An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: UDP-N-acetylglucosamine 6-dehydrogenase
Reaction: UDP-N-acetyl-α-D-glucosamine + 2 NAD+ + H2O = UDP-N-acetyl-2-amino-2-deoxy-α-D-glucuronate + 2 NADH + 2 H+
For diagram of reaction click here.
Other name(s): uridine diphosphoacetylglucosamine dehydrogenase; UDP-acetylglucosamine dehydrogenase; UDP-2-acetamido-2-deoxy-D-glucose:NAD oxidoreductase; UDP-GlcNAc dehydrogenase; WbpA; WbpO
Systematic name: UDP-N-acetyl-α-D-glucosamine:NAD+ 6-oxidoreductase
Comments: This enzyme participates in the biosynthetic pathway for UDP-α-D-ManNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronic acid), an important precursor of B-band lipopolysaccharide.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9054-83-5
References:
1. Fan, D.-F., John, C.E., Zalitis, J. and Feingold, D.S. UDPacetylglucosamine dehydrogenase from Achromobacter georgiopolitanum. Arch. Biochem. Biophys. 135 (1969) 45-49. [PMID: 4312076]
2. Miller, W.L., Wenzel, C.Q., Daniels, C., Larocque, S., Brisson, J.R. and Lam, J.S. Biochemical characterization of WbpA, a UDP-N-acetyl-D-glucosamine 6-dehydrogenase involved in O-antigen biosynthesis in Pseudomonas aeruginosa PAO1. J. Biol. Chem. 279 (2004) 37551-37558. [PMID: 15226302]
EC 1.1.1.328
Accepted name: nicotine blue oxidoreductase
Reaction: 3,3'-bipyridine-2,2',5,5',6,6'-hexol + NAD(P)+ = (E)-2,2',5,5'-tetrahydroxy-6H,6'H-[3,3'-bipyridinylidene]-6,6'-dione + NAD(P)H + H+
For diagram of reaction click here.
Glossary: 3,3'-bipyridine-2,2',5,5',6,6'-hexol = nicotine blue leuco form
Other name(s): nboR (gene name)
Systematic name: 3,3'-bipyridine-2,2',5,5',6,6'-hexol:NADP+ 11-oxidoreductase
Comments: The enzyme, characterized from the nicotine degrading bacterium Arthrobacter nicotinovorans, catalyses the reduction of "nicotine blue" to its hydroquinone form (the opposite direction from that shown). Nicotine blue is the name given to the compound formed by the autocatalytic condensation of two molecules of 2,3,6-trihydroxypyridine, an intermediate in the nicotine degradation pathway. The main role of the enzyme may be to prevent the intracellular formation of nicotine blue semiquinone radicals, which by redox cycling would lead to the formation of toxic reactive oxygen species. The enzyme possesses a slight preference for NADH over NADPH.
References:
1. Mihasan, M., Chiribau, C.B., Friedrich, T., Artenie, V. and Brandsch, R. An NAD(P)H-nicotine blue oxidoreductase is part of the nicotine regulon and may protect Arthrobacter nicotinovorans from oxidative stress during nicotine catabolism. Appl. Environ. Microbiol. 73 (2007) 2479-2485. [PMID: 17293530]
EC 1.1.1.329
Accepted name: 2-deoxy-scyllo-inosamine dehydrogenase
Reaction: 2-deoxy-scyllo-inosamine + NAD(P)+ = 3-amino-2,3-dideoxy-scyllo-inosose + NAD(P)H + H+
Glossary: 2-deoxy-scyllo-inosamine = (1R,2S,3S,4R,5S)-5-aminocyclohexane-1,2,3,4-tetrol
Other name(s): neoA (gene name); kanK (gene name)
Systematic name: 2-deoxy-scyllo-inosamine:NAD(P)+ 1-oxidoreductase
Comments: Requires zinc. Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin, neomycin and ribostamycin. cf. EC 1.1.99.38, 2-deoxy-scyllo-inosamine dehydrogenase (SAM-dependent).
References:
1. Kudo, F., Yamamoto, Y., Yokoyama, K., Eguchi, T. and Kakinuma, K. Biosynthesis of 2-deoxystreptamine by three crucial enzymes in Streptomyces fradiae NBRC 12773. J. Antibiot. (Tokyo) 58 (2005) 766-774. [PMID: 16506694]
2. Nepal, K.K., Oh, T.J. and Sohng, J.K. Heterologous production of paromamine in Streptomyces lividans TK24 using kanamycin biosynthetic genes from Streptomyces kanamyceticus ATCC12853. Mol. Cells 27 (2009) 601-608. [PMID: 19466609]
EC 1.1.1.330
Accepted name: very-long-chain 3-oxoacyl-CoA reductase
Reaction: a very-long-chain (3R)-3-hydroxyacyl-CoA + NADP+ = a very-long-chain 3-oxoacyl-CoA + NADPH + H+
Glossary: a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms
Other name(s): very-long-chain 3-ketoacyl-CoA reductase; very-long-chain β-ketoacyl-CoA reductase; KCR (gene name); IFA38 (gene name)
Systematic name: (3R)-3-hydroxyacyl-CoA:NADP+ oxidoreductase
Comments: The second component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long-chain acyl CoAs. The enzyme is active with substrates with chain length of C16 to C34, depending on the species. cf. EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 4.2.1.134, very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase.
References:
1. Beaudoin, F., Gable, K., Sayanova, O., Dunn, T. and Napier, J.A. A Saccharomyces cerevisiae gene required for heterologous fatty acid elongase activity encodes a microsomal β-keto-reductase. J. Biol. Chem. 277 (2002) 11481-11488. [PMID: 11792704]
2. Han, G., Gable, K., Kohlwein, S.D., Beaudoin, F., Napier, J.A. and Dunn, T.M. The Saccharomyces cerevisiae YBR159w gene encodes the 3-ketoreductase of the microsomal fatty acid elongase. J. Biol. Chem. 277 (2002) 35440-35449. [PMID: 12087109]
3. Beaudoin, F., Wu, X., Li, F., Haslam, R.P., Markham, J.E., Zheng, H., Napier, J.A. and Kunst, L. Functional characterization of the Arabidopsis β-ketoacyl-coenzyme A reductase candidates of the fatty acid elongase. Plant Physiol. 150 (2009) 1174-1191. [PMID: 19439572]
EC 1.1.1.331
Accepted name: secoisolariciresinol dehydrogenase
Reaction: (–)-secoisolariciresinol + 2 NAD+ = (–)-matairesinol + 2 NADH + 2 H+
Systematic name: (–)-secoisolariciresinol:NAD+ oxidoreductase
Comments: Isolated from the plants Forsythia intermedia [1] and Podophyllum peltatum [1-3]. An intermediate lactol is detected in vitro.
References:
1. Xia, Z.Q., Costa, M.A., Pelissier, H.C., Davin, L.B. and Lewis, N.G. Secoisolariciresinol dehydrogenase purification, cloning, and functional expression. Implications for human health protection. J. Biol. Chem. 276 (2001) 12614-12623. [PMID: 11278426]
2. Youn, B., Moinuddin, S.G., Davin, L.B., Lewis, N.G. and Kang, C. Crystal structures of apo-form and binary/ternary complexes of Podophyllum secoisolariciresinol dehydrogenase, an enzyme involved in formation of health-protecting and plant defense lignans. J. Biol. Chem. 280 (2005) 12917-12926. [PMID: 15653677]
3. Moinuddin, S.G., Youn, B., Bedgar, D.L., Costa, M.A., Helms, G.L., Kang, C., Davin, L.B. and Lewis, N.G. Secoisolariciresinol dehydrogenase: mode of catalysis and stereospecificity of hydride transfer in Podophyllum peltatum. Org. Biomol. Chem. 4 (2006) 808-816. [PMID: 16493463]
EC 1.1.1.332
Accepted name: chanoclavine-I dehydrogenase
Reaction: chanoclavine-I + NAD+ = chanoclavine-I aldehyde + NADH + H+
Glossary: chanoclavine-I = (1E)-2-methyl-3-[(4R,5R)-4-(methylamino)-1,3,4,5-tetrahydrobenz[cd]indol-5-yl]prop-2-en-1-ol
Other name(s): easD (gene name); fgaDH (gene name)
Systematic name: chanoclavine-I:NAD+ oxidoreductase
Comments: The enzyme catalyses a step in the pathway of ergot alkaloid biosynthesis in certain fungi.
References:
1. Wallwey, C., Matuschek, M. and Li, S.M. Ergot alkaloid biosynthesis in Aspergillus fumigatus: conversion of chanoclavine-I to chanoclavine-I aldehyde catalyzed by a short-chain alcohol dehydrogenase FgaDH. Arch. Microbiol. 192 (2010) 127-134. [PMID: 20039019]
2. Wallwey, C., Heddergott, C., Xie, X., Brakhage, A.A. and Li, S.M. Genome mining reveals the presence of a conserved gene cluster for the biosynthesis of ergot alkaloid precursors in the fungal family Arthrodermataceae. Microbiology 158 (2012) 1634-1644. [PMID: 22403186]
EC 1.1.1.333
Accepted name: decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose 2-reductase
Reaction: trans,octacis-decaprenylphospho-β-D-arabinofuranose + NAD+ = trans,octacis-decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose + NADH + H+
Other name(s): decaprenylphospho-β-D-ribofuranose 2'-epimerase; Rv3791; DprE2
Systematic name: trans,octacis-decaprenylphospho-β-D-arabinofuranose:NAD+ 2-oxidoreductase
Comments: The reaction is catalysed in the reverse direction. The enzyme, isolated from the bacterium Mycobacterium smegmatis, is involved, along with EC 1.1.98.3, decaprenylphospho-β-D-ribofuranose 2-oxidase, in the epimerization of trans,octacis-decaprenylphospho-β-D-ribofuranose to trans,octacis-decaprenylphospho-β-D-arabinoofuranose, the arabinosyl donor for the biosynthesis of mycobacterial cell wall arabinan polymers.
References:
1. Trefzer, C., Škovierová, H., Buroni, S., Bobovská, A., Nenci, S., Molteni, E., Pojer, F., Pasca, M.R., Makarov, V., Cole, S.T., Riccardi, G., Mikušová, K. and Johnsson, K. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2'-oxidase DprE1. J. Am. Chem. Soc. 134 (2012) 912-915. [PMID: 22188377]
EC 1.1.1.334
Accepted name: methylecgonone reductase
Reaction: ecgonine methyl ester + NADP+ = ecgonone methyl ester + NADPH + H+
Glossary: ecgonine methyl ester = 2β-carbomethoxy-3β-tropine = methyl (1R,2R,3S,5S)-3-hydroxy-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate
Other name(s): MecgoR (gene name)
Systematic name: ecgonine methyl ester:NADP+ oxidoreductase
Comments: The enzyme from the plant Erythroxylum coca catalyses the penultimate step in the biosynthesis of cocaine. In vivo the reaction proceeds in the opposite direction. With NADH instead of NADPH the reaction rate is reduced to 14%. The enzyme also reduces tropinone, nortropinone and 6-hydroxytropinone but with lower reaction rates.
References:
1. Jirschitzka, J., Schmidt, G.W., Reichelt, M., Schneider, B., Gershenzon, J. and D'Auria, J.C. Plant tropane alkaloid biosynthesis evolved independently in the Solanaceae and Erythroxylaceae. Proc. Natl. Acad. Sci. USA 109 (2012) 10304-10309. [PMID: 22665766]
EC 1.1.3.43
Accepted name: paromamine 6'-oxidase
Reaction: paromamine + O2 = 6'-dehydroparomamine + H2O2
Other name(s): btrQ (gene name); neoG (gene name); kanI (gene name); tacB (gene name); neoQ (obsolete gene name)
Systematic name: paromamine:oxygen 6'-oxidoreductase
Comments: Contains FAD. Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin, butirosin, neomycin and ribostamycin. Works in combination with EC 2.6.1.93, neamine transaminase, to replace the 6-hydroxy group of paromamine with an amino group. The enzyme from the bacterium Streptomyces fradiae also catalyses EC 1.1.3.44, 6′′′-hydroxyneomycin C oxidase.
References:
1. Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem. 8 (2007) 283-288. [PMID: 17206729]
2. Yu, Y., Hou, X., Ni, X. and Xia, H. Biosynthesis of 3'-deoxy-carbamoylkanamycin C in a Streptomyces tenebrarius mutant strain by tacB gene disruption. J. Antibiot. (Tokyo) 61 (2008) 63-69. [PMID: 18408324]
3. Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6'-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642-651. [PMID: 21689223]
EC 1.1.3.44
Accepted name: 6′′′-hydroxyneomycin C oxidase
Reaction: 6′′′-deamino-6′′′-hydroxyneomycin C + O2 = 6′′′-deamino-6′′′-oxoneomycin C + H2O2
Other name(s): neoG (gene name); neoQ (obsolete gene name)
Systematic name: 6′′′-deamino-6′′′-hydroxyneomycin C:oxygen 6′′′-oxidoreductase
Comments: Contains FAD. Involved in the biosynthetic pathway of aminoglycoside antibiotics of the neomycin family. Works in combination with EC 2.6.1.95, neomycin C transaminase, to replace the 6′′′-hydroxy group of 6′′′-hydroxyneomycin C with an amino group. Also catalyses EC 1.1.3.43, paromamine 6'-oxidase.
References:
1. Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem. 8 (2007) 283-288. [PMID: 17206729]
2. Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6'-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642-651. [PMID: 21689223]
EC 1.1.98.3
Accepted name: decaprenylphospho-β-D-ribofuranose 2-oxidase
Reaction: trans,octacis-decaprenylphospho-β-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose + FADH2
Other name(s): decaprenylphosphoryl-β-D-ribofuranose 2'-epimerase; Rv3790; DprE1
Systematic name: trans,octacis-decaprenylphospho-β-D-ribofuranose:FAD 2-oxidoreductase
Comments: The enzyme, isolated from the bacterium Mycobacterium smegmatis, is involved, along with EC 1.1.1.333, decaprenylphospho-D-erythro-pentofuranosid-2-ulose 2-reductase, in the epimerization of trans,octacis-decaprenylphospho-β-D-ribofuranose to trans,octacis-decaprenylphospho-β-D-arabinoofuranose, the arabinosyl donor for the biosynthesis of mycobacterial cell wall arabinan polymers.
References:
1. Ribeiro, A.L., Degiacomi, G., Ewann, F., Buroni, S., Incandela, M.L., Chiarelli, L.R., Mori, G., Kim, J., Contreras-Dominguez, M., Park, Y.S., Han, S.J., Brodin, P., Valentini, G., Rizzi, M., Riccardi, G. and Pasca, M.R. Analogous mechanisms of resistance to benzothiazinones and dinitrobenzamides in Mycobacterium smegmatis. PLoS One 6 (2011) e26675. [PMID: 22069462]
2. Trefzer, C., Škovierová, H., Buroni, S., Bobovská, A., Nenci, S., Molteni, E., Pojer, F., Pasca, M.R., Makarov, V., Cole, S.T., Riccardi, G., Mikušová, K. and Johnsson, K. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2'-oxidase DprE1. J. Am. Chem. Soc. 134 (2012) 912-915. [PMID: 22188377]
EC 1.1.99.38
Accepted name: 2-deoxy-scyllo-inosamine dehydrogenase (SAM-dependent)
Reaction: 2-deoxy-scyllo-inosamine + S-adenosyl-L-methionine = 3-amino-2,3-dideoxy-scyllo-inosose + 5'-deoxyadenosine + L-methionine
Other name(s): btrN (gene name)
Systematic name: 2-deoxy-scyllo-inosamine:S-adenosyl-L-methionine 1-oxidoreductase
Comments: Involved in the biosynthetic pathway of the aminoglycoside antibiotics of the butirosin family. The enzyme from Bacillus circulans was shown to be a radical S-adenosyl-L-methionine (SAM) enzyme. cf. EC 1.1.1.329, 2-deoxy-scyllo-inosamine dehydrogenase.
References:
1. Yokoyama, K., Numakura, M., Kudo, F., Ohmori, D. and Eguchi, T. Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin. J. Am. Chem. Soc. 129 (2007) 15147-15155. [PMID: 18001019]
2. Yokoyama, K., Ohmori, D., Kudo, F. and Eguchi, T. Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy. Biochemistry 47 (2008) 8950-8960. [PMID: 18672902]
EC 1.2.1.83
Accepted name: 3-succinoylsemialdehyde-pyridine dehydrogenase
Reaction: 4-oxo-4-(pyridin-3-yl)butanal + NADP+ + H2O = 4-oxo-4-(pyridin-3-yl)butanoate + NADPH + H+
Glossary: 4-oxo-4-(pyridin-3-yl)butanal = 3-succinoylsemialdehyde-pyridine
Systematic name: 4-oxo-4-(pyridin-3-yl)butanal:NADP+ oxidoreductase
Comments: The enzyme has been characterized from the soil bacterium Pseudomonas sp. HZN6. It participates in the nicotine degradation pathway.
