochemistry 67 (2006) 1564-1571. [PMID: 16083926]

[EC 4.2.3.67 created 2011]

EC 4.2.3.68

Accepted name: β-eudesmol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H2O = β-eudesmol + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (β-eudesmol-forming)

Comments: The recombinant enzyme from ginger (Zingiber zerumbet) gives 62.6% β-eudesmol, 16.8% 10-epi-γ-eudesmol, 10% α-eudesmol, and 5.6% aristolene.

References:

1. Yu, F., Harada, H., Yamasaki, K., Okamoto, S., Hirase, S., Tanaka, Y., Misawa, N. and Utsumi, R. Isolation and functional characterization of a β-eudesmol synthase, a new sesquiterpene synthase from Zingiber zerumbet Smith. FEBS Lett. 582 (2008) 565-572. [PMID: 18242187]

[EC 4.2.3.68 created 2011]

EC 4.2.3.69

Accepted name: (+)-α-barbatene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (+)-α-barbatene + diphosphate

Other name(s): AtBS

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-α-barbatene-forming]

Comments: The recombinant enzyme from the plant Arabidopsis thaliana produces 27.3% α-barbatene, 17.8% thujopsene and 9.9% β-chamigrene [1] plus traces of other sesquiterpenoids [2].

References:

1. Wu, S., Schoenbeck, M.A., Greenhagen, B.T., Takahashi, S., Lee, S., Coates, R.M. and Chappell, J. Surrogate splicing for functional analysis of sesquiterpene synthase genes. Plant Physiol. 138 (2005) 1322-1333. [PMID: 15965019]

2. Tholl, D., Chen, F., Petri, J., Gershenzon, J. and Pichersky, E. Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J. 42 (2005) 757-771. [PMID: 15918888]

[EC 4.2.3.69 created 2011]

EC 4.2.3.70

Accepted name: patchoulol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H2O = patchoulol + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (patchoulol-forming)

References:

1. Croteau, R., Munck, S.L., Akoh, C.C., Fisk, H.J. and Satterwhite, D.M. Biosynthesis of the sesquiterpene patchoulol from farnesyl pyrophosphate in leaf extracts of Pogostemon cablin (patchouli): mechanistic considerations. Arch. Biochem. Biophys. 256 (1987) 56-68. [PMID: 3038029]

2. Munck, S.L. and Croteau, R. Purification and characterization of the sesquiterpene cyclase patchoulol synthase from Pogostemon cablin. Arch. Biochem. Biophys. 282 (1990) 58-64. [PMID: 2171435]

3. Faraldos, J.A., Wu, S., Chappell, J. and Coates, R.M. Doubly deuterium-labeled patchouli alcohol from cyclization of singly labeled [2-2H1]farnesyl diphosphate catalyzed by recombinant patchoulol synthase. J. Am. Chem. Soc. 132 (2010) 2998-3008. [PMID: 20148554]

[EC 4.2.3.70 created 2011]

EC 4.2.3.71

Accepted name: (E,E)-germacrene B synthase

Reaction: (2E,6E)-farnesyl diphosphate = (E,E)-germacrene B + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(E,E)-germacrene-B-forming]

References:

1. van Der Hoeven, R.S., Monforte, A.J., Breeden, D., Tanksley, S.D. and Steffens, J.C. Genetic control and evolution of sesquiterpene biosynthesis in Lycopersicon esculentum and L. hirsutum. Plant Cell 12 (2000) 2283-2294. [PMID: 11090225]

[EC 4.2.3.71 created 2011]

EC 4.2.3.72

Accepted name: α-gurjunene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (–)-α-gurjunene + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(–)-α-gurjunene-forming]

Comments: Initial cyclization probably gives biyclogermacrene in an enzyme bound form which is not released to the medium. The enzyme from Solidago canadensis also forms a small amount of (+)-γ-gurjunene [1].

References:

1. Schmidt, C.O., Bouwmeester, H.J., Bulow, N. and Konig, W.A. Isolation, characterization, and mechanistic studies of (–)-α-gurjunene synthase from Solidago canadensis. Arch. Biochem. Biophys. 364 (1999) 167-177. [PMID: 10190971]

[EC 4.2.3.72 created 2011]

EC 4.2.3.73

Accepted name: valencene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (+)-valencene + diphosphate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (valencene-forming)

Comments: The recombinant enzyme from Vitis vinifera gave 49.5% (+)-valencene and 35.5% (–)-7-epi-α-selinene. Initial cyclization gives (+)-germacrene A in an enzyme bound form which is not released to the medium.

References:

1. Lucker, J., Bowen, P. and Bohlmann, J. Vitis vinifera terpenoid cyclases: functional identification of two sesquiterpene synthase cDNAs encoding (+)-valencene synthase and (–)-germacrene D synthase and expression of mono- and sesquiterpene synthases in grapevine flowers and berries. Phytochemistry 65 (2004) 2649-2659. [PMID: 15464152]

[EC 4.2.3.73 created 2011]

*EC 4.3.1.20

Accepted name: erythro-3-hydroxy-L-aspartate ammonia-lyase

Reaction: erythro-3-hydroxy-L-aspartate = oxaloacetate + ammonia

Other name(s): erythro-β-hydroxyaspartate dehydratase; erythro-3-hydroxyaspartate dehydratase; erythro-3-hydroxy-Ls-aspartate hydro-lyase (deaminating); erythro-3-hydroxy-Ls-aspartate ammonia-lyase

Systematic name: erythro-3-hydroxy-L-aspartate ammonia-lyase (oxaloacetate-forming)

Comments: A pyridoxal-phosphate protein. The enzyme, which was characterized from the bacterium Paracoccus denitrificans NCIMB 8944, is highly specific for the L-isomer of erythro-3-hydroxyaspartate. Different from EC 4.3.1.16, threo-3-hydroxy-L-aspartate ammonia-lyase and EC 4.3.1.27, threo-3-hydroxy-D-aspartate ammonia-lyase. Requires a divalent cation such as Mn2+, Mg2+, and Ca2+.

Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 37290-74-7

References:

1. Gibbs, R.G. and Morris, J.G. Purification and properties of erythro-β-hydroxyaspartate dehydratase from Micrococcus denitrificans. Biochem. J. 97 (1965) 547-554. [PMID: 16749162]

[EC 4.3.1.20 created 1972 as EC 4.2.1.38, transfered 2001 to EC 4.3.1.20, modified 2011]

EC 6.4.1.8

Accepted name: acetophenone carboxylase

Reaction: 2 ATP + acetophenone + HCO3- + H2O + H+ = 2 ADP + 2 phosphate + 3-oxo-3-phenylpropanoate

Systematic name: acetophenone:carbon-dioxide ligase (ADP-forming)

Comments: The enzyme is involved in anaerobic degradation of ethylbenzene. No activity with acetone, butanone, 4-hydroxy-acetophenone or 4-amino-acetophenone.

References:

1. Jobst, B., Schuhle, K., Linne, U. and Heider, J. ATP-dependent carboxylation of acetophenone by a novel type of carboxylase. J. Bacteriol. 192 (2010) 1387-1394. [PMID: 20047908]

[EC 6.4.1.8 created 2011]


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