Thr and then ArgIle bonds in prothrombin to form thrombin
Many thanks to those of you who have submitted details of new or missing enzymes, or updates to existing enzymes.
An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: 5-amino-6-(5-phosphoribosylamino)uracil reductase
Reaction: 5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP+ = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH + H+
Other name(s): aminodioxyphosphoribosylaminopyrimidine reductase
Systematic name: 5-amino-6-(5-phospho-D-ribitylamino)uracil:NADP+ 1'-oxidoreductase
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 69020-28-6
References:
1. Burrows, R.B. and Brown, G.M. Presence of Escherichia coli of a deaminase and a reductase involved in biosynthesis of riboflavin. J. Bacteriol. 136 (1978) 657-667. [PMID: 30756]
Accepted name: sulfopropanediol 3-dehydrogenase
Reaction: (R)-2,3-dihydroxypropane-1-sulfonate + 2 NAD+ + H2O = (R)-3-sulfolactate + 2 NADH + 2 H+
Other name(s): DHPS 3-dehydrogenase (sulfolactate forming); 2,3-dihydroxypropane-1-sulfonate 3-dehydrogenase (sulfolactate forming); dihydroxypropanesulfonate 3-dehydrogenase; hpsN (gene name)
Systematic name: (R)-2,3-dihydroxypropane-1-sulfonate:NAD+ 3-oxidoreductase
Comments: The enzyme is involved in degradation of (R)-2,3-dihydroxypropanesulfonate.
References:
1. Mayer, J., Huhn, T., Habeck, M., Denger, K., Hollemeyer, K. and Cook, A.M. 2,3-Dihydroxypropane-1-sulfonate degraded by Cupriavidus pinatubonensis JMP134: purification of dihydroxypropanesulfonate 3-dehydrogenase. Microbiology 156 (2010) 1556-1564. [PMID: 20150239]
Accepted name: phosphonoacetaldehyde reductase (NADH)
Reaction: 2-hydroxyethylphosphonate + NAD+ = phosphonoacetaldehyde + NADH + H+
Other name(s): PhpC
Systematic name: 2-hydroxyethylphosphonate:NAD+ oxidoreductase
Comments: The enzyme from Streptomyces viridochromogenes catalyses a step in the biosynthesis of phosphinothricin tripeptide, the reduction of phosphonoacetaldehyde to 2-hydroxyethylphosphonate. The preferred cofactor is NADH, lower activity with NADPH [1].
References:
1. Blodgett, J.A., Thomas, P.M., Li, G., Velasquez, J.E., van der Donk, W.A., Kelleher, N.L. and Metcalf, W.W. Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide. Nat. Chem. Biol. 3 (2007) 480-485. [PMID: 17632514]
Accepted name: salicylaldehyde dehydrogenase
Reaction: salicylaldehyde + NAD+ + H2O = salicylate + NADH + 2 H+
Glossary: salicylaldehyde = 2-hydroxybenzaldehyde
Systematic name: salicylaldehyde:NAD+ oxidoreductase
Comments: Involved in the naphthalene degradation pathway in some bacteria.
Links to other databases: BRENDA, EXPASY, KEGG, UM-BBD, CAS registry number: 55354-34-2
References:
1. Eaton, R. and Chapman, P.J. Bacterial metabolism of naphthalene: construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxynaphthalene and subsequent reactions. J. Bacteriol. 174 (1992) 7542-7554. [PMID: 1447127]
Accepted name: long-chain acyl-[acyl-carrier-protein] reductase
Reaction: a long-chain aldehyde + acyl-carrier protein + NAD(P)+ = a long-chain acyl-[acyl-carrier protein] + NAD(P)H + H+
Glossary: a long-chain aldehyde = a fatty aldehyde
acyl-carrier protein = ACP = [acp]
Other name(s): long-chain acyl-[acp] reductase; fatty acyl-[acyl-carrier-protein] reductase; acyl-[acp] reductase
Systematic name: long-chain-aldehyde:NAD(P)+ oxidoreductase (acyl-[acyl-carrier protein]-forming)
Comments: Catalyses the reaction in the opposite direction. This enzyme, purified from the cyanobacterium Synechococcus elongatus PCC 7942, catalyses the NAD(P)HĐdependent reduction of an activated fatty acid (acyl-[acp]) to the corresponding aldehyde. Together with EC 4.1.99.5, octadecanal decarbonylase, it is involved in alkane biosynthesis. The natural substrates of the enzyme are C16 to C18 activated fatty acids. Requires Mg2+.
References:
1. Schirmer, A., Rude, M.A., Li, X., Popova, E. and del Cardayre, S.B. Microbial biosynthesis of alkanes. Science 329 (2010) 559-562. [PMID: 20671186]
Accepted name: crotonyl-CoA carboxylase/reductase
Reaction: (2S)-ethylmalonyl-CoA + NADP+ = (E)-but-2-enoyl-CoA + CO2 + NADPH + H+
Glossary: (E)-but-2-enoyl-CoA = crotonyl-CoA
Other name(s): CCR; crotonyl-CoA reductase (carboxylating)
Systematic name: (2S)-ethylmalonyl-CoA:NADP+ oxidoreductase (decarboxylating)
Comments: The reaction is catalysed in the reverse direction. This enzyme, isolated from the bacterium Rhodobacter sphaeroides, catalyses (E)-but-2-enoyl-CoA-dependent oxidation of NADPH in the presence of CO2. When CO2 is absent, the enzyme catalyses the reduction of (E)-but-2-enoyl-CoA to butanoyl-CoA, but with only 10% of maximal activity (relative to (E)-but-2-enoyl-CoA carboxylation).
References:
1. Erb, T.J., Berg, I.A., Brecht, V., Muller, M., Fuchs, G. and Alber, B.E. Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway. Proc. Natl. Acad. Sci. USA 104 (2007) 10631-10636. [PMID: 17548827]
2. Erb, T.J., Brecht, V., Fuchs, G., Muller, M. and Alber, B.E. Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase. Proc. Natl. Acad. Sci. USA 106 (2009) 8871-8876. [PMID: 19458256]
Accepted name: crotonyl-CoA reductase
Reaction: butanoyl-CoA + NADP+ = (E)-but-2-enoyl-CoA + NADPH + H+
Glossary: (E)-but-2-enoyl-CoA = crotonyl-CoA, butanoyl-CoA = butyryl-CoA
Other name(s): butyryl-CoA dehydrogenase; butyryl dehydrogenase; unsaturated acyl-CoA reductase; ethylene reductase; enoyl-coenzyme A reductase; unsaturated acyl coenzyme A reductase; butyryl coenzyme A dehydrogenase; short-chain acyl CoA dehydrogenase; short-chain acyl-coenzyme A dehydrogenase; 3-hydroxyacyl CoA reductase; butanoyl-CoA:(acceptor) 2,3-oxidoreductase; CCR
Systematic name: butanoyl-CoA:NADP+ 2,3-oxidoreductase
Comments: Catalyses the reaction in the reverse direction. This enzyme from Streptomyces collinus is specific for (E)-but-2-enoyl-CoA, and is proposed to provide butanoyl-CoA as a starter unit for straight-chain fatty acid biosynthesis.
References:
1. Wallace, K.K., Bao, Z.Y., Dai, H., Digate, R., Schuler, G., Speedie, M.K. and Reynolds, K.A. Purification of crotonyl-CoA reductase from Streptomyces collinus and cloning, sequencing and expression of the corresponding gene in Escherichia coli. Eur. J. Biochem. 233 (1995) 954-962. [PMID: 8521864]
Accepted name: dye decolorizing peroxidase
Reaction: Reactive Blue 5 + H2O2 + 2 H+ = oxidized Reactive Blue 5 + 2 H2O
Glossary: Reactive Blue 5 = 1-Amino-4-{[3-({4-chloro-6-[(3-sulfophenyl)amino]-1,3,5-triazin-2-yl}amino)-4-sulfophenyl]amino}-9,10-dihydro-9,10-dioxoanthracene-2-sulfonic acid
Other name(s): DyP; DyP-type peroxidase
Systematic name: Reactive-Blue-5:hydrogen-peroxide oxidoreductase
Comments: Heme proteins with proximal histidine secreted by basidiomycetous fungi and eubacteria. They are similar to EC 1.11.1.16 versatile peroxidase (oxidation of Reactive Black 5, phenols, veratryl alcohol), but differ from the latter in their ability to efficiently oxidize a number of recalcitrant anthraquinone dyes, and inability to oxidize Mn(II). The model substrate Reactive Blue 5 is converted with high efficiency via a so far unique mechanism that combines oxidative and hydrolytic steps and leads to the formation of phthalic acid. Bacterial TfuDyP catalyses sulfoxidation.