References:
1. Qiu, J., Ma, Y., Wen, Y., Chen, L., Wu, L. and Liu, W. Functional identification of two novel genes from Pseudomonas sp. strain HZN6 involved in the catabolism of nicotine. Appl. Environ. Microbiol. 78 (2012) 2154-2160. [PMID: 22267672]
EC 1.2.1.84
Accepted name: alcohol-forming fatty acyl-CoA reductase
Reaction: a long-chain acyl-CoA + 2 NADPH + 2 H+ = a long-chain alcohol + 2 NADP+ + coenzyme A
Glossary: a long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 13 to 22 carbon atoms.
Other name(s): FAR (gene name)
Systematic name: long-chain acyl-CoA:NADPH reductase
Comments: The enzyme has been characterized from the plant Simmondsia chinensis (jojoba). The alcohol is formed by a four-electron reduction of fatty acyl-CoA. Although the reaction proceeds through an aldehyde intermediate, a free aldehyde is not released. The recombinant enzyme was shown to accept saturated and mono-unsaturated fatty acyl-CoAs of 16 to 22 carbons.
References:
1. Metz, J.G., Pollard, M.R., Anderson, L., Hayes, T.R. and Lassner, M.W. Purification of a jojoba embryo fatty acyl-coenzyme A reductase and expression of its cDNA in high erucic acid rapeseed. Plant Physiol. 122 (2000) 635-644. [PMID: 10712526]
*EC 1.2.3.1
Accepted name: aldehyde oxidase
Reaction: an aldehyde + H2O + O2 = a carboxylate + H2O2
Other name(s): quinoline oxidase; retinal oxidase
Systematic name: aldehyde:oxygen oxidoreductase
Comments: Contains molybdenum, [2Fe-2S] centres and FAD. The enzyme from liver exhibits a broad substrate specificity, and is involved in the metabolism of xenobiotics, including the oxidation of N-heterocycles and aldehydes and the reduction of N-oxides, nitrosamines, hydroxamic acids, azo dyes, nitropolycyclic aromatic hydrocarbons, and sulfoxides [4,6]. The enzyme is also responsible for the oxidation of retinal, an activity that was initially attributed to a distinct enzyme (EC 1.2.3.11, retinal oxidase) [5,7].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
UM-BBD,
CAS registry number: 9029-07-6
References:
1. Gordon, A.H., Green, D.E. and Subrahmanyan, V. Liver aldehyde oxidase. Biochem. J. 34 (1940) 764-774. [PMID: 16747217]
2. Knox, W.E. The quinine-oxidizing enzyme and liver aldehyde oxidase. J. Biol. Chem. 163 (1946) 699-711. [PMID: 20985642]
3. Mahler, H.R., Mackler, B., Green, D.E. and Bock, R.M. Studies on metalloflavoproteins. III. Aldehyde oxidase: a molybdoflavoprotein. J. Biol. Chem. 210 (1954) 465-480. [PMID: 13201608]
4. Krenitsky, T.A., Neil, S.M., Elion, G.B. and Hitchings, G.H. A comparison of the specificities of xanthine oxidase and aldehyde oxidase. Arch. Biochem. Biophys. 150 (1972) 585-599. [PMID: 5044040]
5. Tomita, S., Tsujita, M. and Ichikawa, Y. Retinal oxidase is identical to aldehyde oxidase. FEBS Lett. 336 (1993) 272-274. [PMID: 8262244]
6. Yoshihara, S. and Tatsumi, K. Purification and characterization of hepatic aldehyde oxidase in male and female mice. Arch. Biochem. Biophys. 338 (1997) 29-34. [PMID: 9015384]
7. Huang, D.-Y., Furukawa, A. and Ichikawa, Y. Molecular cloning of retinal oxidase/aldehyde oxidase cDNAs from rabbit and mouse livers and functional expression of recombinant mouse retinal oxidase cDNA in Escherichia coli. Arch. Biochem. Biophys. 364 (1999) 264-272. [PMID: 10190983]
8. Uchida, H., Kondo, D., Yamashita, A., Nagaosa, Y., Sakurai, T., Fujii, Y., Fujishiro, K., Aisaka, K. and Uwajima, T. Purification and characterization of an aldehyde oxidase from Pseudomonas sp. KY 4690. FEMS Microbiol. Lett. 229 (2003) 31-36. [PMID: 14659539]
[EC 1.2.3.11 Deleted entry: retinal oxidase. Now included with EC 1.2.3.1, aldehyde oxidase (EC 1.2.3.11 created 1990, modified 2002, deleted 2011)]
EC 1.3.1.93
Accepted name: very-long-chain enoyl-CoA reductase
Reaction: a very-long-chain acyl-CoA + NADP+ = a very-long-chain trans-2,3-dehydroacyl-CoA + NADPH + H+
Glossary: a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.
Other name(s): TSC13 (gene name); CER10 (gene name)
Systematic name: very-long-chain acyl-CoA:NADP+ oxidoreductase
Comments: This is the fourth component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long-chain acyl CoAs. cf. EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, and EC 4.2.1.134, very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase.
References:
1. Kohlwein, S.D., Eder, S., Oh, C.S., Martin, C.E., Gable, K., Bacikova, D. and Dunn, T. Tsc13p is required for fatty acid elongation and localizes to a novel structure at the nuclear-vacuolar interface in Saccharomyces cerevisiae. Mol. Cell Biol. 21 (2001) 109-125. [PMID: 11113186]
2. Gable, K., Garton, S., Napier, J.A. and Dunn, T.M. Functional characterization of the Arabidopsis thaliana orthologue of Tsc13p, the enoyl reductase of the yeast microsomal fatty acid elongating system. J. Exp. Bot. 55 (2004) 543-545. [PMID: 14673020]
3. Kvam, E., Gable, K., Dunn, T.M. and Goldfarb, D.S. Targeting of Tsc13p to nucleus-vacuole junctions: a role for very-long-chain fatty acids in the biogenesis of microautophagic vesicles. Mol. Biol. Cell 16 (2005) 3987-3998. [PMID: 15958487]
4. Zheng, H., Rowland, O. and Kunst, L. Disruptions of the Arabidopsis Enoyl-CoA reductase gene reveal an essential role for very-long-chain fatty acid synthesis in cell expansion during plant morphogenesis. Plant Cell 17 (2005) 1467-1481. [PMID: 15829606]
EC 1.3.1.94
Accepted name: polyprenol reductase
Reaction: ditrans,polycis-dolichol + NADP+ = ditrans,polycis-polyprenol + NADPH + H+
Other name(s): SRD5A3 (gene name); DFG10 (gene name)
Systematic name: ditrans,polycis-dolichol:NADP+ 2,3-oxidoreductase
Comments: The reaction occurs in the reverse direction with reduction of the terminal double bond next to the alcohol group. Isolated from human fetal brain tissue but present in all eukaryotes. In mammalian cells dolichols are predominantly 18-21 isoprene units in length.
References:
1. Sagami, H., Kurisaki, A. and Ogura, K. Formation of dolichol from dehydrodolichol is catalyzed by NADPH-dependent reductase localized in microsomes of rat liver. J. Biol. Chem. 268 (1993) 10109-10113. [PMID: 8486680]
2. Cantagrel, V., Lefeber, D.J., Ng, B.G., Guan, Z., Silhavy, J.L., Bielas, S.L., Lehle, L., Hombauer, H., Adamowicz, M., Swiezewska, E., De Brouwer, A.P., Blumel, P., Sykut-Cegielska, J., Houliston, S., Swistun, D., Ali, B.R., Dobyns, W.B., Babovic-Vuksanovic, D., van Bokhoven, H., Wevers, R.A., Raetz, C.R., Freeze, H.H., Morava, E., Al-Gazali, L. and Gleeson, J.G. SRD5A3 is required for converting polyprenol to dolichol and is mutated in a congenital glycosylation disorder. Cell 142 (2010) 203-217. [PMID: 20637498]
*EC 1.3.99.5
Accepted name: 3-oxo-5α-steroid 4-dehydrogenase (acceptor)
Reaction: a 3-oxo-5α-steroid + acceptor = a 3-oxo-Δ4-steroid + reduced acceptor
Other name(s): steroid 5α-reductase; 3-oxosteroid Δ4-dehydrogenase; 3-oxo-5α-steroid Δ4-dehydrogenase; steroid Δ4-5α-reductase; Δ4-3-keto steroid 5α-reductase; Δ4-3-oxo steroid reductase; Δ4-3-ketosteroid5α-oxidoreductase; Δ4-3-oxosteroid-5α-reductase; 3-keto-Δ4-steroid-5α-reductase; 5α-reductase; testosterone 5α-reductase; 4-ene-3-ketosteroid-5α-oxidoreductase; Δ4-5α-dehydrogenase; 3-oxo-5α-steroid:(acceptor) Δ4-oxidoreductase; tesI (gene name)
Systematic name: 3-oxo-5α-steroid:acceptor Δ4-oxidoreductase
Comments: A flavoprotein. This bacterial enzyme, characterized from Comamonas testosteroni, is involved in androsterone degradation. cf. EC 1.3.1.22, 3-oxo-5α-steroid 4-dehydrogenase (NADP+).
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 9036-43-5
References:
1. Levy, H.R. and Talalay, P. Bacterial oxidation of steroids. II. Studies on the enzymatic mechanisms of ring A dehydrogenation. J. Biol. Chem. 234 (1959) 2014-2021. [PMID: 13673006]
2. Florin, C., Kohler, T., Grandguillot, M. and Plesiat, P. Comamonas testosteroni 3-ketosteroid-Δ4(5α)-dehydrogenase: gene and protein characterization. J. Bacteriol. 178 (1996) 3322-3330. [PMID: 8655514]
3. Horinouchi, M., Hayashi, T., Yamamoto, T. and Kudo, T. A new bacterial steroid degradation gene cluster in Comamonas testosteroni TA441 which consists of aromatic-compound degradation genes for seco-steroids and 3-ketosteroid dehydrogenase genes. Appl. Environ. Microbiol. 69 (2003) 4421-4430. [PMID: 12902225]
EC 1.4.3.24
Accepted name: pseudooxynicotine oxidase
Reaction: 4-(methylamino)-1-(pyridin-3-yl)butan-1-one + H2O + O2 = 4-oxo-4-(pyridin-3-yl)butanal + methylamine + H2O2
Glossary: 4-(methylamino)-1-(pyridin-3-yl)butan-1-one = pseudooxynicotine
Systematic name: 4-(methylamino)-1-(pyridin-3-yl)butan-1-one:oxygen oxidoreductase (methylamine releasing)
Comments: Contains one non-covalently bound FAD molecule per dimer. This enzyme, characterized from the soil bacterium Pseudomonas sp. HZN6, is involved the nicotine degradation.
References:
1. Qiu, J., Ma, Y., Wen, Y., Chen, L., Wu, L. and Liu, W. Functional identification of two novel genes from Pseudomonas sp. strain HZN6 involved in the catabolism of nicotine. Appl. Environ. Microbiol. 78 (2012) 2154-2160. [PMID: 22267672]
EC 1.5.3.19
Accepted name: 4-methylaminobutanoate oxidase (formaldehyde-forming)
Reaction: 4-methylaminobutanoate + O2 + H2O = 4-aminobutanoate + formaldehyde + H2O2
For diagram of reaction click here.
Other name(s): mabO (gene name)
Systematic name: 4-methylaminobutanoate:oxygen oxidoreductase (formaldehyde-forming)
Comments: A flavoprotein (FAD). In the enzyme from the soil bacterium Arthrobacter nicotinovorans the cofactor is covalently bound. Participates in the nicotine degradation pathway of this organism.
References:
1. Chiribau, C.B., Sandu, C., Fraaije, M., Schiltz, E. and Brandsch, R. A novel γ-N-methylaminobutyrate demethylating oxidase involved in catabolism of the tobacco alkaloid nicotine by Arthrobacter nicotinovorans pAO1. Eur. J. Biochem. 271 (2004) 4677-4684. [PMID: 15606755]
EC 1.5.3.20
Accepted name: N-alkylglycine oxidase
Reaction: N-alkylglycine + H2O + O2 = alkylamine + glyoxalate + H2O2
Other name(s): N-carboxymethylalkylamine:oxygen oxidoreductase (decarboxymethylating)
Systematic name: N-alkylglycine:oxygen oxidoreductase (alkylamine forming)
Comments: Isolated from the mold Cladosporium sp. G-10. Acts on N6-(carboxymethyl)lysine, 6-[(carboxymethy)amino]hexanoic acid, sarcosine and N-ethylglycine. It has negligible action on glycine (cf. EC 1.4.3.19 glycine oxidase).
References:
1. Gomi, K. and Horiuchi, T. Purification and characterization of a new enzyme, N-alkylglycine oxidase from Cladosporium sp. G-10. Biochim. Biophys. Acta 1429 (1999) 439-445. [PMID: 9989229]
EC 1.5.3.21
Accepted name: 4-methylaminobutanoate oxidase (methylamine-forming)
Reaction: 4-methylaminobutanoate + O2 + H2O = succinate semialdehyde + methylamine + H2O2
For diagram of reaction click here.
Other name(s): mao (gene name) (ambiguous)
Systematic name: 4-methylaminobutanoate methylamidohydrolase
Comments: The enzyme participates in the nicotine degradation pathway of the soil bacterium Arthrobacter nicotinovorans. Has a very weak monoamine oxidase (EC 1.4.3.4) activity with 4-aminobutanoate [1].
References:
1. Chiribau, C.B., Sandu, C., Fraaije, M., Schiltz, E. and Brandsch, R. A novel γ-N-methylaminobutyrate demethylating oxidase involved in catabolism of the tobacco alkaloid nicotine by Arthrobacter nicotinovorans pAO1. Eur. J. Biochem. 271 (2004) 4677-4684. [PMID: 15606755]
2. Chiribau, C.B., Mihasan, M., Ganas, P., Igloi, G.L., Artenie, V. and Brandsch, R. Final steps in the catabolism of nicotine. FEBS J. 273 (2006) 1528-1536. [PMID: 16689938]
EC 1.5.99.14
Accepted name: 6-hydroxypseudooxynicotine dehydrogenase
Reaction: 1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one + acceptor + H2O = 1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one + reduced acceptor
For diagram of reaction click here.
Glossary: 1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one = 6-hydroxypseudooxynicotine
Systematic name: 1-(6-hydroxypyridin-3-yl)-4-(methylamino)butan-1-one:acceptor 6-oxidoreductase (hydroxylating)
Comments: Contains a cytidylyl molybdenum cofactor [3]. The enzyme, which participates in the nicotine degradation pathway, has been characterized from the soil bacterium Arthrobacter nicotinovorans [1,2].
References:
1. Freudenberg, W., Konig, K. and Andreesen, J. R. Nicotine dehydrogenase from Arthrobacter oxidans: A molybdenum-containing hydroxylase. FEMS Microbiology Letters 52 (1988) 13-18.
2. Grether-Beck, S., Igloi, G.L., Pust, S., Schilz, E., Decker, K. and Brandsch, R. Structural analysis and molybdenum-dependent expression of the pAO1-encoded nicotine dehydrogenase genes of Arthrobacter nicotinovorans. Mol. Microbiol. 13 (1994) 929-936. [PMID: 7815950]
3. Sachelaru, P., Schiltz, E. and Brandsch, R. A functional mobA gene for molybdopterin cytosine dinucleotide cofactor biosynthesis is required for activity and holoenzyme assembly of the heterotrimeric nicotine dehydrogenases of Arthrobacter nicotinovorans. Appl. Environ. Microbiol. 72 (2006) 5126-5131. [PMID: 16820521]
*EC 1.13.11.16
Accepted name: 3-carboxyethylcatechol 2,3-dioxygenase
Reaction: (1) 3-(2,3-dihydroxyphenyl)propanoate + O2 = (2Z,4E)-2-hydroxy-6-oxonona-2,4-diene-1,9-dioate
For diagram of reaction click here or click here.
Glossary: (2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate = trans-2,3-dihydroxycinnamate
Other name(s): 2,3-dihydroxy-β-phenylpropionic dioxygenase; 2,3-dihydroxy-β-phenylpropionate oxygenase; 3-(2,3-dihydroxyphenyl)propanoate:oxygen 1,2-oxidoreductase
Systematic name: 3-(2,3-dihydroxyphenyl)propanoate:oxygen 1,2-oxidoreductase (decyclizing)
Comments: An iron protein. This enzyme catalyses a step in the pathway of phenylpropanoid compounds degradation.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
UM-BBD,
CAS registry number: 105503-63-7
References:
1. Dagley, S., Chapman, P.J. and Gibson, D.T. The metabolism of β-phenylpropionic acid by an Achromobacter. Biochem. J. 97 (1965) 643-650. [PMID: 5881653]
2. Lam, W. W. Y and Bugg, T. D. H. Chemistry of extradiol aromatic ring cleavage: isolation of a stable dienol ring fission intermediate and stereochemistry of its enzymatic hydrolytic clevage. J. Chem. Soc., Chem. Commun. 10 (1994) 1163-1164.
3. Díaz, E., Ferrández, A. and García, J.L. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180 (1998) 2915-2923. [PMID: 9603882]
EC 1.13.11.64
Accepted name: 5-nitrosalicylate dioxygenase
Reaction: 5-nitrosalicylate + O2 = 2-oxo-3-(5-oxofuran-2-ylidene)propanoate + nitrite (overall reaction)
Other name(s): naaB (gene name)
Systematic name: 5-nitrosalicylate:oxygen 1,2-oxidoreductase (decyclizing)
Comments: The enzyme, characterized from the soil bacterium Bradyrhizobium sp. JS329, is involved in the pathway of 5-nitroanthranilate degradation. It is unusual in being able to catalyse the ring fission without the requirement for prior removal of the nitro group. The product undergoes spontaneous lactonization, with concurrent elimination of the nitro group.
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]
2. Qu, Y. and Spain, J.C. Molecular and biochemical characterization of the 5-nitroanthranilic acid degradation pathway in Bradyrhizobium sp. strain JS329. J. Bacteriol. 193 (2011) 3057-3063. [PMID: 21498645]
*EC 1.14.13.39
Accepted name: nitric-oxide synthase (NADPH dependent)
Reaction: 2 L-arginine + 3 NADPH + 3 H+ + 4 O2 = 2 L-citrulline + 2 nitric oxide + 3 NADP+ + 4 H2O (overall reaction)
Other name(s): nitric oxide synthetase; endothelium-derived relaxation factor-forming enzyme; endothelium-derived relaxing factor synthase; NO synthase; NADPH-diaphorase
Systematic name: L-arginine,NADPH:oxygen oxidoreductase (nitric-oxide-forming)
Comments: Binds FAD, FMN, heme (iron protoporphyrin IX) and tetrahydrobiopterin. This eukaryotic enzyme, which is found in plants [4] and animals [1-3], consists of oxygenase and reductase domains that are linked via a regulatory calmodulin-binding domain. Upon calcium-induced calmodulin binding, the reductase and oxygenase domains form a complex, allowing electrons to flow from NADPH via FAD and FMN to the active center. May produce superoxide under certain conditions [3]. cf. EC 1.14.13.165, nitric-oxide synthase [NAD(P)H dependent].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 125978-95-2
References:
1. Bredt, D.S. and Snyder, S.H. Isolation of nitric oxide synthetase, a calmodulin-requiring enzyme. Proc. Natl. Acad. Sci. USA 87 (1990) 682-685. [PMID: 1689048]
2. Stuehr, D.J., Kwon, N.S., Nathan, C.F., Griffith, O.W., Feldman, P.L. and Wiseman, J. Nω-hydroxy-L-arginine is an intermediate in the biosynthesis of nitric oxide from L-arginine. J. Biol. Chem. 266 (1991) 6259-6263. [PMID: 1706713]
3. Stuehr, D., Pou, S. and Rosen, G.M. Oxygen reduction by nitric-oxide synthases. J. Biol. Chem. 276 (2001) 14533-14536. [PMID: 11279231]
4. Foresi, N., Correa-Aragunde, N., Parisi, G., Calo, G., Salerno, G. and Lamattina, L. Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent. Plant Cell 22 (2010) 3816-3830. [PMID: 21119059]
EC 1.14.13.163
Accepted name: 6-hydroxy-3-succinoylpyridine 3-monooxygenase
Reaction: 4-(6-hydroxypyridin-3-yl)-4-oxobutanoate + 2 NADH + 2 H+ + O2 = 2,5-dihydroxypyridine + succinate semialdehyde + 2 NAD+ + H2O
Glossary: 4-(6-hydroxypyridin-3-yl)-4-oxobutanoate = 6-hydroxy-3-succinoyl-pyridine
Other name(s): 6-hydroxy-3-succinoylpyridine hydroxylase; hspA (gene name); hspB (gene name)
Systematic name: 4-(6-hydroxypyridin-3-yl)-4-oxobutanoate,NADH:oxygen oxidoreductase (3-hydroxylating, succinate semialdehyde releasing)
Comments: The enzyme catalyses a reaction in the nicotine degradation pathway of Pseudomonas species. One of the enzymes from the soil bacterium Pseudomonas putida S16 contains an FAD cofactor [2].
References:
1. Tang, H., Wang, S., Ma, L., Meng, X., Deng, Z., Zhang, D., Ma, C. and Xu, P. A novel gene, encoding 6-hydroxy-3-succinoylpyridine hydroxylase, involved in nicotine degradation by Pseudomonas putida strain S16. Appl. Environ. Microbiol. 74 (2008) 1567-1574. [PMID: 18203859]
2. Tang, H., Yao, Y., Zhang, D., Meng, X., Wang, L., Yu, H., Ma, L. and Xu, P. A novel NADH-dependent and FAD-containing hydroxylase is crucial for nicotine degradation by Pseudomonas putida. J. Biol. Chem. 286 (2011) 39179-39187. [PMID: 21949128]
EC 1.14.13.165
Accepted name: nitric-oxide synthase [NAD(P)H-dependent]
Reaction: 2 L-arginine + 3 NAD(P)H + 3 H+ + 4 O2 = 2 L-citrulline + 2 nitric oxide + 3 NAD(P)+ + 4 H2O (overall reaction)
Other name(s): nitric oxide synthetase; NO synthase
Systematic name: L-arginine,NAD(P)H:oxygen oxidoreductase (nitric-oxide-forming)
Comments: Binds heme (iron protoporphyrin IX) and tetrahydrobiopterin. Most of the bacterial and archaeal enzymes consist of only an oxidase domain and function together with bacterial ferredoxins [1-2]. The enzyme from the δ-proteobacterium Sorangium cellulosum also includes a reductase domain that binds FAD, FMN and a [2Fe-2S] cluster [3]. The similar enzymes from plants and animals use only NADPH as acceptor (cf. EC 1.14.13.39).
References:
1. Wang, Z.Q., Lawson, R.J., Buddha, M.R., Wei, C.C., Crane, B.R., Munro, A.W. and Stuehr, D.J. Bacterial flavodoxins support nitric oxide production by Bacillus subtilis nitric-oxide synthase. J. Biol. Chem. 282 (2007) 2196-2202. [PMID: 17127770]
2. Gusarov, I., Starodubtseva, M., Wang, Z.Q., McQuade, L., Lippard, S.J., Stuehr, D.J. and Nudler, E. Bacterial nitric-oxide synthases operate without a dedicated redox partner. J. Biol. Chem. 283 (2008) 13140-13147. [PMID: 18316370]
3. Agapie, T., Suseno, S., Woodward, J.J., Stoll, S., Britt, R.D. and Marletta, M.A. NO formation by a catalytically self-sufficient bacterial nitric oxide synthase from Sorangium cellulosum. Proc. Natl. Acad. Sci. USA 106 (2009) 16221-16226. [PMID: 19805284]
EC 1.14.14.13
Accepted name: 4-(L-γ-glutamylamino)butanoyl-[BtrI acyl-carrier protein] monooxygenase
Reaction: 4-(L-γ-glutamylamino)butanoyl-[BtrI acyl-carrier protein] + FMNH2 + O2 = 4-(L-γ-glutamylamino)-(2S)-2-hydroxybutanoyl-[BtrI acyl-carrier protein] + FMN + H2O
Other name(s): btrO (gene name)
Systematic name: 4-(L-γ-glutamylamino)butanoyl-[BtrI acyl-carrier protein],FMN:oxygen oxidoreductase (2-hydroxylating)
Comments: Catalyses a step in the biosynthesis of the side chain of the aminoglycoside antibiotics of the butirosin family. FMNH2 is used as a free cofactor. Forms a complex with a dedicated NAD(P)H:FMN oxidoreductase. The enzyme is not able to hydroxylate free substrates, activation by the acyl-carrier protein is mandatory. Octanoyl-S-[BtrI acyl-carrier protein] is also accepted.
References:
1. Li, Y., Llewellyn, N.M., Giri, R., Huang, F. and Spencer, J.B. Biosynthesis of the unique amino acid side chain of butirosin: possible protective-group chemistry in an acyl carrier protein-mediated pathway. Chem. Biol. 12 (2005) 665-675. [PMID: 15975512]
[EC 1.14.15.2 Transferred entry: camphor 1,2-monooxygenase. Now EC 1.14.13.162, 2,5-diketocamphane 1,2-monooxygenase. (EC 1.14.15.2 created 1972, deleted 2012)]
*EC 1.14.18.1
Accepted name: tyrosinase
Reaction: (1) L-tyrosine + O2 = dopaquinone + H2O (overall reaction)
For diagram of reaction click here.
Other name(s): monophenol monooxygenase; phenolase; monophenol oxidase; cresolase; monophenolase; tyrosine-dopa oxidase; monophenol monooxidase; monophenol dihydroxyphenylalanine:oxygen oxidoreductase; N-acetyl-6-hydroxytryptophan oxidase; monophenol, dihydroxy-L-phenylalanine oxygen oxidoreductase; o-diphenol:O2 oxidoreductase; phenol oxidase
Systematic name: L-tyrosine,L-dopa:oxygen oxidoreductase
Comments: A type III copper protein found in a broad variety of bacteria, fungi, plants, insects, crustaceans, and mammals, which is involved in the synthesis of betalains and melanin. The enzyme, which is activated upon binding molecular oxygen, can catalyse both a monophenolase reaction cycle (reaction 1) or a diphenolase reaction cycle (reaction 2). During the monophenolase cycle, one of the bound oxygen atoms is transferred to a monophenol (such as L-tyrosine), generating an o-diphoenol intermediate, which is subsequently oxidized to an o-quinone and released, along with a water molecule. The enzyme remains in an inactive deoxy state, and is restored to the active oxy state by the binding of a new oxygen molecule. During the diphenolase cycle the enzyme binds an external diphenol molecule (such as L-dopa) and oxidizes it to an o-quinone that is released along with a water molecule, leaving the enzyme in the intermediate met state. The enzyme then binds a second diphenol molecule and repeats the process, ending in a deoxy state [7]. The second reaction is identical to that catalysed by the related enzyme catechol oxidase (EC 1.10.3.1). However, the latter can not catalyse the hydroxylation or monooxygenation of monophenols.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 9002-10-2
References:
1. Dawson, C.R. and Tarpley, W.B. The copper oxidases. In: Sumner, J.B. and Myrbäck, K. (Eds), The Enzymes, 1st edn, vol. 2, Academic Press, New York, 1951, pp. 454-498.
2. Patil, S.S. and Zucker, M. Potato phenolases. Purification and properties. J. Biol. Chem. 240 (1965) 3938-3943. [PMID: 5842066]
3. Pomerantz, S.H. Separation, purification, and properties of two tyrosinases from hamster melanoma. J. Biol. Chem. 238 (1963) 2351-2357. [PMID: 13972077]
4. Robb, D.A. `Tyrosinase. In: Lontie, R. (Ed.), Copper Proteins and Copper Enzymes, vol. 2, CRC Press, Boca Raton, FL, 1984, pp. 207-240.
5. Sanchez-Ferrer, A., Rodriguez-Lopez, J.N., Garcia-Canovas, F. and Garcia-Carmona, F. Tyrosinase: a comprehensive review of its mechanism. Biochim. Biophys. Acta 1247 (1995) 1-11. [PMID: 7873577]
6. Steiner, U., Schliemann, W. and Strack, D. Assay for tyrosine hydroxylation activity of tyrosinase from betalain-forming plants and cell cultures. Anal. Biochem. 238 (1996) 72-75. [PMID: 8660589]
7. Rolff, M., Schottenheim, J., Decker, H. and Tuczek, F. Copper-O2 reactivity of tyrosinase models towards external monophenolic substrates: molecular mechanism and comparison with the enzyme. Chem Soc Rev 40 (2011) 4077-4098. [PMID: 21416076]
*EC 1.21.3.6
Accepted name: aureusidin synthase
Reaction: (1) 2',4,4',6'-tetrahydroxychalcone 4'-O-β-D-glucoside + O2 = aureusidin 6-O-β-D-glucoside + H2O
For diagram of reaction click here.
Glossary: 2',4,4',6'-tetrahydroxychalcone = 3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
Other name(s): AmAS1
Systematic name: 2',4,4',6'-tetrahydroxychalcone 4'-O-β-D-glucoside:oxygen oxidoreductase
Comments: A copper-containing glycoprotein that plays a key role in the yellow coloration of flowers such as Antirrhinum majus (snapdragon). The enzyme is a homologue of plant polyphenol oxidase [1] and catalyses two separate chemical transformations, i.e. 3-hydroxylation and oxidative cyclization (2',-dehydrogenation). H2O2 activates reaction (1) but inhibits reaction (2). Originally considered to act on the phenol but now thought to mainly act on the 4'-O-β-D-glucoside in vivo [4].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 320784-48-3
References:
1. Nakayama, T., Yonekura-Sakakibara, K., Sato, T., Kikuchi, S., Fukui, Y., Fukuchi-Mizutani, M., Ueda, T., Nakao, M., Tanaka, Y., Kusumi, T. and Nishino, T. Aureusidin synthase: A polyphenol oxidase homolog responsible for flower coloration. Science 290 (2000) 1163-1166. [PMID: 11073455]
2. Nakayama, T., Sato, T., Fukui, Y., Yonekura-Sakakibara, K., Hayashi, H., Tanaka, Y., Kusumi, T. and Nishino, T. Specificity analysis and mechanism of aurone synthesis catalyzed by aureusidin synthase, a polyphenol oxidase homolog responsible for flower coloration. FEBS Lett. 499 (2001) 107-111. [PMID: 11418122]
3. Sato, T., Nakayama, T., Kikuchi, S., Fukui, Y., Yonekura-Sakakibara, K., Ueda, T., Nishino, T., Tanaka, Y. and Kusumi, T. Enzymatic formation of aurones in the extracts of yellow snapdragon flowers. Plant Sci. 160 (2001) 229-236. [PMID: 11164594]
4. Ono, E., Fukuchi-Mizutani, M., Nakamura, N., Fukui, Y., Yonekura-Sakakibara, K., Yamaguchi, M., Nakayama, T., Tanaka, T., Kusumi, T. and Tanaka, Y. Yellow flowers generated by expression of the aurone biosynthetic pathway. Proc. Natl. Acad. Sci. USA 103 (2006) 11075-11080. [PMID: 16832053]
*EC 2.1.1.127
Accepted name: [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase
Reaction: 3 S-adenosyl-L-methionine + [ribulose-1,5-bisphosphate carboxylase]-L-lysine = 3 S-adenosyl-L-homocysteine + [ribulose-1,5-bisphosphate carboxylase]-N6,N6,N6-trimethyl-L-lysine
Other name(s): rubisco methyltransferase; ribulose-bisphosphate-carboxylase/oxygenase N-methyltransferase; ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit εN-methyltransferase; S-adenosyl-L-methionine:[3-phospho-D-glycerate-carboxy-lyase (dimerizing)]-lysine 6-N-methyltransferase; RuBisCO methyltransferase; RuBisCO LSMT
Systematic name: S-adenosyl-L-methionine:[3-phospho-D-glycerate-carboxy-lyase (dimerizing)]-lysine N6-methyltransferase
Comments: The enzyme catalyses three successive methylations of Lys-14 in the large subunits of hexadecameric higher plant ribulose-bisphosphate-carboxylase (EC 4.1.1.39). Only the three methylated form is observed [3]. The enzyme from pea (Pisum sativum) also three-methylates a specific lysine in the chloroplastic isoforms of fructose-bisphosphate aldolase (EC 4.1.2.13) [5].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 139171-98-5
References:
1. Wang, P., Royer, M., Houtz, R.L. Affinity purification of ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit εN-methyltransferase. Protein Expr. Purif. 6 (1995) 528-536. [PMID: 8527940]
2. Ying, Z., Janney, N., Houtz, R.L. Organization and characterization of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit N-methyltransferase gene in tobacco. Plant Mol. Biol. 32 (1996) 663-672. [PMID: 8980518]
3. Dirk, L.M., Flynn, E.M., Dietzel, K., Couture, J.F., Trievel, R.C. and Houtz, R.L. Kinetic manifestation of processivity during multiple methylations catalyzed by SET domain protein methyltransferases. Biochemistry 46 (2007) 3905-3915. [PMID: 17338551]
4. Magnani, R., Nayak, N.R., Mazarei, M., Dirk, L.M. and Houtz, R.L. Polypeptide substrate specificity of PsLSMT. A set domain protein methyltransferase. J. Biol. Chem. 282 (2007) 27857-27864. [PMID: 17635932]
5. Mininno, M., Brugiere, S., Pautre, V., Gilgen, A., Ma, S., Ferro, M., Tardif, M., Alban, C. and Ravanel, S. Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as lysine-methylated proteins in plants. J. Biol. Chem. 287 (2012) 21034-21044. [PMID: 22547063]
EC 2.1.1.258
Accepted name: 5-methyltetrahydrofolate:corrinoid/iron-sulfur protein Co-methyltransferase
Reaction: a [methyl-Co(III) corrinoid Fe-S protein] + tetrahydrofolate = a [Co(I) corrinoid Fe-S protein] + 5-methyltetrahydrofolate
Other name(s): acsE (gene name)
Systematic name: 5-methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase
Comments: Catalyses the transfer of a methyl group from the N5 group of methyltetrahydrofolate to the 5-methoxybenzimidazolylcobamide cofactor of a corrinoid/Fe-S protein. Involved, together with EC 1.2.7.4, carbon-monoxide dehydrogenase (ferredoxin) and EC 2.3.1.169, CO-methylating acetyl-CoA synthase, in the reductive acetyl coenzyme A (Wood-Ljungdahl) pathway of autotrophic carbon fixation in various bacteria and archaea.