References:
1. Kim, S.J. and Shoda, M. Purification and characterization of a novel peroxidase from Geotrichum candidum dec 1 involved in decolorization of dyes. Appl. Environ. Microbiol. 65 (1999) 1029-1035. [PMID: 10049859]
2. Sugano, Y., Ishii, Y. and Shoda, M. Role of H164 in a unique dye-decolorizing heme peroxidase DyP. Biochem. Biophys. Res. Commun. 322 (2004) 126-132. [PMID: 15313183]
3. Zubieta, C., Joseph, R., Krishna, S.S., McMullan, D., Kapoor, M., Axelrod, H.L., Miller, M.D., Abdubek, P., Acosta, C., Astakhova, T., Carlton, D., Chiu, H.J., Clayton, T., Deller, M.C., Duan, L., Elias, Y., Elsliger, M.A., Feuerhelm, J., Grzechnik, S.K., Hale, J., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Kozbial, P., Kumar, A., Marciano, D., Morse, A.T., Murphy, K.D., Nigoghossian, E., Okach, L., Oommachen, S., Reyes, R., Rife, C.L., Schimmel, P., Trout, C.V., van den Bedem, H., Weekes, D., White, A., Xu, Q., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A. and Wilson, I.A. Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA. Proteins 69 (2007) 234-243. [PMID: 17654547]
4. Sugano, Y., Matsushima, Y., Tsuchiya, K., Aoki, H., Hirai, M. and Shoda, M. Degradation pathway of an anthraquinone dye catalyzed by a unique peroxidase DyP from Thanatephorus cucumeris Dec 1. Biodegradation 20 (2009) 433-440. [PMID: 19009358]
5. Sugano, Y. DyP-type peroxidases comprise a novel heme peroxidase family. Cell. Mol. Life Sci. 66 (2009) 1387-1403. [PMID: 19099183]
6. Ogola, H.J., Kamiike, T., Hashimoto, N., Ashida, H., Ishikawa, T., Shibata, H. and Sawa, Y. Molecular characterization of a novel peroxidase from the cyanobacterium Anabaena sp. strain PCC 7120. Appl. Environ. Microbiol. 75 (2009) 7509-7518. [PMID: 19801472]
7. van Bloois, E., Torres Pazmino, D.E., Winter, R.T. and Fraaije, M.W. A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily. Appl. Microbiol. Biotechnol. 86 (2010) 1419-1430. [PMID: 19967355]
8. Liers, C., Bobeth, C., Pecyna, M., Ullrich, R. and Hofrichter, M. DyP-like peroxidases of the jelly fungus Auricularia auricula-judae oxidize nonphenolic lignin model compounds and high-redox potential dyes. Appl. Microbiol. Biotechnol. 85 (2010) 1869-1879. [PMID: 19756587]
9. Hofrichter, M., Ullrich, R., Pecyna, M.J., Liers, C. and Lundell, T. New and classic families of secreted fungal heme peroxidases. Appl. Microbiol. Biotechnol. 87 (2010) 871-897. [PMID: 20495915]
EC 1.11.2 With H2O2 as acceptor, one oxygen atom of which is incorporated into the product
EC 1.11.2.1
Accepted name: unspecific peroxygenase
Reaction: RH + H2O2 = ROH + H2O
Other name(s): aromatic peroxygenase; mushroom peroxygenase; haloperoxidase-peroxygenase; Agrocybe aegerita peroxidase
Systematic name: substrate:hydrogen peroxide oxidoreductase (RH-hydroxylating or -epoxidising)
Comments: A heme-thiolate protein (P450). Enzymes of this type include glycoproteins secreted by agaric basidiomycetes. They catalyse the insertion of an oxygen atom from H2O2 into a wide variety of substrates, including aromatic rings such as naphthalene, toluene, phenanthrene, pyrene and p-nitrophenol, recalcitrant heterocycles such as pyridine, dibenzofuran, various ethers (resulting in O-dealkylation) and alkanes such as propane, hexane and cyclohexane. Reactions catalysed include hydroxylation, epoxidation, N-oxidation, sulfooxidation, O- and N-dealkylation, bromination and one-electron oxidations. They have little or no activity toward chloride. Mechanistically, the catalytic cycle of unspecific (mono)-peroxygenases combines elements of the "shunt" pathway of cytochrome P450s (a side activity that utilizes a peroxide in place of dioxygen and NAD[P]H) and the classic heme peroxidase cycle.
References:
1. Ullrich, R., Nuske, J., Scheibner, K., Spantzel, J. and Hofrichter, M. Novel haloperoxidase from the agaric basidiomycete Agrocybe aegerita oxidizes aryl alcohols and aldehydes. Appl. Environ. Microbiol. 70 (2004) 4575-4581. [PMID: 15294788]
2. Ullrich, R. and Hofrichter, M. The haloperoxidase of the agaric fungus Agrocybe aegerita hydroxylates toluene and naphthalene. FEBS Lett. 579 (2005) 6247-6250. [PMID: 16253244]
3. Anh, D.H., Ullrich, R., Benndorf, D., Svatos, A., Muck, A. and Hofrichter, M. The coprophilous mushroom Coprinus radians secretes a haloperoxidase that catalyzes aromatic peroxygenation. Appl. Environ. Microbiol. 73 (2007) 5477-5485. [PMID: 17601809]
4. Aranda, E., Kinne, M., Kluge, M., Ullrich, R. and Hofrichter, M. Conversion of dibenzothiophene by the mushrooms Agrocybe aegerita and Coprinellus radians and their extracellular peroxygenases. Appl. Microbiol. Biotechnol. 82 (2009) 1057-1066. [PMID: 19039585]
5. Kinne, M., Poraj-Kobielska, M., Aranda, E., Ullrich, R., Hammel, K.E., Scheibner, K. and Hofrichter, M. Regioselective preparation of 5-hydroxypropranolol and 4'-hydroxydiclofenac with a fungal peroxygenase. Bioorg. Med. Chem. Lett. 19 (2009) 3085-3087. [PMID: 19394224]
6. Kluge, M., Ullrich, R., Dolge, C., Scheibner, K. and Hofrichter, M. Hydroxylation of naphthalene by aromatic peroxygenase from Agrocybe aegerita proceeds via oxygen transfer from H2O2 and intermediary epoxidation. Appl. Microbiol. Biotechnol. 81 (2009) 1071-1076. [PMID: 18815784]
7. Ullrich, R., Dolge, C., Kluge, M. and Hofrichter, M. Pyridine as novel substrate for regioselective oxygenation with aromatic peroxygenase from Agrocybe aegerita. FEBS Lett. 582 (2008) 4100-4106. [PMID: 19022254]
8. Aranda, E., Kinne, M., Kluge, M., Ullrich, R. and Hofrichter, M. Conversion of dibenzothiophene by the mushrooms Agrocybe aegerita and Coprinellus radians and their extracellular peroxygenases. Appl. Microbiol. Biotechnol. 82 (2009) 1057-1066. [PMID: 19039585]
9. Kinne, M., Poraj-Kobielska, M., Ralph, S.A., Ullrich, R., Hofrichter, M. and Hammel, K.E. Oxidative cleavage of diverse ethers by an extracellular fungal peroxygenase. J. Biol. Chem. 284 (2009) 29343-29349. [PMID: 19713216]
10. Pecyna, M.J., Ullrich, R., Bittner, B., Clemens, A., Scheibner, K., Schubert, R. and Hofrichter, M. Molecular characterization of aromatic peroxygenase from Agrocybe aegerita. Appl. Microbiol. Biotechnol. 84 (2009) 885-897. [PMID: 19434406]
Accepted name: 3-demethylubiquinol 3-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 3-demethylubiquinol-n = S-adenosyl-L-homocysteine + ubiquinol-n
Glossary: 3-demethylubiquinol-n = 3-hydroxy-2-methoxy-5-methyl-6-(all-trans-polyprenyl)-1,4-benzoquinol
Other name(s): 5-demethylubiquinone-9 methyltransferase; OMHMB-methyltransferase; 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase; S-adenosyl-L-methionine:2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone-O-methyltransferase; COQ3 (gene name); Coq3 O-methyltransferase; ubiG (gene name, ambiguous)
Systematic name: S-adenosyl-L-methionine:3-hydroxy-2-methoxy-5-methyl-6-(all-trans-polyprenyl)-1,4-benzoquinol 3-O-methyltransferase
Comments: This enzyme is involved in ubiquinone biosynthesis. Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone-9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units. For example, the human COQ3 enzyme can restore biosynthesis of ubiquinone-6 in coq3 deletion mutants of yeast [3]. The enzymes from yeast, Escherichia coli and rat also catalyse the methylation of 3,4-dihydroxy-5-all-trans-polyprenylbenzoate [3] (a reaction that is classified as EC 2.1.1.114, polyprenyldihydroxybenzoate methyltransferase).