References:
1. Roberts, D.L., Zhao, S., Doukov, T. and Ragsdale, S.W. The reductive acetyl coenzyme A pathway: sequence and heterologous expression of active methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase from Clostridium thermoaceticum. J. Bacteriol. 176 (1994) 6127-6130. [PMID: 7928975]
2. Doukov, T., Seravalli, J., Stezowski, J.J. and Ragsdale, S.W. Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. Structure 8 (2000) 817-830. [PMID: 10997901]
3. Doukov, T.I., Hemmi, H., Drennan, C.L. and Ragsdale, S.W. Structural and kinetic evidence for an extended hydrogen-bonding network in catalysis of methyl group transfer. Role of an active site asparagine residue in activation of methyl transfer by methyltransferases. J. Biol. Chem. 282 (2007) 6609-6618. [PMID: 17172470]
EC 2.1.1.259
Accepted name: [fructose-bisphosphate aldolase]-lysine N-methyltransferase
Reaction: 3 S-adenosyl-L-methionine + [fructose-bisphosphate aldolase]-L-lysine = 3 S-adenosyl-L-homocysteine + [fructose-bisphosphate aldolase]-N6,N6,N6-trimethyl-L-lysine
Other name(s): rubisco methyltransferase; ribulose-bisphosphate-carboxylase/oxygenase N-methyltransferase; ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit εN-methyltransferase; S-adenosyl-L-methionine:[3-phospho-D-glycerate-carboxy-lyase (dimerizing)]-lysine 6-N-methyltransferase
Systematic name: S-adenosyl-L-methionine:[fructose-bisphosphate aldolase]-lysine N6-methyltransferase
Comments: The enzyme methylates a conserved lysine in the C-terminal part of higher plant fructose-bisphosphate aldolase (EC 4.1.2.13). The enzyme from pea (Pisum sativum) also methylates Lys-14 in the large subunits of hexadecameric higher plant ribulose-bisphosphate-carboxylase (EC 4.1.1.39) [2], but that from Arabidopsis thaliana does not.
References:
1. Magnani, R., Nayak, N.R., Mazarei, M., Dirk, L.M. and Houtz, R.L. Polypeptide substrate specificity of PsLSMT. A set domain protein methyltransferase. J. Biol. Chem. 282 (2007) 27857-27864. [PMID: 17635932]
2. Mininno, M., Brugiere, S., Pautre, V., Gilgen, A., Ma, S., Ferro, M., Tardif, M., Alban, C. and Ravanel, S. Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as lysine-methylated proteins in plants. J. Biol. Chem. 287 (2012) 21034-21044. [PMID: 22547063]
EC 2.3.1.199
Accepted name: very-long-chain 3-oxoacyl-CoA synthase
Reaction: a very-long-chain acyl-CoA + malonyl-CoA = a very-long-chain 3-oxoacyl-CoA + CO2 + coenzyme A
Glossary: a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.
Other name(s): very-long-chain 3-ketoacyl-CoA synthase; very-long-chain β-ketoacyl-CoA synthase; condensing enzyme; CUT1 (gene name); CER6 (gene name); FAE1 (gene name); KCS (gene name); ELO (gene name)
Systematic name: malonyl-CoA:very-long-chain acyl-CoA malonyltransferase (decarboxylating and thioester-hydrolysing)
Comments: This is the first component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long-chain acyl CoAs. Multiple forms exist with differing preferences for the substrate, and thus the specific form expressed determines the local composition of very-long-chain fatty acids [6,7]. For example, the FAE1 form from the plant Arabidopsis thaliana accepts only 16 and 18 carbon substrates, with oleoyl-CoA (18:1) being the preferred substrate [5], while CER6 from the same plant prefers substrates with chain length of C22 to C32 [4,8]. cf. EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, EC 4.2.1.134, very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase
References:
1. Toke, D.A. and Martin, C.E. Isolation and characterization of a gene affecting fatty acid elongation in Saccharomyces cerevisiae. J. Biol. Chem. 271 (1996) 18413-18422. [PMID: 8702485]
2. Oh, C.S., Toke, D.A., Mandala, S. and Martin, C.E. ELO2 and ELO3, homologues of the Saccharomyces cerevisiae ELO1 gene, function in fatty acid elongation and are required for sphingolipid formation. J. Biol. Chem. 272 (1997) 17376-17384. [PMID: 9211877]
3. Dittrich, F., Zajonc, D., Huhne, K., Hoja, U., Ekici, A., Greiner, E., Klein, H., Hofmann, J., Bessoule, J.J., Sperling, P. and Schweizer, E. Fatty acid elongation in yeast--biochemical characteristics of the enzyme system and isolation of elongation-defective mutants. Eur. J. Biochem. 252 (1998) 477-485. [PMID: 9546663]
4. Millar, A.A., Clemens, S., Zachgo, S., Giblin, E.M., Taylor, D.C. and Kunst, L. CUT1, an Arabidopsis gene required for cuticular wax biosynthesis and pollen fertility, encodes a very-long-chain fatty acid condensing enzyme. Plant Cell 11 (1999) 825-838. [PMID: 10330468]
5. Ghanevati, M. and Jaworski, J.G. Engineering and mechanistic studies of the Arabidopsis FAE1 β-ketoacyl-CoA synthase, FAE1 KCS. Eur. J. Biochem. 269 (2002) 3531-3539. [PMID: 12135493]
6. Blacklock, B.J. and Jaworski, J.G. Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases. Biochem. Biophys. Res. Commun. 346 (2006) 583-590. [PMID: 16765910]
7. Denic, V. and Weissman, J.S. A molecular caliper mechanism for determining very long-chain fatty acid length. Cell 130 (2007) 663-677. [PMID: 17719544]
8. Tresch, S., Heilmann, M., Christiansen, N., Looser, R. and Grossmann, K. Inhibition of saturated very-long-chain fatty acid biosynthesis by mefluidide and perfluidone, selective inhibitors of 3-ketoacyl-CoA synthases. Phytochemistry 76 (2012) 162-171. [PMID: 22284369]
EC 2.3.1.200
Accepted name: lipoyl amidotransferase
Reaction: [glycine cleavage system H]-N6-lipoyl-L-lysine + a [lipoyl-carrier protein] = glycine cleavage system H + a [lipoyl-carrier protein]-N6-lipoyl-L-lysine
Glossary: lipoic acid = 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid
Other name(s): LipL (gene name, ambiguous)
Systematic name: [glycine cleavage system H]-N6-lipoyl-L-lysine:[lipoyl-carrier protein]-N6-L-lysine lipoyltransferase
Comments: In the bacterium Listeria monocytogenes the enzyme takes part in a pathway for scavenging of lipoic acid. The enzyme is bound to 2-oxo-acid dehydrogenases such as the pyruvate dehydrogenase complex, where it transfers the lipoyl moiety from lipoyl-[glycine cleavage system H] to the E2 subunits of the complexes.
References:
1. Christensen, Q.H., Hagar, J.A., O'Riordan, M.X. and Cronan, J.E. A complex lipoate utilization pathway in Listeria monocytogenes. J. Biol. Chem. 286 (2011) 31447-31456. [PMID: 21768091]
EC 2.3.1.201
Accepted name: UDP-2-acetamido-3-amino-2,3-dideoxy-glucuronate N-acetyltransferase
Reaction: acetyl-CoA + UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucuronate = CoA + UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronate
Other name(s): WbpD; WlbB
Systematic name: acetyl-CoA:UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucuronate N-acetyltransferase
Comments: This enzyme participates in the biosynthetic pathway for UDP-α-D-ManNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronic acid), an important precursor of B-band lipopolysaccharide.
References:
1. Westman, E.L., McNally, D.J., Charchoglyan, A., Brewer, D., Field, R.A. and Lam, J.S. Characterization of WbpB, WbpE, and WbpD and reconstitution of a pathway for the biosynthesis of UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronic acid in Pseudomonas aeruginosa. J. Biol. Chem. 284 (2009) 11854-11862. [PMID: 19282284]
2. Larkin, A. and Imperiali, B. Biosynthesis of UDP-GlcNAc(3NAc)A by WbpB, WbpE, and WbpD: enzymes in the Wbp pathway responsible for O-antigen assembly in Pseudomonas aeruginosa PAO1. Biochemistry 48 (2009) 5446-5455. [PMID: 19348502]
EC 2.3.1.202
Accepted name: UDP-4-amino-4,6-dideoxy-N-acetyl-β-L-altrosamine N-acetyltransferase
Reaction: acetyl-CoA + UDP-4-amino-4,6-dideoxy-N-acetyl-β-L-altrosamine = CoA + UDP-2,4-bis(acetamido)-2,4,6-trideoxy-β-L-altropyranose
Other name(s): PseH
Systematic name: acetyl-CoA:UDP-4-amino-4,6-dideoxy-N-acetyl-β-L-altrosamine N-acetyltransferase
Comments: Isolated from Helicobacter pylori. The enzyme is involved in the biosynthesis of pseudaminic acid.
References:
1. Schoenhofen, I.C., McNally, D.J., Brisson, J.R. and Logan, S.M. Elucidation of the CMP-pseudaminic acid pathway in Helicobacter pylori: synthesis from UDP-N-acetylglucosamine by a single enzymatic reaction. Glycobiology 16 (2006) 8C-14C. [PMID: 16751642]
EC 2.3.1.203
Accepted name: UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine N-acetyltransferase
Reaction: acetyl-CoA + UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine = CoA + UDP-N,N'-diacetylbacillosamine
Glossary: UDP-N,N'-diacetylbacillosamine = UDP-2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose
Other name(s): PglD
Systematic name: acetyl-CoA:UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine N-acetyltransferase
Comments: The product, UDP-N,N'-diacetylbacillosamine, is an intermediate in protein glycosylation pathways in several bacterial species, including N-linked glycosylation of certain L-aspargine residues in Campylobacter species [1,2] and O-linked glycosylation of certain L-serine residues in Neisseria species [3].
References:
1. Olivier, N.B., Chen, M.M., Behr, J.R. and Imperiali, B. In vitro biosynthesis of UDP-N,N'-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system. Biochemistry 45 (2006) 13659-13669. [PMID: 17087520]
2. Rangarajan, E.S., Ruane, K.M., Sulea, T., Watson, D.C., Proteau, A., Leclerc, S., Cygler, M., Matte, A. and Young, N.M. Structure and active site residues of PglD, an N-acetyltransferase from the bacillosamine synthetic pathway required for N-glycan synthesis in Campylobacter jejuni. Biochemistry 47 (2008) 1827-1836. [PMID: 18198901]
3. Hartley, M.D., Morrison, M.J., Aas, F.E., Borud, B., Koomey, M. and Imperiali, B. Biochemical characterization of the O-linked glycosylation pathway in Neisseria gonorrhoeae responsible for biosynthesis of protein glycans containing N,N'-diacetylbacillosamine. Biochemistry 50 (2011) 4936-4948. [PMID: 21542610]
EC 2.3.2.19
Accepted name: ribostamycin:4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoyl-[BtrI acyl-carrier protein] 4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoate transferase
Reaction: 4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoyl-[BtrI acyl-carrier protein] + ribostamycin = γ-L-glutamyl-butirosin B + BtrI acyl-carrier protein
Other name(s): btrH (gene name)
Systematic name: ribostamycin:4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoyl-[BtrI acyl-carrier protein] 4-(γ-L-glutamylamino)-(S)-2-hydroxybutanoate transferase
Comments: The enzyme attaches the side chain of the aminoglycoside antibiotics of the butirosin family. The side chain confers resistance against several aminoglycoside-modifying enzymes.
References:
1. Llewellyn, N.M., Li, Y. and Spencer, J.B. Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain. Chem. Biol. 14 (2007) 379-386. [PMID: 17462573]
*EC 2.4.1.60
Accepted name: abequosyltransferase
Reaction: CDP-D-abequose + α-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-β-D-galactopyranosyl-diphosphodecaprenol = CDP + α-D-abequopyranosyl-(1→3)-α-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-β-D-galactopyranosyl-diphosphodecaprenol
Glossary: abequose = 3,6-deoxy-D-xylo-hexose = 3,6-deoxy-D-galactose = 3-deoxy-D-fucose
Other name(s): trihexose diphospholipid abequosyltransferase
Systematic name: CDP-D-abequose:Man(α1→4)Rha(α1→3)Gal(β-1)-diphospholipid D-abequosyltransferase
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 37277-67-1
References:
1. Osborn, M.J. and Weiner, I.M. Biosynthesis of a bacterial lipopolysaccharide. VI. Mechanism of incorporation of abequose into the O-antigen of Salmonella typhimurium. J. Biol. Chem. 243 (1968) 2631-2639. [PMID: 4297268]
2. Liu, D., Lindqvist, L. and Reeves, P.R. Transferases of O-antigen biosynthesis in Salmonella enterica: dideoxyhexosyltransferases of groups B and C2 and acetyltransferase of group C2. J. Bacteriol. 177 (1995) 4084-4088. [PMID: 7541787]
*EC 2.4.1.131
Accepted name: GDP-Man:Man3GlcNAc2-PP-dolichol α-1,2-mannosyltransferase
Reaction: 2 GDP-α-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 = 2 GDP + 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
For diagram of reaction click here.
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; GDP-mannose:glycolipid 2-α-D-mannosyltransferase; GDP-Man:Man3GlcNAc2-PP-Dol α-1,2-mannosyltransferase
Systematic name: GDP-α-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 2-α-D-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 2.4.1.202
Accepted name: 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one 2-D-glucosyltransferase
Reaction: (1) UDP-α-D-glucose + 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one = UDP + (2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside
For diagram of reaction click here.
Glossary: 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one = DIBOA
Other name(s): uridine diphosphoglucose-2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one 2-glucosyltransferase; BX8; BX9; benzoxazinoid glucosyltransferase; DIMBOA glucosyltransferase
Systematic name: UDP-α-D-glucose:2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one 2-β-D-glucosyltransferase
Comments: The enzyme is involved in the detoxification of the benzoxazinoids DIBOA (2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one) and DIMBOA (2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one) which are stored as the respective non-toxic glucosides in the vacuoles in some plants, most commonly from the family of Poaceae (grasses). Benzoxazinoids are known to exhibit antimicrobial, antifeedant, and antiinsecticidal effects and are involved in the interaction of plants with other plants, insects, or microorganisms.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 122544-56-3
References:
1. Bailey, B.A. and Larson, R.L. Hydroxamic acid glucosyltransferases from maize seedlings. Plant Physiol. 90 (1989) 1071-1076. [PMID: 16666853]
2. von Rad, U., Huttl, R., Lottspeich, F., Gierl, A. and Frey, M. Two glucosyltransferases are involved in detoxification of benzoxazinoids in maize. Plant J. 28 (2001) 633-642. [PMID: 11851909]
*EC 2.4.1.256
Accepted name: dolichyl-P-Glc:Glc2Man9GlcNAc2-PP-dolichol α-1,2-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
For diagram of reaction click here.
Other name(s): ALG10; Dol-P-Glc:Glc2Man9GlcNAc2-PP-Dol α-1,2-glucosyltransferase
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 2-α-D-glucosyltransferase
Comments: This eukaryotic 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. The lipid-linked oligosaccharide is involved in N-linked protein glycosylation of selected asparagine residues of nascent polypeptide chains in eukaryotic cells.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number:
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 2.4.1.257
Accepted name: GDP-Man:Man2GlcNAc2-PP-dolichol 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
For diagram of reaction click here.
Other name(s): GDP-Man:Man2GlcNAc2-PP-Dol α-1,6-mannosyltransferase; 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].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number:
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 2.4.1.261
Accepted name: dolichyl-P-Man:Man8GlcNAc2-PP-dolichol 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
For diagram of reaction click here.
Other name(s): ALG9; ALG9 α1,2 mannosyltransferase; dolichylphosphomannose-dependent ALG9 mannosyltransferase; ALG9 mannosyltransferase; Dol-P-Man:Man8GlcNAc2-PP-Dol α-1,2-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 2-α-D-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).
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number:
References:
1. Vleugels, W., Keldermans, L., Jaeken, J., Butters, T.D., Michalski, J.C., Matthijs, G. and Foulquier, F. Quality control of glycoproteins bearing truncated glycans in an ALG9-defective (CDG-IL) patient. Glycobiology 19 (2009) 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 2.4.1.282
Accepted name: 3-O-α-D-glucosyl-L-rhamnose phosphorylase
Reaction: 3-O-α-D-glucopyranosyl-L-rhamnopyranose + phosphate = L-rhamnopyranose + β-D-glucose 1-phosphate
Other name(s): cphy1019 (gene name)
Systematic name: 3-O-α-D-glucopyranosyl-L-rhamnopyranose:phosphate β-D-glucosyltransferase
Comments: The enzyme does not phosphorylate α,α-trehalose, kojibiose, nigerose, or maltose. In the reverse phosphorolysis reaction the enzyme is specific for L-rhamnose as acceptor and β-D-glucose 1-phosphate as donor.
References:
1. Nihira, T., Nakai, H. and Kitaoka, M. 3-O-α-D-Glucopyranosyl-L-rhamnose phosphorylase from Clostridium phytofermentans. Carbohydr. Res. 350 (2012) 94-97. [PMID: 22277537]
EC 2.4.1.283
Accepted name: 2-deoxystreptamine N-acetyl-D-glucosaminyltransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + 2-deoxystreptamine = UDP + 2'-N-acetylparomamine
Other name(s): btrM (gene name); neoD (gene name); kanF (gene name)
Systematic name: UDP-N-acetyl-α-D-glucosamine:2-deoxystreptamine N-acetyl-D-glucosaminyltransferase
Comments: Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin, butirosin, neomycin and ribostamycin. Unlike the enzyme from the bacterium Streptomyces kanamyceticus, which can also accept UDP-D-glucose [2] (cf. EC 2.4.1.284, 2-deoxystreptamine glucosyltransferase), the enzyme from Bacillus circulans can only accept UDP-N-acetyl-α-D-glucosamine [1].
References:
1. Yokoyama, K., Yamamoto, Y., Kudo, F. and Eguchi, T. Involvement of two distinct N-acetylglucosaminyltransferases and a dual-function deacetylase in neomycin biosynthesis. ChemBioChem. 9 (2008) 865-869. [PMID: 18311744]
2. Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843-852. [PMID: 21983602]
EC 2.4.1.284
Accepted name: 2-deoxystreptamine glucosyltransferase
Reaction: UDP-α-D-glucose + 2-deoxystreptamine = UDP + 2'-deamino-2'-hydroxyparomamine
Glossary: 2'-deamino-2'-hydroxyparomamine = 4-O-α-D-glucopyranosyl-2-deoxy-D-streptamine
Other name(s): kanF (gene name)
Systematic name: UDP-α-D-glucose:2-deoxystreptamine 6-α-D-glucosyltransferase
Comments: Involved in the biosynthesis of kanamycin B and kanamycin C. Also catalyses EC 2.4.1.283, 2-deoxystreptamine N-acetyl-D-glucosaminyltransferase, but activity is only one fifth of that with UDP-α-D-glucose.
References:
1. Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843-852. [PMID: 21983602]
EC 2.4.1.285
Accepted name: UDP-GlcNAc:ribostamycin N-acetylglucosaminyltransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + ribostamycin = UDP + 2′′′-acetyl-6′′′-hydroxyneomycin C
Other name(s): neoK (gene name)
Systematic name: UDP-N-acetyl-α-D-glucosamine:ribostamycin N-acetylglucosaminyltransferase
Comments: Involved in biosynthesis of the aminoglycoside antibiotic neomycin. Requires a divalent metal ion, optimally Mg2+, Mn2+ or Co2+.
References:
1. Yokoyama, K., Yamamoto, Y., Kudo, F. and Eguchi, T. Involvement of two distinct N-acetylglucosaminyltransferases and a dual-function deacetylase in neomycin biosynthesis. ChemBioChem. 9 (2008) 865-869. [PMID: 18311744]
EC 2.4.1.286
Accepted name: chalcone 4'-O-glucosyltransferase
Reaction: (1) UDP-α-D-glucose + 2',4,4',6'-tetrahydroxychalcone = UDP + 2',4,4',6'-tetrahydroxychalcone 4'-O-β-D-glucoside
For diagram of reaction click here.
Glossary: 2',4,4',6'-tetrahydroxychalcone = 3-(4-hydroxyphemyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
Other name(s): 4’CGT
Systematic name: UDP-α-D-glucose:2',4,4',6'-tetrahydroxychalcone 4'-O-β-D-glucosyltransferase
Comments: Isolated from the plant Antirrhinum majus (snapdragon). Involved in the biosynthesis of aurones, plant flavonoids that provide yellow color to the flowers.
References:
1. Ono, E., Fukuchi-Mizutani, M., Nakamura, N., Fukui, Y., Yonekura-Sakakibara, K., Yamaguchi, M., Nakayama, T., Tanaka, T., Kusumi, T. and Tanaka, Y. Yellow flowers generated by expression of the aurone biosynthetic pathway. Proc. Natl. Acad. Sci. USA 103 (2006) 11075-11080. [PMID: 16832053]
EC 2.4.1.287
Accepted name: rhamnopyranosyl-N-acetylglucosaminyl-diphospho-decaprenol β-1,3/1,4-galactofuranosyltransferase
Reaction: 2 UDP-α-D-galactofuranose + α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol = 2 UDP + β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol (overall reaction)
Other name(s): arabinogalactan galactofuranosyl transferase 1; GlfT1
Systematic name: UDP-α-D-galactofuranose:α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol 3-β/4-β-galactofuranosyltransferase
Comments: Isolated from Mycobacterium tuberculosis and M. smegmatis, the enzyme has dual β-(1→4) and β-(1→5) transferase action. Involved in the formation of the cell wall in mycobacteria.
References:
1. Mikusová, K., Belánová, M., Korduláková, J., Honda, K., McNeil, M.R., Mahapatra, S., Crick, D.C. and Brennan, P.J. Identification of a novel galactosyl transferase involved in biosynthesis of the mycobacterial cell wall. J. Bacteriol. 188 (2006) 6592-6598. [PMID: 16952951]
2. Belánová, M., Dianisková, P., Brennan, P.J., Completo, G.C., Rose, N.L., Lowary, T.L. and Mikusová, K. Galactosyl transferases in mycobacterial cell wall synthesis. J. Bacteriol. 190 (2008) 1141-1145. [PMID: 18055597]
EC 2.4.1.288
Accepted name: galactofuranosylgalactofuranosylrhamnosyl-N-acetylglucosaminyl-diphospho-decaprenol β-1,5/1,6-galactofuranosyltransferase
Reaction: 28 UDP-α-D-galactofuranose + β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol = 28 UDP + [β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→6)]14-β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol
Other name(s): GlfT2
Systematic name: UDP-α-D-galactofuranose:β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol 4-β/5-β-D-galactofuranosyltransferase
Comments: Isolated from Mycobacterium tuberculosis. The enzyme adds approximately twenty-eight galactofuranosyl residues with alternating 1→5 and 1→6 links forming a galactan domain with approximately thirty galactofuranosyl residues. Involved in the formation of the cell wall in mycobacteria.
References:
1. Rose, N.L., Zheng, R.B., Pearcey, J., Zhou, R., Completo, G.C. and Lowary, T.L. Development of a coupled spectrophotometric assay for GlfT2, a bifunctional mycobacterial galactofuranosyltransferase. Carbohydr. Res. 343 (2008) 2130-2139. [PMID: 18423586]
2. May, J.F., Splain, R.A., Brotschi, C. and Kiessling, L.L. A tethering mechanism for length control in a processive carbohydrate polymerization. Proc. Natl. Acad. Sci. USA 106 (2009) 11851-11856. [PMID: 19571009]
3. Wheatley, R.W., Zheng, R.B., Richards, M.R., Lowary, T.L. and Ng, K.K. Tetrameric structure of GlfT2 reveals a scaffold for the assembly of mycobacterial arabinogalactan. J. Biol. Chem. (2012) . [PMID: 22707726]
EC 2.4.2.45
Accepted name: decaprenyl-phosphate phosphoribosyltransferase
Reaction: trans,octacis-decaprenyl phosphate + 5-phospho-α-D-ribose 1-diphosphate = trans,octacis-decaprenylphospho-β-D-ribofuranose 5-phosphate + diphosphate
Other name(s): 5-phospho-α-D-ribose-1-diphosphate:decaprenyl-phosphate 5-phosphoribosyltransferase; 5-phospho-α-D-ribose 1-pyrophosphate:decaprenyl phosphate 5-phosphoribosyltransferase; DPPR synthase; Rv3806
Systematic name: trans,octacis-decaprenylphospho-β-D-ribofuranose 5-phosphate:diphosphate phospho-α-D-ribosyltransferase
Comments: Requires Mg2+. Isolated from Mycobacterium tuberculosis. Has some activity with other polyprenyl phosphates.
References:
1. Huang, H., Scherman, M.S., D'Haeze, W., Vereecke, D., Holsters, M., Crick, D.C. and McNeil, M.R. Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-α-D-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-D-arabinose synthesis. J. Biol. Chem. 280 (2005) 24539-24543. [PMID: 15878857]
EC 2.4.2.46
Accepted name: galactan 5-O-arabinofuranosyltransferase
Reaction: Adds an α-D-arabinofuranosyl group from trans,octacis-decaprenylphospho-β-D-arabinofuranose at the 5-O-position of the eighth, tenth and twelfth galactofuranose unit of the galactofuranan chain of [β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→6)]14-β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol
Other name(s): AftA; Rv3792
Systematic name: galactofuranan:trans,octacis-decaprenylphospho-β-D-arabinofuranose 5-O-α-D-arabinofuranosyltransferase
Comments: Isolated from Mycobacterium tuberculosis and Corynebacterium glutamicum. These arabinofuranosyl groups form the start of an arabinofuranan chain as part of the of the cell wall in mycobacteria.
References:
1. Alderwick, L.J., Seidel, M., Sahm, H., Besra, G.S. and Eggeling, L. Identification of a novel arabinofuranosyltransferase (AftA) involved in cell wall arabinan biosynthesis in Mycobacterium tuberculosis. J. Biol. Chem. 281 (2006) 15653-15661. [PMID: 16595677]
EC 2.4.2.47
Accepted name: arabinofuranan 3-O-arabinosyltransferase
Reaction: Adds an α-D-arabinofuranosyl group from trans,octacis-decaprenylphospho-β-D-arabinofuranose at the 3-O-position of an α-(1→5)-arabinofuranan chain attached to a β-(1→5)-galactofuranan chain
Other name(s): AftC
Systematic name: α-(1→5)-arabinofuranan:trans,octacis-decaprenylphospho-β-D-arabinofuranose 3-O-α-D-arabinofuranosyltransferase
Comments: Isolated from Mycobacterium smegmatis. Involved in the formation of the cell wall in mycobacteria.
References:
1. Birch, H.L., Alderwick, L.J., Bhatt, A., Rittmann, D., Krumbach, K., Singh, A., Bai, Y., Lowary, T.L., Eggeling, L. and Besra, G.S. Biosynthesis of mycobacterial arabinogalactan: identification of a novel α(1-→3) arabinofuranosyltransferase. Mol. Microbiol. 69 (2008) 1191-1206. [PMID: 18627460]
2. Zhang, J., Angala, S.K., Pramanik, P.K., Li, K., Crick, D.C., Liav, A., Jozwiak, A., Swiezewska, E., Jackson, M. and Chatterjee, D. Reconstitution of functional mycobacterial arabinosyltransferase AftC proteoliposome and assessment of decaprenylphosphorylarabinose analogues as arabinofuranosyl donors. ACS Chem. Biol. 6 (2011) 819-828. [PMID: 21595486]
EC 2.4.99.17
Accepted name: S-adenosylmethionine:tRNA ribosyltransferase-isomerase
Reaction: S-adenosyl-L-methionine + 7-aminomethyl-7-carbaguanosine34 in tRNA = L-methionine + adenine + epoxyqueuosine34 in tRNA
Glossary: 7-aminomethyl-7-carbaguanine = 7-aminomethyl-7-deazaguanine = preQ1
Other name(s): QueA enzyme; queuosine biosynthesis protein QueA
Systematic name: S-adenosyl-L-methionine:7-aminomethyl-7-deazaguanosine ribosyltransferase (ribosyl isomerizing; L-methionine, adenine releasing)
Comments: The reaction is a combined transfer and isomerization of the ribose moiety of S-adenosyl-L-methionine to the modified guanosine base in the wobble position in tRNAs specific for Tyr, His, Asp or Asn. It is part of the queuosine biosynthesis pathway.
References:
1. Slany, R.K., Bosl, M., Crain, P.F. and Kersten, H. A new function of S-adenosylmethionine: the ribosyl moiety of AdoMet is the precursor of the cyclopentenediol moiety of the tRNA wobble base queuine. Biochemistry 32 (1993) 7811-7817. [PMID: 8347586]
2. Slany, R.K., Bosl, M. and Kersten, H. Transfer and isomerization of the ribose moiety of AdoMet during the biosynthesis of queuosine tRNAs, a new unique reaction catalyzed by the QueA protein from Escherichia coli. Biochimie 76 (1994) 389-393. [PMID: 7849103]
3. Kinzie, S.D., Thern, B. and Iwata-Reuyl, D. Mechanistic studies of the tRNA-modifying enzyme QueA: a chemical imperative for the use of AdoMet as a "ribosyl" donor. Org. Lett. 2 (2000) 1307-1310. [PMID: 10810734]
4. Van Lanen, S.G. and Iwata-Reuyl, D. Kinetic mechanism of the tRNA-modifying enzyme S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). Biochemistry 42 (2003) 5312-5320. [PMID: 12731872]
5. Mathews, I., Schwarzenbacher, R., McMullan, D., Abdubek, P., Ambing, E., Axelrod, H., Biorac, T., Canaves, J.M., Chiu, H.J., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Hornsby, M., Jaroszewski, L., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., Miller, M.D., Moy, K., Nigoghossian, E., Ouyang, J., Paulsen, J., Quijano, K., Reyes, R., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J. and Wilson, I.A. Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 Å resolution reveals a new fold. Proteins 59 (2005) 869-874. [PMID: 15822125]
6. Grimm, C., Ficner, R., Sgraja, T., Haebel, P., Klebe, G. and Reuter, K. Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase. Biochem. Biophys. Res. Commun. 351 (2006) 695-701. [PMID: 17083917]
EC 2.6.1.93
Accepted name: neamine transaminase
Reaction: neamine + 2-oxoglutarate = 6'-dehydroparomamine + L-glutamate
Other name(s): glutamate—6'-dehydroparomamine aminotransferase; btrB (gene name); neoN (gene name); kacL (gene name)
Systematic name: neamine:2-oxoglutarate aminotransferase
Comments: The reaction occurs in vivo in the opposite direction. Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin B, butirosin, neomycin and ribostamycin. Works in combination with EC 1.1.3.43, paromamine 6-oxidase, to replace the 6'-hydroxy group of paromamine with an amino group. The enzyme from the bacterium Streptomyces kanamyceticus can also catalyse EC 2.6.1.94, 2'-deamino-2'-hydroxyneamine transaminase, which leads to production of kanamycin A [3]. The enzyme from the bacterium Streptomyces fradiae can also catalyse EC 2.6.1.95, leading to production of neomycin C [2].