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 63774-48-1
References:
1. Houser, R.M. and Olson, R.E. 5-Demethylubiquinone-9-methyltransferase from rat liver mitochondria. Characterization, localization, and solubilization. J. Biol. Chem. 252 (1977) 4017-4021. [PMID: 863914]
2. Leppik, R.A., Stroobant, P., Shineberg, B., Young, I.G. and Gibson, F. Membrane-associated reactions in ubiquinone biosynthesis. 2-Octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase. Biochim. Biophys. Acta 428 (1976) 146-156. [PMID: 769831]
3. Poon, W.W., Barkovich, R.J., Hsu, A.Y., Frankel, A., Lee, P.T., Shepherd, J.N., Myles, D.C. and Clarke, C.F. Yeast and rat Coq3 and Escherichia coli UbiG polypeptides catalyze both O-methyltransferase steps in coenzyme Q biosynthesis. J. Biol. Chem. 274 (1999) 21665-21672. [PMID: 10419476]
4. Jonassen, T. and Clarke, C.F. Isolation and functional expression of human COQ3, a gene encoding a methyltransferase required for ubiquinone biosynthesis. J. Biol. Chem. 275 (2000) 12381-12387. [PMID: 10777520]
Accepted name: polyprenyldihydroxybenzoate methyltransferase
Reaction: S-adenosyl-L-methionine + 3,4-dihydroxy-5-all-trans-polyprenylbenzoate = S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-5-all-trans-polyprenylbenzoate
Other name(s): 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase; dihydroxyhexaprenylbenzoate methyltransferase; COQ3 (gene name); Coq3 O-methyltransferase
Systematic name: S-adenosyl-L-methionine:3,4-dihydroxy-5-all-trans-polyprenylbenzoate 3-O-methyltransferase
Comments: This enzyme is involved in ubiquinone biosynthesis. Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone-9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units. For example, the human COQ3 enzyme can restore biosynthesis of ubiquinone-6 in coq3 deletion mutants of yeast [3]. The enzymes from yeast and rat also catalyse the methylation of 3-demethylubiquinol-6 and 3-demethylubiquinol-9, respectively [2] (this activity is classified as EC 2.1.1.64, 3-demethylubiquinol 3-O-methyltransferase).
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 139569-31-6
References:
1. Clarke, C.F., Williams, W., Teruya, J.H. Ubiquinone biosynthesis in Saccharomyces cerevisiae. Isolation and sequence of COQ3, the 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase gene. J. Biol. Chem. 266 (1991) 16636-16641. [PMID: 1885593]
2. Poon, W.W., Barkovich, R.J., Hsu, A.Y., Frankel, A., Lee, P.T., Shepherd, J.N., Myles, D.C. and Clarke, C.F. Yeast and rat Coq3 and Escherichia coli UbiG polypeptides catalyze both O-methyltransferase steps in coenzyme Q biosynthesis. J. Biol. Chem. 274 (1999) 21665-21672. [PMID: 10419476]
3. Jonassen, T. and Clarke, C.F. Isolation and functional expression of human COQ3, a gene encoding a methyltransferase required for ubiquinone biosynthesis. J. Biol. Chem. 275 (2000) 12381-12387. [PMID: 10777520]
Accepted name: GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphosphoundecaprenol 4-β-mannosyltransferase
Reaction: GDP-mannose + GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol = GDP + D-Man-β-(1→4)- GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol
Other name(s): GumI
Systematic name: GDP-mannose:GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol 4-β-mannosyltransferase
Comments: The enzyme is involved in the biosynthesis of the exopolysaccharide xanthan.
References:
1. Katzen, F., Ferreiro, D.U., Oddo, C.G., Ielmini, M.V., Becker, A., Puhler, A. and Ielpi, L. Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence. J. Bacteriol. 180 (1998) 1607-1617. [PMID: 9537354]
2. Ielpi, L., Couso, R.O. and Dankert, M.A. Sequential assembly and polymerization of the polyprenol-linked pentasaccharide repeating unit of the xanthan polysaccharide in Xanthomonas campestris. J. Bacteriol. 175 (1993) 2490-2500. [PMID: 7683019]
3. Kim, S.Y., Kim, J.G., Lee, B.M. and Cho, J.Y. Mutational analysis of the gum gene cluster required for xanthan biosynthesis in Xanthomonas oryzae pv oryzae. Biotechnol. Lett. 31 (2009) 265-270. [PMID: 18854951]
Accepted name: GDP-mannose:cellobiosyl-diphosphopolyprenol α-mannosyltransferase
Reaction: GDP-mannose + D-Glc-β-(1→4)-Glc-α-1-diphospho-ditrans,octacis-undecaprenol = GDP + D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol
Other name(s): GumH; AceA; α1,3-mannosyltransferase AceA
Systematic name: GDP-mannose:D-Glc-β-(1→4)-Glc-α-1-diphospho-ditrans,octacis-undecaprenol 3-α-mannosyltransferase
Comments: In the bacterium Gluconacetobacter xylinus (previously known as Acetobacter xylinum) the enzyme is involved in the biosynthesis of the exopolysaccharide acetan [1]. In Xanthomonas campestris the enzyme is involved in the biosynthesis of the exopolysaccharide xanthan [5].
References:
1. Geremia, R.A., Roux, M., Ferreiro, D.U., Dauphin-Dubois, R., Lellouch, A.C. and Ielpi, L. Expression and biochemical characterisation of recombinant AceA, a bacterial α-mannosyltransferase. Mol. Gen. Genet. 261 (1999) 933-940. [PMID: 10485283]
2. Abdian, P.L., Lellouch, A.C., Gautier, C., Ielpi, L. and Geremia, R.A. Identification of essential amino acids in the bacterial α-mannosyltransferase aceA. J. Biol. Chem. 275 (2000) 40568-40575. [PMID: 11001941]
3. Petroni, E.A. and Ielpi, L. Isolation and nucleotide sequence of the GDP-mannose:cellobiosyl-diphosphopolyprenol α-mannosyltransferase gene from Acetobacter xylinum. J. Bacteriol. 178 (1996) 4814-4821. [PMID: 8759843]
4. Lellouch, A.C., Watt, G.M., Geremia, R.A. and Flitsch, S.L. Phytanyl-pyrophosphate-linked substrate for a bacterial α-mannosyltransferase. Biochem. Biophys. Res. Commun. 272 (2000) 290-292. [PMID: 10872841]
5. Katzen, F., Ferreiro, D.U., Oddo, C.G., Ielmini, M.V., Becker, A., Puhler, A. and Ielpi, L. Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence. J. Bacteriol. 180 (1998) 1607-1617. [PMID: 9537354]
Accepted name: baicalein 7-O-glucuronosyltransferase
Reaction: UDP-D-glucuronate + baicalein = UDP + baicalin
Glossary: baicalin = 5,6,7-trihydroxyflavone-7-O-β-D-glucuronate = 5,6-dihydroxy-4-oxo-2-phenyl-4H-chromen-7-yl β-D-glucupyranosiduronic acid
baicalein = 5,6,7-trihydroxyflavone = 5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one
wogonin = 5,7-dihydroxy-8-methoxyflavone = 5,7-dihydroxy-8-methoxy-2-phenyl-4H-chromen-4-one
scutellarein = 4,5,6,7-tetrahydroxyflavone-7-O-β-D-glucoronate = 5,6,7-trihydroxy-2-(4-hydroxyphenyl)chromen-4-one
Other name(s): UBGAT
Systematic name: UDP-D-glucuronate:5,6,7-trihydroxyflavone 7-O-glucuronosyltransferase
Comments: The enzyme is specific for UDP-D-glucuronate as a sugar donor and flavones with substitution ortho- to the 7-OH group such as baicalein (6-OH), scutellarein (6-OH) and wogonin (8-OMe).