References:
1. Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem. 8 (2007) 283-288. [PMID: 17206729]
2. Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6'-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642-651. [PMID: 21689223]
3. Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843-852. [PMID: 21983602]
EC 2.6.1.94
Accepted name: 2'-deamino-2'-hydroxyneamine transaminase
Reaction: 2'-deamino-2'-hydroxyneamine + 2-oxoglutarate = 2'-deamino-2'-hydroxy-6'-dehydroparomamine + L-glutamate
Other name(s): kacL (gene name)
Systematic name: 2'-deamino-2'-hydroxyneamine:2-oxoglutarate aminotransferase
Comments: The reaction occurs in vivo in the opposite direction. Involved in the biosynthetic pathway of kanamycin A and kanamycin D. The enzyme, characterized from the bacterium Streptomyces kanamyceticus, can also catalyse EC 2.6.1.93, neamine transaminase.
References:
1. Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843-852. [PMID: 21983602]
EC 2.6.1.95
Accepted name: neomycin C transaminase
Reaction: neomycin C + 2-oxoglutarate = 6′′′-deamino-6′′′-oxoneomycin C + L-glutamate
Other name(s): neoN (gene name)
Systematic name: 2-oxoglutarate:neomycin C aminotransferase
Comments: The reaction occurs in vivo in the opposite direction. Involved in the biosynthetic pathway of aminoglycoside antibiotics of the neomycin family. Works in combination with EC 1.1.3.44, 6′′′-hydroxyneomycin C oxidase, to replace the 6′′′-hydroxy group of 6′′′-deamino-6′′′-hydroxyneomycin C with an amino group. The enzyme, characterized from the bacterium Streptomyces fradiae, can also catalyse EC 2.6.1.93, neamine transaminase.
References:
1. Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem. 8 (2007) 283-288. [PMID: 17206729]
2. Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6'-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642-651. [PMID: 21689223]
*EC 2.7.1.31
Accepted name: glycerate 3-kinase
Reaction: ATP + D-glycerate = ADP + 3-phospho-D-glycerate
Other name(s): glycerate kinase (phosphorylating) (ambiguous); D-glycerate 3-kinase; D-glycerate kinase (ambiguous); glycerate-kinase (ambiguous); GK (ambiguous); D-glyceric acid kinase (ambiguous); ATP:(R)-glycerate 3-phosphotransferase
Systematic name: ATP:D-glycerate 3-phosphotransferase
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 9026-61-3
References:
1. Doughty, C.C., Hayashi, J.A. and Guenther, H.L. Purification and properties of D-glycerate 3-kinase from Escherichia coli. J. Biol. Chem. 241 (1966) 568-572. [PMID: 5325263]
2. Ichihara, A. and Greenberg, D.M. Studies on the purification and properties of D-glyceric acid kinase of liver. J. Biol. Chem. 225 (1957) 949-958. [PMID: 13416296]
EC 2.7.1.177
Accepted name: L-threonine kinase
Reaction: ATP + L-threonine = ADP + O-phospho-L-threonine
For diagram of reaction click here.
Other name(s): PduX
Systematic name: ATP:L-threonine O3-phosphotransferase
Comments: The enzyme is involved in the de novo synthesis of adenosylcobalamin. It is specific for ATP and free L-threonine. In the bacterium Salmonella enterica the activity with CTP, GTP, or UTP is 6, 11, and 3% of the activity with ATP.
References:
1. Fan, C. and Bobik, T.A. The PduX enzyme of Salmonella enterica is an L-threonine kinase used for coenzyme B12 synthesis. J. Biol. Chem. 283 (2008) 11322-11329. [PMID: 18308727]
2. Fan, C., Fromm, H.J. and Bobik, T.A. Kinetic and functional analysis of L-threonine kinase, the PduX enzyme of Salmonella enterica. J. Biol. Chem. 284 (2009) 20240-20248. [PMID: 19509296]
EC 2.7.4.26
Accepted name: isopentenyl phosphate kinase
Reaction: ATP + isopentenyl phosphate = ADP + isopentenyl diphosphate
Systematic name: ATP:isopentenyl phosphate phosphotransferase
Comments: The enzyme is involved in the mevalonate pathway in Archaea [1]. The activity has also been identified in the plant Mentha piperita (peppermint) [2]. It is strictly specific for ATP but can use other phosphate acceptors such as dimethylallyl phosphate, geranyl phosphate, or fosfomycin.
References:
1. Grochowski, L.L., Xu, H. and White, R.H. Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate. J. Bacteriol. 188 (2006) 3192-3198. [PMID: 16621811]
2. Lange, B.M. and Croteau, R. Isopentenyl diphosphate biosynthesis via a mevalonate-independent pathway: isopentenyl monophosphate kinase catalyzes the terminal enzymatic step. Proc. Natl. Acad. Sci. USA 96 (1999) 13714-13719. [PMID: 10570138]
3. Chen, M. and Poulter, C.D. Characterization of thermophilic archaeal isopentenyl phosphate kinases. Biochemistry 49 (2010) 207-217. [PMID: 19928876]
4. Mabanglo, M.F., Schubert, H.L., Chen, M., Hill, C.P. and Poulter, C.D. X-ray structures of isopentenyl phosphate kinase. ACS Chem. Biol. 5 (2010) 517-527. [PMID: 20402538]
EC 2.7.8.35
Accepted name: UDP-N-acetylglucosamine—decaprenyl-phosphate N-acetylglucosaminephosphotransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + trans,octacis-decaprenyl phosphate = UMP + N-acetyl-α-D-glucosaminyl-diphospho-trans,octacis-decaprenol
Other name(s): GlcNAc-1-phosphate transferase; UDP-GlcNAc:undecaprenyl phosphate GlcNAc-1-phosphate transferase; WecA; WecA transferase
Systematic name: UDP-N-acetyl-α-D-glucosamine:trans,octacis-decaprenyl-phosphate N-acetylglucosaminephosphotransferase
Comments: Isolated from Mycobacterium tuberculosis and Mycobacterium smegmatis. This enzyme catalyses the synthesis of monotrans,octacis-decaprenyl-N-acetyl-α-D-glucosaminyl diphosphate (mycobacterial lipid I), an essential lipid intermediate for the biosynthesis of various bacterial cell envelope components. cf. EC 2.7.8.33, UDP-GlcNAc:undecaprenyl-phosphate GlcNAc-1-phosphate transferase.
References:
1. Jin, Y., Xin, Y., Zhang, W. and Ma, Y. Mycobacterium tuberculosis Rv1302 and Mycobacterium smegmatis MSMEG_4947 have WecA function and MSMEG_4947 is required for the growth of M. smegmatis. FEMS Microbiol. Lett. 310 (2010) 54-61. [PMID: 20637039]
EC 3.1.1.91
Accepted name: 2-oxo-3-(5-oxofuran-2-ylidene)propanoate lactonase
Reaction: 2-oxo-3-(5-oxofuran-2-ylidene)propanoate + H2O = maleylpyruvate
Other name(s): naaC (gene name)
Systematic name: 2-oxo-3-(5-oxofuran-2-ylidene)propanoate lactonohydrolase
Comments: This enzyme, characterized from the soil bacterium Bradyrhizobium sp. JS329, is involved in the pathway of 5-nitroanthranilate degradation.
References:
1. Qu, Y. and Spain, J.C. Molecular and biochemical characterization of the 5-nitroanthranilic acid degradation pathway in Bradyrhizobium sp. strain JS329. J. Bacteriol. 193 (2011) 3057-3063. [PMID: 21498645]
EC 3.1.1.92
Accepted name: 4-sulfomuconolactone hydrolase
Reaction: 4-sulfomuconolactone + H2O = maleylacetate + sulfite
Glossary: 4-sulfomuconolactone = 4-carboxymethylen-4-sulfobut-2-en-olide = 2-(5-oxo-2-sulfo-2,5-dihydrofuran-2-yl)acetic acid
Systematic name: 4-sulfomuconolactone sulfohydrolase
Comments: The enzyme was isolated from the bacteria Hydrogenophaga intermedia and Agrobacterium radiobacter S2. It catalyses a step in the degradation of 4-sulfocatechol.
References:
1. Halak, S., Basta, T., Burger, S., Contzen, M., Wray, V., Pieper, D.H. and Stolz, A. 4-sulfomuconolactone hydrolases from Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2. J. Bacteriol. 189 (2007) 6998-7006. [PMID: 17660282]
EC 3.1.1.93
Accepted name: mycophenolic acid acyl-glucuronide esterase
Reaction: mycophenolic acid O-acyl-glucuronide + H2O = mycophenolate + D-glucuronate
Glossary: mycophenolate = (4E)-6-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)-4-methylhex-4-enoate
Other name(s): mycophenolic acid acyl-glucuronide deglucuronidase; AcMPAG deglucuronidase
Systematic name: mycophenolic acid O-acyl-glucuronide-ester hydrolase
Comments: This liver enzyme deglucuronidates mycophenolic acid O-acyl-glucuronide, a metabolite of the immunosuppressant drug mycophenolate that is thought to be immunotoxic.
References:
1. Iwamura, A., Fukami, T., Higuchi, R., Nakajima, M. and Yokoi, T. Human α/β hydrolase domain containing 10 (ABHD10) is responsible enzyme for deglucuronidation of mycophenolic acid acyl-glucuronide in liver. J. Biol. Chem. 287 (2012) 9240-9249. [PMID: 22294686]
EC 3.1.3.88
Accepted name: 5"-phosphoribostamycin phosphatase
Reaction: 5"-phosphoribostamycin + H2O = ribostamycin + phosphate
Other name(s): btrP (gene name); neoI (gene name)
Systematic name: 5"-phosphoribostamycin phosphohydrolase
Comments: Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including ribostamycin, neomycin and butirosin. No metal is required for activity.
References:
1. Kudo, F., Fujii, T., Kinoshita, S. and Eguchi, T. Unique O-ribosylation in the biosynthesis of butirosin. Bioorg. Med. Chem. 15 (2007) 4360-4368. [PMID: 17482823]
*EC 3.2.1.89
Accepted name: arabinogalactan endo-β-1,4-galactanase
Reaction: The enzyme specifically hydrolyses (1→4)-β-D-galactosidic linkages in type I arabinogalactans.
Other name(s): endo-1,4-β-galactanase; galactanase (ambiguous); arabinogalactanase; ganB (gene name)
Systematic name: arabinogalactan 4-β-D-galactanohydrolase
Comments: This enzyme, isolated from the bacterium Bacillus subtilis, hydrolyses the β(1→4) bonds found in type I plant arabinogalactans, which are a component of the primary cell walls of dicots. The predominant product is a tetrasaccharide. cf. EC 3.2.1.181, galactan endo-β-1,3-galactanase.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 58182-40-4
References:
1. Emi, S. and Yamamoto, T. Purification and properties of several galactanases of Bacillus subtilis var. amylosacchariticus. Agric. Biol. Chem. 36 (1972) 1945-1954.
2. Labavitch, J.M., Freeman, L.E. and Albersheim, P. Structure of plant cell walls. Purification and characterization of a β-1,4-galactanase which degrades a structural component of the primary cell walls of dicots. J. Biol. Chem. 251 (1976) 5904-5910. [PMID: 823153]
3. Shipkowski, S. and Brenchley, J.E. Bioinformatic, genetic, and biochemical evidence that some glycoside hydrolase family 42 β-galactosidases are arabinogalactan type I oligomer hydrolases. Appl. Environ. Microbiol. 72 (2006) 7730-7738. [PMID: 17056685]
EC 3.2.1.181
Accepted name: galactan endo-β-1,3-galactanase
Reaction: The enzyme specifically hydrolyses β-1,3-galactan and β-1,3-galactooligosaccharides
Other name(s): endo-β-1,3-galactanase
Systematic name: arabinogalactan 3-β-D-galactanohydrolase
Comments: The enzyme from the fungus Flammulina velutipes (winter mushroom) hydrolyses the β(1→3) bonds found in type II plant arabinogalactans, which occur in cell walls of dicots and cereals. The enzyme is an endohydrolase, and requires at least 3 contiguous β-1,3-residues. cf. EC 3.2.1.89, arabinogalactan endo-β-1,4-galactanase and EC 3.2.1.145, galactan 1,3-β-galactosidase.
References:
1. Kotake, T., Hirata, N., Degi, Y., Ishiguro, M., Kitazawa, K., Takata, R., Ichinose, H., Kaneko, S., Igarashi, K., Samejima, M. and Tsumuraya, Y. Endo-β-1,3-galactanase from winter mushroom Flammulina velutipes. J. Biol. Chem. 286 (2011) 27848-27854. [PMID: 21653698]
*EC 3.5.99.5
Accepted name: 2-aminomuconate deaminase
Reaction: 2-aminomuconate + H2O = (3E)-2-oxohex-3-enedioate + NH3
Other name(s): amnD (gene name); nbaF (gene name)
Systematic name: 2-aminomuconate aminohydrolase
Comments: 2-Aminomuconate is an intermediate in the bacterial biodegradation of nitrobenzene. The enzyme has been isolated from several species, including Pseudomonas pseudocaligenes JS45, Pseudomonas fluorescens KU-7, Pseudomonas sp. AP3 and Burkholderia cenocepacia J2315. The reaction is spontaneous in acid conditions.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 201098-29-5
References:
1. He, Z and Spain, J.C. Studies of the catabolic pathway of degradation of nitrobenzene by Pseudomonas pseudoalcaligenes JS45: removal of the amino group from 2-aminomuconic semialdehyde. Appl. Environ. Microbiol. 63 (1997) 4839-4843. [PMID: 9471964]
2. He, Z. and Spain, J.C. A novel 2-aminomuconate deaminase in the nitrobenzene degradation pathway of Pseudomonas pseudoalcaligenes JS45. J. Bacteriol. 180 (1998) 2502-2506. [PMID: 9573204]
3. Takenaka, S., Murakami, S., Kim, Y.J. and Aoki, K. Complete nucleotide sequence and functional analysis of the genes for 2-aminophenol metabolism from Pseudomonas sp. AP-3. Arch. Microbiol. 174 (2000) 265-272. [PMID: 11081795]
4. Muraki, T., Taki, M., Hasegawa, Y., Iwaki, H. and Lau, P.C. Prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of Pseudomonas fluorescens strain KU-7. Appl. Environ. Microbiol. 69 (2003) 1564-1572. [PMID: 12620844]
EC 3.5.99.9
Accepted name: 2-nitroimidazole nitrohydrolase
Reaction: 2-nitroimidazole + H2O = imidazol-2-one + nitrite
Other name(s): NnhA; 2NI nitrohydrolase; 2NI denitrase
Systematic name: 2-nitroimidazole nitrohydrolase
Comments: The enzyme catalyses the initial step in the biodegradation of 2-nitroimidazole by the soil bacterium Mycobacterium sp. JS330
References:
1. Qu, Y. and Spain, J.C. Catabolic pathway for 2-nitroimidazole involves a novel nitrohydrolase that also confers drug resistance. Environ Microbiol 13 (2011) 1010-1017. [PMID: 21244596]
*EC 3.6.1.27
Accepted name: undecaprenyl-diphosphate phosphatase
Reaction: ditrans,octacis-undecaprenyl diphosphate + H2O = ditrans,octacis-undecaprenyl phosphate + phosphate
For diagram of reaction click here or click here.
Other name(s): C55-isoprenyl diphosphatase; C55-isoprenyl pyrophosphatase; isoprenyl pyrophosphatase (ambiguous); undecaprenyl pyrophosphate phosphatase; undecaprenyl pyrophosphate pyrophosphatase; UPP phosphatase; Und-PP pyrophosphatase; UppP (ambiguous); BacA; undecaprenyl-diphosphate phosphohydrolase; undecaprenyl-diphosphatase
Systematic name: ditrans,octacis-undecaprenyl-diphosphate phosphohydrolase
Comments: Isolated from the bacteria Micrococcus lysodeikticus [1], Escherichia coli [2,3,5,6] and Bacillus subtilis [4]. The product of the reaction, ditrans,octacis-undecaprenyl phosphate, is essential for cell wall polysaccharide biosynthesis in these strains.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 9077-80-9
References:
1. Goldman, R. and Strominger, J.L. Purification and properties of C55-isoprenylpyrophosphate phosphatase from Micrococcus lysodeikticus. J. Biol. Chem. 247 (1972) 5116-5122. [PMID: 4341539]
2. El Ghachi, M., Bouhss, A., Blanot, D. and Mengin-Lecreulx, D. The bacA gene of Escherichia coli encodes an undecaprenyl pyrophosphate phosphatase activity. J. Biol. Chem. 279 (2004) 30106-30113. [PMID: 15138271]
3. El Ghachi, M., Derbise, A., Bouhss, A. and Mengin-Lecreulx, D. Identification of multiple genes encoding membrane proteins with undecaprenyl pyrophosphate phosphatase (UppP) activity in Escherichia coli. J. Biol. Chem. 280 (2005) 18689-18695. [PMID: 15778224]
4. Bernard, R., El Ghachi, M., Mengin-Lecreulx, D., Chippaux, M. and Denizot, F. BcrC from Bacillus subtilis acts as an undecaprenyl pyrophosphate phosphatase in bacitracin resistance. J. Biol. Chem. 280 (2005) 28852-28857. [PMID: 15946938]
5. Tatar, L.D., Marolda, C.L., Polischuk, A.N., van Leeuwen, D. and Valvano, M.A. An Escherichia coli undecaprenyl-pyrophosphate phosphatase implicated in undecaprenyl phosphate recycling. Microbiology 153 (2007) 2518-2529. [PMID: 17660416]
6. Touze, T., Blanot, D. and Mengin-Lecreulx, D. Substrate specificity and membrane topology of Escherichia coli PgpB, an undecaprenyl pyrophosphate phosphatase. J. Biol. Chem. 283 (2008) 16573-16583. [PMID: 18411271]
*EC 3.7.1.14
Accepted name: 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase
Reaction: (1) (2Z,4E)-2-hydroxy-6-oxonona-2,4-diene-1,9-dioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + succinate
For diagram of reaction click here or click here.
Other name(s): mhpC (gene name)
Systematic name: (2Z,4E)-2-hydroxy-6-oxona-2,4-dienedioate succinylhydrolase
Comments: This enzyme catalyses a step in a pathway of phenylpropanoid compounds degradation. The first step of the enzyme mechanism involves a reversible keto-enol tautomerization [4].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
UM-BBD,
CAS registry number:
References:
1. Burlingame, R. and Chapman, P.J. Catabolism of phenylpropionic acid and its 3-hydroxy derivative by Escherichia coli. J. Bacteriol. 155 (1983) 113-121. [PMID: 6345502]
2. Burlingame, R.P., Wyman, L. and Chapman, P.J. Isolation and characterization of Escherichia coli mutants defective for phenylpropionate degradation. J. Bacteriol. 168 (1986) 55-64. [PMID: 3531186]
3. Lam, W. W. Y and Bugg, T. D. H. Chemistry of extradiol aromatic ring cleavage: isolation of a stable dienol ring fission intermediate and stereochemistry of its enzymatic hydrolytic clevage. J. Chem. Soc., Chem. Commun. 10 (1994) 1163-1164.
4. Lam, W.W. and Bugg, T.D. Purification, characterization, and stereochemical analysis of a C-C hydrolase: 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase. Biochemistry 36 (1997) 12242-12251. [PMID: 9315862]
5. Ferrández, A., García, J.L. and Díaz, E. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12. J. Bacteriol. 179 (1997) 2573-2581. [PMID: 9098055]
6. Díaz, E., Ferrández, A. and García, J.L. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180 (1998) 2915-2923. [PMID: 9603882]
EC 3.7.1.19
Accepted name: 2,6-dihydroxypseudooxynicotine hydrolase
Reaction: 1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one + H2O = 2,6-dihydroxypyridine + 4-methylaminobutanoate
For diagram of reaction click here.
Glossary: 1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one = 2,6-dihydroxypseudooxynicotine
Systematic name: 1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one hydrolase
Comments: The enzyme, characterized from the soil bacterium Arthrobacter nicotinovorans, participates in nicotine degradation.
References:
1. Gherna, R.L., Richardson, S.H. and Rittenberg, S.C. The bacterial oxidation of nicotine. VI. The metabolism of 2,6-dihydroxypseudooxynicotine. J. Biol. Chem. 240 (1965) 3669-3674. [PMID: 5835946]
2. Sachelaru, P., Schiltz, E., Igloi, G.L. and Brandsch, R. An α/β-fold C—C bond hydrolase is involved in a central step of nicotine catabolism by Arthrobacter nicotinovorans. J. Bacteriol. 187 (2005) 8516-8519. [PMID: 16321959]
*EC 4.1.1.77
Accepted name: 2-oxo-3-hexenedioate decarboxylase
Reaction: (3E)-2-oxohex-3-enedioate = 2-oxopent-4-enoate + CO2
Other name(s): 4-oxalocrotonate carboxy-lyase (misleading); 4-oxalocrotonate decarboxylase (misleading); cnbF (gene name); praD (gene name); amnE (gene name); nbaG (gene name); xylI (gene name)
Systematic name: (3E)-2-oxohex-3-enedioate carboxy-lyase (2-oxopent-4-enoate-forming)
Comments: Involved in the meta-cleavage pathway for the degradation of phenols, modified phenols and catechols. The enzyme has been reported to accept multiple tautomeric forms [1-4]. However, careful analysis of the stability of the different tautomers, as well as characterization of the enzyme that produces its substrate, EC 5.3.2.6, 2-hydroxymuconate tautomerase, showed that the actual substrate for the enzyme is (3E)-2-oxohex-3-enedioate [4].
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]
2. Takenaka, S., Murakami, S., Shinke, R. and Aoki, K. Metabolism of 2-aminophenol by Pseudomonas sp. AP-3: modified meta-cleavage pathway. Arch. Microbiol. 170 (1998) 132-137. [PMID: 9683650]
3. Stanley, T.M., Johnson, W.H., Jr., Burks, E.A., Whitman, C.P., Hwang, C.C. and Cook, P.F. Expression and stereochemical and isotope effect studies of active 4-oxalocrotonate decarboxylase. Biochemistry 39 (2000) 718-726. [PMID: 10651637]
4. Wang, S.C., Johnson, W.H., Jr., Czerwinski, R.M., Stamps, S.L. and Whitman, C.P. Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions. Biochemistry 46 (2007) 11919-11929. [PMID: 17902707]
5. Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758-6768. [PMID: 19717587]
EC 4.1.1.95
Accepted name: L-glutamyl-[BtrI acyl-carrier protein] decarboxylase
Reaction: L-glutamyl-[BtrI acyl-carrier protein] = 4-amino butanoyl-[BtrI acyl-carrier protein] + CO2
Other name(s): btrK (gene name)
Systematic name: L-glutamyl-[BtrI acyl-carrier protein] carboxy-lyase
Comments: Binds pyridoxal 5'-phosphate. Catalyses a step in the biosynthesis of the side chain of the aminoglycoside antibiotics of the butirosin family. Has very low activity with substrates not bound to an acyl-carrier protein.
References:
1. Li, Y., Llewellyn, N.M., Giri, R., Huang, F. and Spencer, J.B. Biosynthesis of the unique amino acid side chain of butirosin: possible protective-group chemistry in an acyl carrier protein-mediated pathway. Chem. Biol. 12 (2005) 665-675. [PMID: 15975512]
EC 4.1.1.96
Accepted name: carboxynorspermidine decarboxylase
Reaction: (1) carboxynorspermidine = bis(3-aminopropyl)amine + CO2
Glossary: bis(3-aminopropyl)amine = norspermidine
Other name(s): carboxyspermidine decarboxylase; CANSDC; VC1623 (gene name)
Systematic name: carboxynorspermidine carboxy-lyase (bis(3-aminopropyl)amine-forming)
Comments: A pyridoxal 5'-phosphate enzyme. Part of a bacterial polyamine biosynthesis pathway. The enzyme is essential for biofilm formation in the bacterium Vibrio cholerae [1]. The enzyme from Campylobacter jejuni only produces spermidine in vivo even though it shows activity with carboxynorspermidine in vitro [3].
References:
1. Lee, J., Sperandio, V., Frantz, D.E., Longgood, J., Camilli, A., Phillips, M.A. and Michael, A.J. An alternative polyamine biosynthetic pathway is widespread in bacteria and essential for biofilm formation in Vibrio cholerae. J. Biol. Chem. 284 (2009) 9899-9907. [PMID: 19196710]
2. Deng, X., Lee, J., Michael, A.J., Tomchick, D.R., Goldsmith, E.J. and Phillips, M.A. Evolution of substrate specificity within a diverse family of β/α-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine. J. Biol. Chem. 285 (2010) 25708-25719. [PMID: 20534592]
3. Hanfrey, C.C., Pearson, B.M., Hazeldine, S., Lee, J., Gaskin, D.J., Woster, P.M., Phillips, M.A. and Michael, A.J. Alternative spermidine biosynthetic route is critical for growth of Campylobacter jejuni and is the dominant polyamine pathway in human gut microbiota. J. Biol. Chem. 286 (2011) 43301-43312. [PMID: 22025614]
*EC 4.1.3.17
Accepted name: 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Reaction: (1) 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate
For diagram of reaction click here.
Other name(s): pyruvate aldolase; γ-methyl-γ-hydroxy-α-ketoglutaric aldolase; 4-hydroxy-4-methyl-2-ketoglutarate aldolase; 4-hydroxy-4-methyl-2-oxoglutarate pyruvate-lyase; HMG aldolase; CHA aldolase; 4-carboxy-4-hydroxy-2-oxoadipate aldolase
Systematic name: 4-hydroxy-4-methyl-2-oxoglutarate pyruvate-lyase (pyruvate-forming)
Comments: Requires a divalent metal ion [3]. This enzyme participates in the degradation of protocatechuate (via the meta-cleavage pathway), phthalate, syringate and gallate [1-3]. The enzyme from Pseudomonas ochraceae can also cleave 4-hydroxy-2-oxoglutarate to glyoxylate and pyruvate, and also catalyses the reaction of EC 4.1.1.3 (oxaloacetate decarboxylase) [3].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 37290-65-6
References:
1. Tack, B.F., Chapman, P.J. and Dagley, S. Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase. J. Biol. Chem. 247 (1972) 6444-6449. [PMID: 5076765]
2. Wood, W.A. 2-Keto-3-deoxy-6-phosphogluconic and related aldolases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 281-302.
3. Maruyama, K. Purification and properties of 2-pyrone-4,6-dicarboxylate hydrolase. J. Biochem. (Tokyo) 93 (1983) 557-565. [PMID: 6841353]
4. Nogales, J., Canales, A., Jimenez-Barbero, J., Serra, B., Pingarron, J.M., Garcia, J.L. and Diaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359-374. [PMID: 21219457]
*EC 4.2.1.33
Accepted name: 3-isopropylmalate dehydratase
Reaction: (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate (overall reaction)
For diagram of reaction click here.
Glossary: α-isopropylmalate = (2S)-2-isopropylmalate
Other name(s): (2R,3S)-3-isopropylmalate hydro-lyase; β-isopropylmalate dehydratase; isopropylmalate isomerase; α-isopropylmalate isomerase; 3-isopropylmalate hydro-lyase
Systematic name: (2R,3S)-3-isopropylmalate hydro-lyase (2-isopropylmaleate-forming)
Comments: Forms part of the leucine biosynthesis pathway. The enzyme brings about the interconversion of the two isomers of isopropylmalate. It contains an iron-sulfur cluster.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 37290-72-5
References:
1. Gross, S.R., Burns, R.O. and Umbarger, H.E. The biosynthesis of leucine. II. The enzymic isomerization of β-carboxy-β-hydroxyisocaproate and α-hydroxy-β-carboxyisocaproate. Biochemistry 2 (1963) 1046-1052. [PMID: 14087357]
2. Calvo, J. M., Stevens, C. M., Kalyanpur, M. G., and Umbarger, H. E. The absolute configuration of α-hydroxy-β-carboxyisocaproic acid (3-isopropylmalic acid), an intermediate in leucine biosynthesis. Biochemistry 3 (1964) 2024-2027. [PMID: 14269331]
3. Cole, F.E., Kalyanpur, M. G. and Stevens, C. M. Absolute configuration of α-isopropylmalate and the mechanism of its conversion to β-isopropylmalate in the biosynthesis of leucine. Biochemistry 12 (1973) 3346-3350. [PMID: 4270046]
4. Jang, S. and Imlay, J.A. Micromolar intracellular hydrogen peroxide disrupts metabolism by damaging iron-sulfur enzymes. J. Biol. Chem. 282 (2007) 929-937. [PMID: 17102132]
[EC 4.2.1.58 Deleted entry: crotonoyl-[acyl-carrier-protein] hydratase. The reaction described is covered by EC 4.2.1.59. (EC 4.2.1.58 created 1972, deleted 2012)]
*EC 4.2.1.59
Accepted name: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
Reaction: a (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H2O
Other name(s): fabZ (gene name); fabA (gene name); D-3-hydroxyoctanoyl-[acyl carrier protein] dehydratase; D-3-hydroxyoctanoyl-acyl carrier protein dehydratase; β-hydroxyoctanoyl-acyl carrier protein dehydrase; β-hydroxyoctanoyl thioester dehydratase; β-hydroxyoctanoyl-ACP-dehydrase; (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase; (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase (oct-2-enoyl-[acyl-carrier protein]-forming); 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase
Systematic name: (3R)-3-hydroxyoctanoyl-[acyl-carrier protein] hydro-lyase (oct-2-enoyl-[acyl-carrier protein]-forming)
Comments: This enzyme is responsible for the dehydration step of the dissociated (type II) fatty-acid biosynthesis system that occurs in plants and bacteria. The enzyme uses fatty acyl thioesters of ACP in vivo. Different forms of the enzyme may have preferences for substrates with different chain length. For example, the activity of FabZ, the ubiquitous enzyme in bacteria, decreases with increasing chain length. Gram-negative bacteria that produce unsaturated fatty acids, such as Escherichia coli, have another form (FabA) that prefers intermediate chain length, and also catalyses EC 5.3.3.14, trans-2-decenoyl-[acyl-carrier protein] isomerase. Despite the differences both forms can catalyse all steps leading to the synthesis of palmitate (C16:0). FabZ, but not FabA, can also accept unsaturated substrates [4].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 9030-85-7
References:
1. Mizugaki, M., Swindell, A.C. and Wkil, S.J. Intermediate- and long-chain β-hydroxyacyl-ACP dehydrases from E. coli fatty acid synthetase. Biochem. Biophys. Res. Commun. 33 (1968) 520-527. [PMID: 4881058]
2. Sharma, A., Henderson, B.S., Schwab, J.M. and Smith, J.L. Crystallization and preliminary X-ray analysis of β-hydroxydecanoyl
thiol ester dehydrase from Escherichia coli. J. Biol. Chem. 265 (1990) 5110-5112. [PMID: 2180957]
3. Mohan, S., Kelly, T.M., Eveland, S.S., Raetz, C.R. and Anderson, M.S. An Escherichia coli gene (FabZ) encoding (3R)-hydroxymyristoyl acyl carrier protein dehydrase. Relation to fabA and suppression of mutations in lipid A biosynthesis. J. Biol. Chem. 269 (1994) 32896-32903. [PMID: 7806516]
4. Heath, R.J. and Rock, C.O. Roles of the FabA and FabZ β-hydroxyacyl-acyl carrier protein dehydratases in Escherichia coli fatty acid biosynthesis. J. Biol. Chem. 271 (1996) 27795-27801. [PMID: 8910376]
[EC 4.2.1.60 Deleted entry: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase. The reaction described is covered by EC 4.2.1.59. (EC 4.2.1.60 created 1972, modified 2006, deleted 2012)]
[EC 4.2.1.61 Deleted entry: 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase. The reaction described is covered by EC 4.2.1.59. (EC 4.2.1.61 created 1972, deleted 2012)]
EC 4.2.1.134
Accepted name: very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase
Reaction: a very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] = a very-long-chain trans-2,3-dehydroacyl-[acyl-carrier protein] + H2O
Glossary: a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.
Other name(s): PHS1 (gene name); PAS2 (gene name)
Systematic name: very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] hydro-lyase
Comments: This is the third component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long chain acyl CoAs. cf. EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase.
References:
1. Bach, L., Michaelson, L.V., Haslam, R., Bellec, Y., Gissot, L., Marion, J., Da Costa, M., Boutin, J.P., Miquel, M., Tellier, F., Domergue, F., Markham, J.E., Beaudoin, F., Napier, J.A. and Faure, J.D. The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTICCINO2 is essential and limiting for plant development. Proc. Natl. Acad. Sci. USA 105 (2008) 14727-14731. [PMID: 18799749]
2. Kihara, A., Sakuraba, H., Ikeda, M., Denpoh, A. and Igarashi, Y. Membrane topology and essential amino acid residues of Phs1, a 3-hydroxyacyl-CoA dehydratase involved in very long-chain fatty acid elongation. J. Biol. Chem. 283 (2008) 11199-11209. [PMID: 18272525]
*EC 4.2.3.32
Accepted name: levopimaradiene synthase
Reaction: (+)-copalyl diphosphate = abieta-8(14),12-diene + diphosphate
For diagram of reaction click here.