References:
1. Nagashima, S., Hirotani, M. and Yoshikawa, T. Purification and characterization of UDP-glucuronate: baicalein 7-O-glucuronosyltransferase from Scutellaria baicalensis Georgi. cell suspension cultures. Phytochemistry 53 (2000) 533-538. [PMID: 10724177]
Accepted name: adenosyl-chloride synthase
Reaction: S-adenosyl-L-methionine + chloride = 5-deoxy-5-chloroadenosine + L-methionine
Glossary: 5-deoxy-5-chloroadenosine = 5'-chloro-5'-deoxyadenosine
Other name(s): chlorinase; 5'-chloro-5'-deoxyadenosine synthase
Systematic name: S-adenosyl-L-methionine:chloride adenosyltransferase
Comments: This enzyme, isolated from the marine bacterium Salinispora tropica, catalyses an early step in the pathway leading to biosynthesis of the proteosome inhibitor salinosporamide A. The enzyme is very similar to EC 2.5.1.63, adenosyl-fluoride synthase, but does not accept fluoride.
References:
1. Eustaquio, A.S., Pojer, F., Noel, J.P. and Moore, B.S. Discovery and characterization of a marine bacterial SAM-dependent chlorinase. Nat. Chem. Biol. 4 (2008) 69-74. [PMID: 18059261]
Accepted name: pantoate kinase
Reaction: ATP + (R)-pantoate = ADP + (R)-4-phosphopantoate
Other name(s): PoK; TK2141 protein
Systematic name: ATP:(R)-pantoate 4-phosphotransferase
Comments: The conversion of (R)-pantoate to (R)-4'-phosphopantothenate is part of the pathway leading to biosynthesis of 4'-phosphopantetheine, an essential cofactor of coenzyme A and acyl-carrier protein. In bacteria and eukaryotes this conversion is performed by condensation with β-alanine, followed by phosphorylation (EC 6.3.2.1 and EC 2.7.1.33, respectively). In archaea the order of these two steps is reversed, and phosphorylation precedes condensation with β-alanine.
References:
1. Yokooji, Y., Tomita, H., Atomi, H. and Imanaka, T. Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. J. Biol. Chem. 284 (2009) 28137-28145. [PMID: 19666462]
Accepted name: UMP/CMP kinase
Reaction: (1) ATP + (d)CMP = ADP + (d)CDP
(2) ATP + UMP = ADP + UDP
Glossary: CMP = cytidine monophosphate
dCMP = deoxycytidine monophosphate
CDP = cytidine diphosphate
dCDP = deoxycytidine diphosphate
UMP = uridine monophosphate
UDP = uridine diphosphate
Other name(s): cytidylate kinase; deoxycytidylate kinase; CTP:CMP phosphotransferase; dCMP kinase; deoxycytidine monophosphokinase; UMP-CMP kinase; ATP:UMP-CMP phosphotransferase; pyrimidine nucleoside monophosphate kinase; uridine monophosphate-cytidine monophosphate phosphotransferase
Systematic name: ATP:CMP(UMP) phosphotransferase
Comments: This eukaryotic enzyme is a bifunctional enzyme that catalyses the phosphorylation of both CMP and UMP with similar efficiency. dCMP can also act as acceptor. Different from the monofunctional prokaryotic enzymes EC 2.7.4.25, CMP kinase and EC 2.7.4.22, UMP kinase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, PDB, CAS registry number: 37278-21-0
References:
1. Hurwitz, J. The enzymatic incorporation of ribonucleotides into polydeoxynucleotide material. J. Biol. Chem. 234 (1959) 2351-2358. [PMID: 14405566]
2. Ruffner, B.W., Jr. and Anderson, E.P. Adenosine triphosphate: uridine monophosphate-cytidine monophosphate phosphotransferase from Tetrahymena pyriformis. J. Biol. Chem. 244 (1969) 5994-6002. [PMID: 5350952]
3. Scheffzek, K., Kliche, W., Wiesmuller, L. and Reinstein, J. Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 Å: implications for water-mediated specificity. Biochemistry 35 (1996) 9716-9727. [PMID: 8703943]
4. Zhou, L., Lacroute, F. and Thornburg, R. Cloning, expression in Escherichia coli, and characterization of Arabidopsis thaliana UMP/CMP kinase. Plant Physiol. 117 (1998) 245-254. [PMID: 9576794]
5. Van Rompay, A.R., Johansson, M. and Karlsson, A. Phosphorylation of deoxycytidine analog monophosphates by UMP-CMP kinase: molecular characterization of the human enzyme. Mol. Pharmacol. 56 (1999) 562-569. [PMID: 10462544]
Accepted name: (d)CMP kinase
Reaction: ATP + (d)CMP = ADP + (d)CDP
Glossary: CMP = cytidine monophosphate
dCMP = deoxycytidine monophosphate
CDP = cytidine diphosphate
dCDP = deoxycytidine diphosphate
UMP = uridine monophosphate
UDP = uridine diphosphate
Other name(s): prokaryotic cytidylate kinase; deoxycytidylate kinase; dCMP kinase; deoxycytidine monophosphokinase
Systematic name: ATP:(d)CMP phosphotransferase
Comments: The prokaryotic cytidine monophosphate kinase specifically phosphorylates CMP (or dCMP), using ATP as the preferred phosphoryl donor. Unlike EC 2.7.4.14, a eukaryotic enzyme that phosphorylates UMP and CMP with similar efficiency, the prokaryotic enzyme phosphorylates UMP with very low rates, and this function is catalysed in prokaryotes by EC 2.7.4.22, UMP kinase. The enzyme phosphorylates dCMP nearly as well as it does CMP [1].
References:
1. Bertrand, T., Briozzo, P., Assairi, L., Ofiteru, A., Bucurenci, N., Munier-Lehmann, H., Golinelli-Pimpaneau, B., Barzu, O. and Gilles, A.M. Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme. J. Mol. Biol. 315 (2002) 1099-1110. [PMID: 11827479]
2. Thum, C., Schneider, C.Z., Palma, M.S., Santos, D.S. and Basso, L.A. The Rv1712 Locus from Mycobacterium tuberculosis H37Rv codes for a functional CMP kinase that preferentially phosphorylates dCMP. J. Bacteriol. 191 (2009) 2884-2887. [PMID: 19181797]
Accepted name: undecaprenyl-phosphate glucose phosphotransferase
Reaction: UDP-glucose + ditrans,octacis-undecaprenyl phosphate = UMP + α-D-glucopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): GumD; undecaprenylphosphate glucosylphosphate transferase
Systematic name: UDP-glucose:-ditrans,octacis-undecaprenyl-phosphate glucose phosphotransferase
Comments: The enzyme is involved in biosynthesis of xanthan.
References:
1. Ielpi, L., Couso, R.O. and Dankert, M.A. Sequential assembly and polymerization of the polyprenol-linked pentasaccharide repeating unit of the xanthan polysaccharide in Xanthomonas campestris. J. Bacteriol. 175 (1993) 2490-2500. [PMID: 7683019]
2. Katzen, F., Ferreiro, D.U., Oddo, C.G., Ielmini, M.V., Becker, A., Puhler, A. and Ielpi, L. Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence. J. Bacteriol. 180 (1998) 1607-1617. [PMID: 9537354]
3. Kim, S.Y., Kim, J.G., Lee, B.M. and Cho, J.Y. Mutational analysis of the gum gene cluster required for xanthan biosynthesis in Xanthomonas oryzae pv oryzae. Biotechnol. Lett. 31 (2009) 265-270. [PMID: 18854951]
Accepted name: baicalin-β-D-glucuronidase
Reaction: baicalin + H2O = baicalein + D-glucuronate
Glossary: baicalin = 5,6,7-trihydroxyflavone-7-O-β-D-glucuronate = 5,6-dihydroxy-4-oxo-2-phenyl-4H-chromen-7-yl β-D-glucupyranosiduronic acid
baicalein = 5,6,7-trihydroxyflavone = 5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one
wogonin = 5,7-dihydroxy-8-methoxyflavone = 5,7-dihydroxy-8-methoxy-2-phenyl-4H-chromen-4-one
oroxylin = 5,7-dihydroxy-6-methoxyflavone = 5,7-dihydroxy-6-methoxy-2-phenyl-4H-1-benzopyran-4-one
Other name(s): baicalinase
Systematic name: 5,6,7-trihydroxyflavone-7-O-β-D-glucupyranosiduronate glucuronosylhydrolase
Comments: The enzyme also hydrolyses wogonin 7-O-β-D-glucuronide and oroxylin 7-O-β-D-glucuronide with lower efficiency [4]. Neglegible activity with p-nitrophenyl-β-D-glucuronide [2].
References:
1. Ikegami, F., Matsunae, K., Hisamitsu, M., Kurihara, T., Yamamoto, T. and Murakoshi, I. Purification and properties of a plant β-D-glucuronidase form Scutellaria root. Biol. Pharm. Bull. 18 (1995) 1531-1534. [PMID: 8593473]
2. Zhang, C., Zhang, Y., Chen, J. and Liang, X. Purification and characterization of baicalin-β-D-glucuronidase hydrolyzing baicalin to baicalein from fresh roots of Scutellaria viscidula Bge. Proc. Biochem. 40 (2005) 1911-1915.
3. Sasaki, K., Taura, F., Shoyama, Y. and Morimoto, S. Molecular characterization of a novel β-glucuronidase from Scutellaria baicalensis Georgi. J. Biol. Chem. 275 (2000) 27466-27472. [PMID: 10858442]
4. Morimoto, S., Harioka, T. and Shoyama, Y. Purification and characterization of flavone-specific β-glucuronidase from callus cultures of Scutellaria baicalensis Georgi. Planta 195 (1995) 535-540.
Accepted name: hesperidin 6-O-α-L-rhamnosyl-β-D-glucosidase
Reaction: hesperidin + H2O = hesperitin + rutinose
Glossary: hesperitin = 5,7,3'-trihydroxy-4'-methoxyflavanone
hesperidin = hesperitin 7-(6-O-α-L-rhamnopyranosyl)-β-D-glucopyranoside
rutinose = 6-O-α-L-rhamnopyranosyl-D-glucose
Systematic name: hesperetin 7-(6-O-α-L-rhamnopyranosyl-β-D-glucopyranoside) 6-O-α-rhamnopyranosyl-β-glucohydrolase
Comments: The enzyme exhibits high specificity towards 7-O-linked flavonoid β-rutinosides.
References:
1. Mazzaferro, L., Pinuel, L., Minig, M. and Breccia, J.D. Extracellular monoenzyme deglycosylation system of 7-O-linked flavonoid β-rutinosides and its disaccharide transglycosylation activity from Stilbella fimetaria. Arch. Microbiol. 192 (2010) 383-393. [PMID: 20358178]
Accepted name: coagulation factor Xa
Reaction: Selective cleavage of ArgThr and then ArgIle bonds in prothrombin to form thrombin
Other name(s): thrombokinase; prothrombase; prothrombinase; activated blood-coagulation factor X; autoprothrombin C; thromboplastin; plasma thromboplastin; factor Xa; activated Stuart-Prower factor; activated factor X
Comments: A blood coagulation factor formed from the proenzyme factor X by limited proteolysis. Factor X is a glycoprotein composed of a heavy chain and a light chain, which are generated from a precursor protein by the excision of the tripeptide RKR and held together by one or more disulfide bonds. The activated factor Xa converts prothrombin to thrombin in the presence of factor Va, Ca2+ and phospholipids. Scutelarin (EC 3.4.21.60) has similar specificity, but does not require factor Va.
Links to other databases: BRENDA, KEGG, MEROPS, PDB, CAS registry number: 9002-05-5
References:
1. Fujikawa, K. and Davie, E.W. Bovine factor X (Stuart factor). Methods Enzymol. 45 (1976) 89-95. [PMID: 1012041]
2. Jesty, J. and Nemerson, Y. The activation of bovine coagulation factor X. Methods Enzymol. 45 (1976) 95-107. [PMID: 1012042]
3. Davie, E.W., Fujikawa, K., Kurachi, K. and Kisiel, W. The role of serine proteases in the blood coagulation cascade. Adv. Enzymol. 48 (1979) 277-318. [PMID: 367103]
4. Jackson, C.M. and Nemerson, Y. Blood coagulation. Annu. Rev. Biochem. 49 (1980) 765-811. [PMID: 6996572]
5. McMullen, B.A., Fujikawa, K., Kisiel, W., Sasagawa, T., Howald, W.N., Kwa, E.Y. and Weinstein, B. Complete amino acid sequence of the light chain of human blood coagulation factor X: evidence for identification of residue 63 as β-hydroxyaspartic acid. Biochemistry 22 (1983) 2875-2884. [PMID: 6871167]
6. Cho, K., Tanaka, T., Cook, R.R., Kisiel, W., Fujikawa, K., Kurachi, K. and Powers, J.C. Active-site mapping of bovine and human blood coagulation serine proteases using synthetic peptide 4-nitroanilide and thio ester substrates. Biochemistry 23 (1984) 644-650. [PMID: 6370301]
Accepted name: scutelarin
Reaction: Selective cleavage of ArgThr and ArgIle in prothrombin to form thrombin and two inactive fragments
Other name(s): taipan activator; Oxyuranus scutellatus prothrombin-activating proteinase
Comments: From the venom of the Taipan snake (Oxyuranus scutellatus). Converts prothrombin to thrombin. Specificity is similar to that of Factor Xa (EC 3.4.21.6). However, unlike Factor Xa this enzyme can cleave its target in the absence of coagulation Factor Va. Activity is potentiated by phospholipid and Ca2+ which binds via γ-carboxyglutamic acid residues. Similar enzymes are known from the venom of other Australian elapid snakes, including Pseudonaja textilis textilis. Oxyuranus microlepidotus and Demansia nuchalis affinis.
Links to other databases: BRENDA, EXPASY, KEGG, MEROPS, CAS registry number: 93389-45-8
References:
1. Walker, F.J., Owen, W.G. and Esmon, C.T. Characterization of the prothrombin activator from the venom of Oxyuranus scutellatus scutellatus (taipan venom). Biochemistry 19 (1980) 1020-1023. [PMID: 6986908]
2. Speijer, H., Govers-Reimslag, J.W., Zwaal, R.F. and Rosing, J. Prothrombin activation by an activator from the venom of Oxyuranus scutellatus (taipan snake). J. Biol. Chem. 261 (1986) 13258-13267. [PMID: 3531198]
Accepted name: (R)-amidase
Reaction: (1) (R)-piperazine-2-carboxamide + H2O = (R)-piperazine-2-carboxylic acid + NH3
(2) β-alaninamide + H2O = β-alanine + NH3
Other name(s): R-stereospecific amidase; R-amidase
Systematic name: (R)-piperazine-2-carboxamide amidohydrolase
Comments: In addition (R)-piperidine-3-carboxamide is hydrolysed to (R)-piperidine-3-carboxylic acid and NH3, and (R)-N-tert-butylpiperazine-2-carboxamide is hydrolysed to (R)-piperazine-2-carboxylic acid and tert-butylamine with lower activity. The enzyme does not act on the other amide substrates which are hydrolysed by EC 3.5.1.4 (amidase).
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:
References:
1. Komeda, H., Harada, H., Washika, S., Sakamoto, T., Ueda, M. and Asano, Y. A novel R-stereoselective amidase from Pseudomonas sp. MCI3434 acting on piperazine-2-tert-butylcarboxamide. Eur. J. Biochem. 271 (2004) 1580-1590. [PMID: 15066183]
Accepted name: 2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase
Reaction: 2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + H2O = 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + formate
Other name(s): ArfB
Systematic name: 2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one amidohydrolase
Comments: The enzyme catalyses the second step in archaeal riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin biosynthesis. The first step is catalysed by EC 3.5.4.29 (GTP cyclohydrolase IIa). The bacterial enzyme, EC 3.5.4.25 (GTP cyclohydrolase II) catalyses both reactions.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:
References:
1. Grochowski, L.L., Xu, H. and White, R.H. An iron(II) dependent formamide hydrolase catalyzes the second step in the archaeal biosynthetic pathway to riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin. Biochemistry 48 (2009) 4181-4188. [PMID: 19309161]
Accepted name: streptothricin hydrolase
Reaction: streptothricin-F + H2O = streptothricin-F acid
Other name(s): sttH (gene name)
Systematic name: streptothricin-F hydrolase
Comments: The enzyme also catalyses the hydrolysis of streptothricin-D to streptothricin-D acid [1]. The enzyme is responsible for streptothricin resistance in Streptomyces albulus and Streptomyces noursei [1,2].
References:
1. Maruyama, C. and Hamano, Y. The biological function of the bacterial isochorismatase-like hydrolase SttH. Biosci. Biotechnol. Biochem. 73 (2009) 2494-2500. [PMID: 19897889]
2. Hamano, Y., Matsuura, N., Kitamura, M. and Takagi, H. A novel enzyme conferring streptothricin resistance alters the toxicity of streptothricin D from broad-spectrum to bacteria-specific. J. Biol. Chem. 281 (2006) 16842-16848. [PMID: 16641084]
Accepted name: GTP cyclohydrolase II
Reaction: GTP + 3 H2O = formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate
Other name(s): guanosine triphosphate cyclohydrolase II; GTP-8-formylhydrolase
Systematic name: GTP 7,8-8,9-dihydrolase (diphosphate-forming)
Comments: Two C-N bonds are hydrolysed, releasing formate, with simultaneous removal of the terminal diphosphate.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 56214-35-8
References:
1. Foor, F. and Brown, G.M. Purification and properties of guanosine triphosphate cyclohydrolase II from Escherichia coli. J. Biol. Chem. 250 (1975) 3545-3551. [PMID: 235552]
Accepted name: diaminohydroxyphosphoribosylaminopyrimidine deaminase
Reaction: 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + H2O = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NH3
Systematic name: 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine 2-aminohydrolase
Comments: The substrate is the product of EC 3.5.4.25 GTP cyclohydrolase II.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 68994-19-4
References:
1. Burrows, R.B. and Brown, G.M. Presence of Escherichia coli of a deaminase and a reductase involved in biosynthesis of riboflavin. J. Bacteriol. 136 (1978) 657-667. [PMID: 30756]
Accepted name: GTP cyclohydrolase IIa
Reaction: GTP + 3 H2O = 2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + 2 phosphate
For diagram of reaction, click here
Systematic name: GTP 8,9-hydrolase (phosphate-forming)
Comments: Requires Mg2+. This enzyme catalyses the hydrolysis of the imidazole ring of guanosine 5'-triphosphate, N7-methylguanosine 5'-triphosphate or inosine 5'-triphosphate. Xanthosine 5'-triphosphate and ATP are not substrates. It also catalyses the hydrolysis of diphosphate to form two equivalents of phosphate. Unlike GTP cyclohydrolase II (EC 3.5.4.25), this enzyme does not release formate, but does hydrolyse the diphosphate from GTP to phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number:
References:
1. Graham, D.E., Xu, H. and White, R.H. A member of a new class of GTP cyclohydrolases produces formylaminopyrimidine nucleotide monophosphates. Biochemistry 41 (2002) 15074-15084. [PMID: 12475257]
Accepted name: 5-nitroanthranilic acid aminohydrolase
Reaction: 5-nitroanthranilate + H2O = 5-nitrosalicylate + NH3
Other name(s): naaA (gene name); 5NAA deaminase
Systematic name: 5-nitroanthranilate amidohydrolase
Comments: The enzyme catalyses the initial step in biodegradation of 5-nitroanthranilic acid by Bradyrhizobium sp. strain JS329.
References:
1. Qu, Y. and Spain, J.C. Biodegradation of 5-nitroanthranilic acid by Bradyrhizobium sp. strain JS329. Appl. Environ. Microbiol. 76 (2010) 1417-1422. [PMID: 20081004]
Accepted name: (R)-mandelonitrile lyase
Reaction: (R)-mandelonitrile = cyanide + benzaldehyde
Other name(s): (R)-oxynitrilase; oxynitrilase; D-oxynitrilase; D-α-hydroxynitrile lyase; mandelonitrile benzaldehyde-lyase; PaHNL; AtHNL; PhaMDL; (R)-HNL; (R)-PeHNL; (R)-hydroxynitrile lyase; R-selective hydroxynitrile lyase; R-selective HNL; (R)-(+)-mandelonitrile lyase
Systematic name: (R)-mandelonitrile benzaldehyde-lyase (cyanide-forming)
Comments: A variety of enzymes from different sources and with different properties. Some are flavoproteins, others are not. Active towards a number of aromatic and aliphatic hydroxynitriles (cyanohydrins).
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9024-43-5
References:
1. Ueatrongchit, T., Kayo, A., Komeda, H., Asano, Y. and H-Kittikun, A. Purification and characterization of a novel (R)-hydroxynitrile lyase from Eriobotrya japonica (Loquat). Biosci. Biotechnol. Biochem. 72 (2008) 1513-1522. [PMID: 18540101]
2. Lin, G., Han, S. and Li, Z. Enzymic synthesis of (R)-cyanohydrins by three (R)-oxynitrilase sources in micro-aqueous organic medium. Tetrahedron 55 (1999) 3531-3540.
3. de Gonzalo, G., Brieva, R. and Gotor, V. (R)-Oxynitrilase-catalyzed transformation of ω-hydroxyalkanals. J. Mol. Catal. B 19-20 (2002) 223-230.
4. Ueatrongchit, T., Tamura, K., Ohmiya, T., H-Kittikun, A. and Asano, Y. Hydroxynitrile lyase from Passiflora edulis. Purification, characteristics and application in asymmetric synthesis of (R)-mandelonitrile. Enzyme Microb. Technol. 46 (2010) 456-465.
5. Andexer, J., von Langermann, J., Mell, A., Bocola, M., Kragl, U., Eggert, T. and Pohl, M. An R-selective hydroxynitrile lyase from Arabidopsis thaliana with an α/β-hydrolase fold. Angew. Chem. Int. Ed. Engl. 46 (2007) 8679-8681. [PMID: 17907254]
6. Guterl, J.K., Andexer, J.N., Sehl, T., von Langermann, J., Frindi-Wosch, I., Rosenkranz, T., Fitter, J., Gruber, K., Kragl, U., Eggert, T. and Pohl, M. Uneven twins: comparison of two enantiocomplementary hydroxynitrile lyases with α/β-hydrolase fold. J. Biotechnol. 141 (2009) 166-173. [PMID: 19433222]
[EC 4.1.2.37 Deleted entry: hydroxynitrilase. Now covered by EC 4.1.2.46 [aliphatic (R)-hydroxynitrile lyase] and EC 4.1.2.47 [(S)-hydroxynitrile ketone-lyase (cyanide forming)] (EC 4.1.2.37 created 1992 (EC 4.1.2.39 created 1999, incorporated 2007), deleted 2011)]
Accepted name: trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
Reaction: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate + H2O = salicylaldehyde + pyruvate
For diagram of reaction, click here
Glossary: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate = (E)-2'-hydroxybenzylidenepyruvate
salicylaldehyde = 2-hydroxybenzaldehyde
Other name(s): 2'-hydroxybenzalpyruvate aldolase; NsaE; tHBPA hydratase-aldolase
Systematic name: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate hydro-lyase
Comments: This enzyme is involved in naphthalene degradation. The enzyme catalyses a retro-aldol reaction in vitro, and it accepts a broad range of aldehydes and 4-substituted 2-oxobut-3-enoates as substrates [4].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number:
References:
1. Kuhm, A.E., Knackmuss, H.J. and Stolz, A. Purification and properties of 2'-hydroxybenzalpyruvate aldolase from a bacterium that degrades naphthalenesulfonates. J. Biol. Chem. 268 (1993) 9484-9489. [PMID: 8486638]
2. Keck, A., Conradt, D., Mahler, A., Stolz, A., Mattes, R. and Klein, J. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152 (2006) 1929-1940. [PMID: 16804169]
3. Eaton, R.W. Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J. Bacteriol. 176 (1994) 7757-7762. [PMID: 8002605]
4. Eaton, R.W. trans-o-Hydroxybenzylidenepyruvate hydratase-aldolase as a biocatalyst. Appl. Environ. Microbiol. 66 (2000) 2668-2672. [PMID: 10831455]
Accepted name: aliphatic (R)-hydroxynitrile lyase
Reaction: (2R)-2-hydroxy-2-methylbutanenitrile = cyanide + butan-2-one
Other name(s): (R)-HNL; (R)-oxynitrilase; (R)-hydroxynitrile lyase; LuHNL
Systematic name: (2R)-2-hydroxy-2-methylbutanenitrile butan-2-one-lyase (cyanide forming)
Comments: The enzyme contains Zn2+ [1]. The enzyme catalyses the stereoselective synthesis of aliphatic (R)-cyanohydrins [1]. No activity towards mandelonitrile and 4-hydroxymandelonitrile [5]. Natural substrates for the (R)-oxynitrilase from Linum usitatissimum are acetone and butan-2-one, which are the building blocks of the cyanogen glycosides in Linum, linamarin and lotaustralin, or linustatin and neolinustatin, respectively [4].
References:
1. Trummler, K., Roos, J., Schwaneberg, U., Effenberger, F., Frster, S., Pfizenmaier, K., Wajant, H. Expression of the Zn2+-containing hydroxynitrile lyase from flax (Linum usitatissimum) in Pichia pastoris - utilization of the recombinant enzyme for enzymatic analysis and site-directed mutagenesis. Plant Sci. 139 (1998) 19-27.
2. Trummler, K. and Wajant, H. Molecular cloning of acetone cyanohydrin lyase from flax (Linum usitatissimum). Definition of a novel class of hydroxynitrile lyases. J. Biol. Chem. 272 (1997) 4770-4774. [PMID: 9030531]
3. Albrecht, J., Jansen, I.and Kula, M.R. Improved purification of an (R)-oxynitrilase from Linum usitatissimum (flax) and investigation of the substrate range. Biotechnol. Appl. Biochem. 17 (1993) 191-203.
4. Xu, L.-L., Singh, B.K. and Conn, E.E. Purification and characterization of acetone cyanohydrin lyase from Linum usitatissimum. Arch. Biochem. Biophys. 263 (1988) 256-263. [PMID: 3377504]
5. Cabirol, F.L., Tan, P.L., Tay, B., Cheng, S., Hanefeld, U. and Sheldon, R.A. Linum usitatissimum hydroxynitrile lyase cross-linked enzyme aggregates: a recyclable enantioselective catalyst. Adv. Synth. Catal. 350 (2008) 2329-2338.
6. Breithaupt, H., Pohl, M., Bnigk, W., Heim, P., Schimz, K.-L. and Kula, M.-R. Cloning and expression of (R)-hydroxynitrile lyase from Linum usitatissimum (flax). J. Mol. Catal. B 6 (1999) 315-332.
Accepted name: (S)-hydroxynitrile lyase
Reaction: (1) an aliphatic (S)-hydroxynitrile = cyanide + an aliphatic aldehyde or ketone
(2) an aromatic (S)-hydroxynitrile = cyanide + an aromatic aldehyde
Other name(s): (S)-cyanohydrin producing hydroxynitrile lyase; (S)-oxynitrilase; (S)-HbHNL; (S)-MeHNL; hydroxynitrile lyase; oxynitrilase; HbHNL; MeHNL; (S)-selective hydroxynitrile lyase; (S)-cyanohydrin carbonyl-lyase (cyanide forming)
Systematic name: (S)-cyanohydrin lyase (cyanide forming)
Comments: Hydroxynitrile lyases catalyses the the cleavage of hydroxynitriles into cyanide and the corresponding aldehyde or ketone. In nature the liberation of cyanide serves as a defense mechanism against herbivores and microbial attack in plants. In vitro the enzymes from Manihot esculenta and Hevea brasiliensis accept a broad range of aliphatic and aromatic carbonyl compounds as substrates and catalyse the formation of (S)-hydroxynitriles [1,10].
References:
1. Förster, S., Roos, J., Effenberger, F., Wajant, H. and Sprauer, A. The first recombinant hydroxynitrile lyase and its application in the synthesis of (S)-cyanohydrins. Angew. Chem. Int. Ed. 35 (1996) 437-439.
2. Bühler, H., Effenberger, F., Förster, S., Roos, J. and Wajant, H. Substrate specificity of mutants of the hydroxynitrile lyase from Manihot esculenta. Chembiochem. 4 (2003) 211-216. [PMID: 12616635]
3. Semba, H., Dobashi, Y. and Matsui, T. Expression of hydroxynitrile lyase from Manihot esculenta in yeast and its application in (S)-mandelonitrile production using an immobilized enzyme reactor. Biosci. Biotechnol. Biochem. 72 (2008) 1457-1463. [PMID: 18540112]
4. Avi, M., Wiedner, R.M., Griengl, H. and Schwab, H. Improvement of a stereoselective biocatalytic synthesis by substrate and enzyme engineering: 2-hydroxy-(4'-oxocyclohexyl)acetonitrile as the model. Chemistry 14 (2008) 11415-11422. [PMID: 19006143]
5. von Langermann, J., Guterl, J.K., Pohl, M., Wajant, H. and Kragl, U. Hydroxynitrile lyase catalyzed cyanohydrin synthesis at high pH-values. Bioprocess Biosyst Eng 31 (2008) 155-161. [PMID: 18204865]
6. Schmidt, A., Gruber, K., Kratky, C. and Lamzin, V.S. Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis. J. Biol. Chem. 283 (2008) 21827-21836. [PMID: 18524775]
7. Gartler, G., Kratky, C. and Gruber, K. Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis. J. Biotechnol. 129 (2007) 87-97. [PMID: 17250917]
8. Wagner, U.G., Schall, M., Hasslacher, M., Hayn, M., Griengl, H., Schwab, H. and Kratky, C. Crystallization and preliminary X-ray diffraction studies of a hydroxynitrile lyase from Hevea brasiliensis. Acta Crystallogr. D Biol. Crystallogr. 52 (1996) 591-593. [PMID: 15299689]
9. Schmidt, M., Herve, S., Klempier, N. and Griengl, H. Preparation of optically active cyanohydrins using the (S)-hydroxynitrile lyase from Hevea brasiliensis. Tetrahedron 52 (1996) 7833-7840.
10. Klempier, N. and Griengl, H. Aliphatic (S)-cyanohydrins by enzyme catalyzed synthesis. Tetrahedron Lett. 34 (1993) 4769-4772.
Accepted name: L-erythro-3-hydroxyaspartate aldolase
Reaction: L-erythro-3-hydroxy-aspartate = glycine + glyoxylate
Other name(s): L-erythro-β-hydroxyaspartate aldolase; L-erythro-β-hydroxyaspartate glycine-lyase; erythro-3-hydroxy-Ls-aspartate glyoxylate-lyase
Systematic name: L-erythro-3-hydroxy-aspartate glyoxylate-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Paracoccus denitrificans NCIMB 8944, is strictly specific for the L-erythro stereoisomer of 3-hydroxyaspartate. Different from EC 4.1.3.41, erythro-3-hydroxy-D-aspartate aldolase. Requires a divalent cation.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 37290-64-5
References:
1. Gibbs, R.G. and Morris, J.G. Assay and properties of β-hydroxyaspartate aldolase from Micrococcus denitrificans. Biochim. Biophys. Acta 85 (1964) 501-503. [PMID: 14194868]
Accepted name: 3-hydroxy-D-aspartate aldolase
Reaction: (1) threo-3-hydroxy-D-aspartate = glycine + glyoxylate
(2) D-erythro-3-hydroxyaspartate = glycine + glyoxylate
Other name(s): D-3-hydroxyaspartate aldolase
Systematic name: 3-hydroxy-D-aspartate glyoxylate-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Paracoccus denitrificans IFO 13301, is strictly D-specific as to the α-position of the substrate, but accepts both the threo and erythro forms at the β-position. The erythro form is a far better substrate (about 100 fold). The enzyme can also accept D-allothreonine, D-threonine, erythro-3-phenyl-D-serine and threo-3-phenyl-D-serine. Different from EC 4.1.3.14, erythro-3-hydroxy-L-aspartate aldolase. Requires a divalent cation, such as Mg2+, Mn2+ or Co2+.
References:
1. Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M. and Shimizu, S. A novel enzyme, D-3-hydroxyaspartate aldolase from Paracoccus denitrificans IFO 13301: purification, characterization, and gene cloning. Appl. Microbiol. Biotechnol. 62 (2003) 53-60. [PMID: 12835921]
Accepted name: octadecanal decarbonylase
Reaction: octadecanal + reduced ferredoxin = heptadecane + CO + oxidized ferredoxin
Other name(s): decarbonylase; aldehyde decarbonylase
Systematic name: octadecanal alkane-lyase
Comments: Involved in the biosynthesis of alkanes. The enzyme from the cyanobacterium Nostoc punctiforme PCC 73102 requires reduced ferredoxin for activity, and produces mostly C15 to C17 alkanes [2]. The enzyme from pea (Pisum sativum) produces alkanes of chain length C18 to C32 and is inhibited by metal-chelating agents [1]. The substrate for this enzyme is formed by EC 1.2.1.80, acyl-[acyl-carrier protein] reductase.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 94185-90-7
References:
1. Cheesbrough, T.M. and, K olattukudy, P.E. Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum. Proc. Natl. Acad. Sci. USA 81 (1984) 6613-6617. [PMID: 6593720]
2. Schirmer, A., Rude, M.A., Li, X., Popova, E. and del Cardayre, S.B. Microbial biosynthesis of alkanes. Science 329 (2010) 559-562. [PMID: 20671186]
Accepted name: colneleate synthase
Reaction: (9S,10E,12Z)-9-hydroperoxyoctadeca-10,12-dienoate = (8E)-9-[(1E,3Z)-nona-1,3-dien-1-yloxy]non-8-enoate + H2O
Glossary: colneleate = (8E)-9-[(1E,3Z)-nona-1,3-dien-1-yloxy]non-8-enoate
Other name(s): 9-divinyl ether synthase; 9-DES; CYP74D; CYP74D1; CYP74 cytochrome P-450; DES1
Systematic name: (8E)-9-[(1E,3E)-nona-1,3-dien-1-yloxy]non-8-enoate synthase
Comments: A heme-thiolate protein (P450) [2]. It catalyses the selective removal of pro-R hydrogen at C-8 in the biosynthesis of colneleic acid [4]. It forms also (8E)-9-[(1E,3Z,6Z)-nona-1,3,6-trien-1-yloxy]non-8-enoic acid (i.e. colnelenate) from (9S,10E,12Z,15Z)-9-hydroperoxy-10,12,15-octadecatrienoate. The corresponding 13-hydroperoxides are poor substrates [1,3]. The divinyl ethers colneleate and colnelenate have antimicrobial activity.
References:
1. Stumpe, M., Kandzia, R., Gobel, C., Rosahl, S. and Feussner, I. A pathogen-inducible divinyl ether synthase (CYP74D) from elicitor-treated potato suspension cells. FEBS Lett. 507 (2001) 371-376. [PMID: 11696374]
2. Itoh, A. and Howe, G.A. Molecular cloning of a divinyl ether synthase. Identification as a CYP74 cytochrome P-450. J. Biol. Chem. 276 (2001) 3620-3627. [PMID: 11060314]
3. Fammartino, A., Cardinale, F., Gobel, C., Mene-Saffrane, L., Fournier, J., Feussner, I. and Esquerre-Tugaye, M.T. Characterization of a divinyl ether biosynthetic pathway specifically associated with pathogenesis in tobacco. Plant Physiol. 143 (2007) 378-388. [PMID: 17085514]
4. Hamberg, M. Hidden stereospecificity in the biosynthesis of divinyl ether fatty acids. FEBS J. 272 (2005) 736-743. [PMID: 15670154]
Accepted name: threo-3-hydroxy-L-aspartate ammonia-lyase
Reaction: threo-3-hydroxy-L-aspartate = oxaloacetate + NH3
Other name(s): L-threo-3-hydroxyaspartate dehydratase; threo-3-hydroxyaspartate ammonia-lyase
Systematic name: threo-3-hydroxy-L-aspartate ammonia-lyase (oxaloacetate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Pseudomonas sp. T62, is highly specific, and does not accept any other stereoisomer of 3-hydroxyaspartate. Different from EC 4.3.1.20, erythro-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+, or Ca2+.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 248270-70-4
References:
1. Wada, M., Matsumoto, T., Nakamori, S., Sakamoto, M., Kataoka, M., Liu, J.-Q., Itoh, N., Yamada, H. and Shimizu, S. Purification and characterization of a novel enzyme, L-threo-3-hydroxyaspartate dehydratase, from Pseudomonas sp. T62. FEMS Microbiol. Lett. 179 (1999) 147-151. [PMID: 10481099]
Accepted name: erythro-3-hydroxy-L-aspartate ammonia-lyase
Reaction: erythro-3-hydroxy-L-aspartate = oxaloacetate + NH3
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+, or Ca2+.
Links to other databases: BRENDA, EXPASY, KEGG, METACYC, 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]
Accepted name: threo-3-hydroxy-D-aspartate ammonia-lyase
Reaction: threo-3-hydroxy-D-aspartate = oxaloacetate + NH3
Other name(s): D-threo-3-hydroxyaspartate dehydratase
Systematic name: threo-3-hydroxy-D-aspartate ammonia-lyase (oxaloacetate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Delftia sp. HT23, also has activity against L-threo-3-hydroxyaspartate, L-erythro-3-hydroxyaspartate, and D-serine. Different from EC 4.3.1.20, erythro-3-hydroxy-L-aspartate ammonia-lyase and EC 4.3.1.16, threo-3-hydroxy-L-aspartate ammonia-lyase. Requires a divalent cation such as Mn2+, Co2+ or Ni2+.
References:
1. Maeda, T., Takeda, Y., Murakami, T., Yokota, A. and Wada, M. Purification, characterization and amino acid sequence of a novel enzyme, D-threo-3-hydroxyaspartate dehydratase, from Delftia sp. HT23. J. Biochem. 148 (2010) 705-712. [PMID: 20843822]
Accepted name: 4-phosphopantoate—β-alanine ligase
Reaction: ATP + (R)-4-phosphopantoate + β-alanine = AMP + diphosphate + (R)-4'-phosphopantothenate
Other name(s): phosphopantothenate synthetase; TK1686 protein
Systematic name: (R)-4-phosphopantoate:β-alanine ligase (AMP-forming)
Comments: The conversion of (R)-pantoate to (R)-4'-phosphopantothenate is part of the pathway leading to biosynthesis of 4'-phosphopantetheine, an essential cofactor of coenzyme A and acyl-carrier protein. In bacteria and eukaryotes this conversion is performed by condensation with β-alanine, followed by phosphrylation (EC 6.3.2.1 [pantoate—β-alanine ligase] and EC 2.7.1.33 [pantothenate kinase], respectively). In archaea the order of these two steps is reversed, and phosphorylation precedes condensation with β-alanine. The two archaeal enzymes that catalyse this conversion are EC 2.7.1.169, pantoate kinase, and this enzyme.
References:
1. Yokooji, Y., Tomita, H., Atomi, H. and Imanaka, T. Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. J. Biol. Chem. 284 (2009) 28137-28145. [PMID: 19666462]