Glossary: levopimaradiene = abieta-8(14),12-diene
Other name(s): PtTPS-LAS; LPS; copalyl-diphosphate diphosphate-lyase [abieta-8(14),12-diene-forming]
Systematic name: (+)-copalyl-diphosphate diphosphate-lyase [abieta-8(14),12-diene-forming]
Comments: In Ginkgo, the enzyme catalyses the initial cyclization step in the biosynthesis of ginkgolides, a structurally unique family of diterpenoids that are highly specific platelet-activating-factor receptor antagonists [1]. Levopimaradiene is widely distributed in higher plants. In some species the enzyme also forms abietadiene, palustradiene, and neoabietadiene [2].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number:
References:
1. Schepmann, H.G., Pang, J. and Matsuda, S.P. Cloning and characterization of Ginkgo biloba levopimaradiene synthase which catalyzes the first committed step in ginkgolide biosynthesis. Arch. Biochem. Biophys. 392 (2001) 263-269. [PMID: 11488601]
2. Ro, D.K. and Bohlmann, J. Diterpene resin acid biosynthesis in loblolly pine (Pinus taeda): functional characterization of abietadiene/levopimaradiene synthase (PtTPS-LAS) cDNA and subcellular targeting of PtTPS-LAS and abietadienol/abietadienal oxidase (PtAO, CYP720B1). Phytochemistry 67 (2006) 1572-1578. [PMID: 16497345]
EC 4.2.3.131
Accepted name: miltiradiene synthase
Reaction: (+)-copalyl diphosphate = miltiradiene + diphosphate
For diagram of reaction click here.
Other name(s): SmMDS; SmiKSL
Systematic name: (+)-copaly-diphosphate diphosphate-lyase (cyclizing, miltiradiene-forming)
Comments: Isolated from the plant Selaginella moellendorffii as a mutifunctional enzyme that also catalyses EC 5.5.1.12, copalyl diphosphate synthase [2]. In the plant Salvia miltiorrhiza the two enzymes are separate entities [1].
References:
1. Gao, W., Hillwig, M.L., Huang, L., Cui, G., Wang, X., Kong, J., Yang, B. and Peters, R.J. A functional genomics approach to tanshinone biosynthesis provides stereochemical insights. Org. Lett. 11 (2009) 5170-5173. [PMID: 19905026]
2. Sugai, Y., Ueno, Y., Hayashi, K., Oogami, S., Toyomasu, T., Matsumoto, S., Natsume, M., Nozaki, H. and Kawaide, H. Enzymatic 13C labeling and multidimensional NMR analysis of miltiradiene synthesized by bifunctional diterpene cyclase in Selaginella moellendorffii. J. Biol. Chem. 286 (2011) 42840-42847. [PMID: 22027823]
EC 4.2.3.132
Accepted name: neoabietadiene synthase
Reaction: (+)-copalyl diphosphate = neoabietadiene + diphosphate
For diagram of reaction click here.
Glossary: neoabietadiene = abieta-8(14),13(15)-diene
Other name(s): AgAS; PtTPS-LAS
Systematic name: (+)-copaly-diphosphate diphosphate-lyase (cyclizing, neoabietadiene-forming)
Comments: Isolated from Abies grandis (grand fir) [1]. This class I enzyme forms about equal proportions of abietadiene, levopimaradiene and neoabietadiene. See also EC 4.2.3.18, abieta-7,13-diene synthase and EC 4.2.3.32, levopimaradiene synthase. An X-ray study of this multifunctional enzyme showed that the class I activity is in the α domain, while (+)-copalyl diphosphate synthase activity (EC 5.5.1.12, a class II activity) is in the β and γ domains [2]. In Pinus taeda (loblolly pine) the major product is levopimaradiene, with less abietadiene and neoabietadiene [3].
References:
1. Peters, R.J., Flory, J.E., Jetter, R., Ravn, M.M., Lee, H.J., Coates, R.M. and Croteau, R.B. Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. Biochemistry 39 (2000) 15592-15602. [PMID: 11112547]
2. Zhou, K., Gao, Y., Hoy, J.A., Mann, F.M., Honzatko, R.B. and Peters, R.J. Insights into diterpene cyclization from structure of bifunctional abietadiene synthase from Abies grandis. J. Biol. Chem. 287 (2012) 6840-6850. [PMID: 22219188]
3. Ro, D.K. and Bohlmann, J. Diterpene resin acid biosynthesis in loblolly pine (Pinus taeda): functional characterization of abietadiene/levopimaradiene synthase (PtTPS-LAS) cDNA and subcellular targeting of PtTPS-LAS and abietadienol/abietadienal oxidase (PtAO, CYP720B1). Phytochemistry 67 (2006) 1572-1578. [PMID: 16497345]
EC 4.2.3.133
Accepted name: α-copaene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (–)-α-copaene + diphosphate
For diagram of reaction click here.
Glossary: (–)-α-copaene = (1R,2S,6S,7S,8S)-1,3-dimethyl-8-(propan-2-yl)tricyclo[4.4.0.02,7]dec-3-ene
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, α-copaene-forming)
Comments: Isolated from Helianthus annuus (sunflower). The enzyme also produces β-caryophyllene, δ-cadinene and traces of other sesquiterpenoids. See EC 4.2.3.13 (+)-δ-cadinene synthase, EC 4.2.3.57 (–)-β-caryophyllene synthase.
References:
1. Gopfert, J.C., Macnevin, G., Ro, D.K. and Spring, O. Identification, functional characterization and developmental regulation of sesquiterpene synthases from sunflower capitate glandular trichomes. BMC Plant Biol. 9 (2009) 86. [PMID: 19580670]
2. Xie, X., Kirby, J. and Keasling, J.D. Functional characterization of four sesquiterpene synthases from Ricinus communis (castor bean). Phytochemistry 78 (2012) 20-28. [PMID: 22459969]
EC 4.3.2.6
Accepted name: γ-L-glutamyl-butirosin B γ-glutamyl cyclotransferase
Reaction: γ-L-glutamyl-butirosin B = butirosin B + 5-oxoproline
Glossary: γ-L-glutamyl-butirosin B = (1R,2R,3S,4R,6S)-6-amino-4-{[(2R)-4-(L-γ-glutamylamino)-2-hydroxybutanoyl]amino}-3-hydroxy-2-(α-D-ribofuranosyloxy)cyclohexyl
Other name(s): btrG (gene name)
Systematic name: γ-L-glutamyl-butirosin B γ-glutamyl cyclotransferase (5-oxoproline producing)
Comments: The enzyme catalyses the last step in the biosynthesis of the aminoglycoside antibiotic butirosin B. The enzyme acts as a cyclotransferase, cleaving the amide bond via transamidation using the α-amine of the terminal γ-L-glutamate of the side chain, releasing it as the cyclic 5-oxoproline.
References:
1. Llewellyn, N.M., Li, Y. and Spencer, J.B. Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain. Chem. Biol. 14 (2007) 379-386. [PMID: 17462573]
EC 5.3.2.6
Accepted name: 2-hydroxymuconate tautomerase
Reaction: (2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (3E)-2-oxohex-3-enedioate
Glossary: (2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (2Z,4E)-2-hydroxymuconate
Other name(s): 4-oxalocrotonate tautomerase (misleading); 4-oxalocrotonate isomerase (misleading); cnbG (gene name); praC (gene name); xylH (gene name)
Systematic name: (2Z,4E)-2-hydroxyhexa-2,4-dienedioate keto—enol isomerase
Comments: Involved in the meta-cleavage pathway for the degradation of phenols, modified phenols and catechols. The enol form (2Z,4E)-2-hydroxyhexa-2,4-dienedioate is produced as part of this pathway and is converted to the keto form (3E)-2-oxohex-3-enedioate by the enzyme [6]. Another keto form, (4E)-2-oxohex-4-enedioate (4-oxalocrotonate), was originally thought to be produced by the enzyme [1,2] but later shown to be produced non-enzymatically [5].
References:
1. Whitman, C.P., Aird, B.A., Gillespie, W.R. and Stolowich, N.J. Chemical and enzymatic ketonization of 2-hydroxymuconate, a conjugated enol. J. Am. Chem. Soc. 113 (1991) 3154-3162.
2. Whitman, C.P., Hajipour, G., Watson, R.J., Johnson, W.H., Jr., Bembenek, M.E. and Stolowich, N.J. Stereospecific ketonization of 2-hydroxymuconate by 4-oxalocrotonate tautomerase and 5-(carboxymethyl)-2-hydroxymuconate isomerase. J. Am. Chem. Soc. 114 (1992) 10104-10110.
3. Subramanya, H.S., Roper, D.I., Dauter, Z., Dodson, E.J., Davies, G.J., Wilson, K.S. and Wigley, D.B. Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases. Biochemistry 35 (1996) 792-802. [PMID: 8547259]
4. Stivers, J.T., Abeygunawardana, C., Mildvan, A.S., Hajipour, G., Whitman, C.P. and Chen, L.H. Catalytic role of the amino-terminal proline in 4-oxalocrotonate tautomerase: affinity labeling and heteronuclear NMR studies. Biochemistry 35 (1996) 803-813. [PMID: 8547260]
5. Wang, S.C., Johnson, W.H., Jr., Czerwinski, R.M., Stamps, S.L. and Whitman, C.P. Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions. Biochemistry 46 (2007) 11919-11929. [PMID: 17902707]
6. Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M. and Masai, E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 191 (2009) 6758-6768. [PMID: 19717587]
EC 5.4.3.9
Accepted name: glutamate 2,3-aminomutase
Reaction: L-glutamate = 3-aminopentanedioate
Glossary: 3-aminopentanedioate = isoglutamate
Systematic name: L-glutamate 2,3-aminomutase
Comments: This enzyme is a member of the 'AdoMet radical' (radical SAM) family. It contains pyridoxal phosphate and a [4Fe-4S] cluster, which is coordinated by 3 cysteines and binds an exchangeable S-adenosyl-L-methionine molecule. During the reaction cycle, the AdoMet forms a 5'-deoxyadenosyl radical, which is regenerated at the end of the reaction.
References:
1. Ruzicka, F.J. and Frey, P.A. Glutamate 2,3-aminomutase: a new member of the radical SAM superfamily of enzymes. Biochim. Biophys. Acta 1774 (2007) 286-296. [PMID: 17222594]
*EC 5.5.1.12
Accepted name: copalyl diphosphate synthase
Reaction: geranylgeranyl diphosphate = (+)-copalyl diphosphate
For diagram of reaction click here.
Systematic name: (+)-copalyl-diphosphate lyase (decyclizing)
Comments: In some plants, such as Salvia miltiorrhiza, this enzyme is monofunctional. In other plants this activity is often a part of a bifunctional enzyme. For example, in Selaginella moellendorffii this activity is catalysed by a bifunctional enzyme that also catalyses EC 4.2.3.131, miltiradiene synthase, while in the tree Abies grandis (grand fir) it is catalysed by a bifunctional enzyme that also catalyses EC 4.2.3.18, abietadiene synthase.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 157972-08-2
References:
1. Peters, R.J., Ravn, M.M., Coates, R.M. and Croteau, R.B. Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites. J. Am. Chem. Soc. 123 (2001) 8974-8978. [PMID: 11552804]
2. Sugai, Y., Ueno, Y., Hayashi, K., Oogami, S., Toyomasu, T., Matsumoto, S., Natsume, M., Nozaki, H. and Kawaide, H. Enzymatic 13C labeling and multidimensional NMR analysis of miltiradiene synthesized by bifunctional diterpene cyclase in Selaginella moellendorffii. J. Biol. Chem. 286 (2011) 42840-42847. [PMID: 22027823]
3. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement. Proc. Natl. Acad. Sci. USA 99 (2002) 580-584. [PMID: 11805316]
4. Ravn, M.M., Peters, R.J., Coates, R.M. and Croteau, R. Mechanism of abietadiene synthase catalysis: stereochemistry and stabilization of the cryptic pimarenyl carbocation intermediates. J. Am. Chem. Soc. 124 (2002) 6998-7006. [PMID: 12059223]
5. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate. Biochemistry 41 (2002) 1836-1842. [PMID: 11827528]
EC 6.2.1.39
Accepted name: [butirosin acyl-carrier protein]—L-glutamate ligase
Reaction: (1) ATP + L-glutamate + BtrI acyl-carrier protein = ADP + phosphate + L-glutamyl-[BtrI acyl-carrier protein]
Other name(s): [BtrI acyl-carrier protein]—L-glutamate ligase; BtrJ
Systematic name: [BtrI acyl-carrier protein]:L-glutamate ligase (ADP-forming)
Comments: Catalyses two steps in the biosynthesis of the side chain of the aminoglycoside antibiotics of the butirosin family. The enzyme adds one molecule of L-glutamate to a dedicated acyl-carrier protein, and following decarboxylation of the product by EC 4.1.1.95, L-glutamyl-[BtrI acyl-carrier protein] decarboxylase, adds a second L-glutamate molecule.
Requires Mg2+ or Mn2+, and activity is enhanced in the presence of Mn2+.
References:
1. Li, Y., Llewellyn, N.M., Giri, R., Huang, F. and Spencer, J.B. Biosynthesis of the unique amino acid side chain of butirosin: possible protective-group chemistry in an acyl carrier protein-mediated pathway. Chem. Biol. 12 (2005) 665-675. [PMID: 15975512]
[EC 6.3.2.27 Deleted entry: The activity is covered by two independent enzymes, EC 6.3.2.38 N2-citryl-N6-acetyl-N6-hydroxylysine synthase, and EC 6.3.2.39, aerobactin synthase (EC 6.3.2.27 created 2002, modified 2006, deleted 2012)]
EC 6.3.2.38
Accepted name: N2-citryl-N6-acetyl-N6-hydroxylysine synthase
Reaction: 2 ATP + citrate + N6-acetyl-N6-hydroxy-L-lysine + H2O = 2 ADP + 2 phosphate + N2-citryl-N6-acetyl-N6-hydroxy-L-lysine
For diagram of reaction click here.
Other name(s): Nα-citryl-Nε-acetyl-Nε-hydroxylysine synthase; iucA (gene name)
Systematic name: citrate:N6-acetyl-N6-hydroxy-L-lysine ligase (ADP-forming)
Comments: Requires Mg2+. Aerobactin is one of a group of high-affinity iron chelators known as siderophores and is produced under conditions of iron deprivation [5]. It is a dihydroxamate comprising two molecules of N6-acetyl-N6-hydroxy-L-lysine and one molecule of citrate. This enzyme catalyses the first of two synthase reactions to link N6-acetyl-N6-hydroxy-L-lysine and citrate [4,5].
References:
1. Appanna, D.L., Grundy, B.J., Szczepan, E.W. and Viswanatha, T. Aerobactin synthesis in a cell-free system of Aerobacter aerogenes 62-1. Biochim. Biophys. Acta 801 (1984) 437-443.
2. Gibson, F. and Magrath, D.I. The isolation and characterization of a hydroxamic acid (aerobactin) formed by Aerobacter aerogenes 62-I. Biochim. Biophys. Acta 192 (1969) 175-184. [PMID: 4313071]
3. Maurer, P.J. and Miller, M. Microbial iron chelators: total synthesis of aerobactin and its constituent amino acid, N6-acetyl-N6-hydroxylysine. J. Am. Chem. Soc. 104 (1982) 3096-3101.
4. de Lorenzo, V., Bindereif, A., Paw, B.H. and Neilands, J.B. Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12. J. Bacteriol. 165 (1986) 570-578. [PMID: 2935523]
5. Challis, G.L. A widely distributed bacterial pathway for siderophore biosynthesis
independent of nonribosomal peptide synthetases. ChemBioChem 6 (2005) 601-611. [PMID: 15719346]
EC 6.3.2.39
Accepted name: aerobactin synthase
Reaction: 2 ATP + N2-citryl-N6-acetyl-N6-hydroxy-L-lysine + N6-acetyl-N6-hydroxy-L-lysine + H2O = 2 ADP + 2 phosphate + aerobactin
For diagram of reaction click here.
Other name(s): iucC (gene name)
Systematic name: N2-citryl-N6-acetyl-N6-hydroxy-L-lysine:N6-acetyl-N6-hydroxy-L-lysine ligase (ADP-forming)
Comments: Requires Mg2+. Aerobactin is one of a group of high-affinity iron chelators known as siderophores and is produced under conditions of iron deprivation [6]. It is a dihydroxamate comprising two molecules of N6-acetyl-N6-hydroxy-L-lysine and one molecule of citric acid. This enzyme catalyses the second of two synthase reactions to link N6-acetyl-N6-hydroxy-L-lysine and citrate [3,4,5].
References:
1. Appanna, D.L., Grundy, B.J., Szczepan, E.W. and Viswanatha, T. Aerobactin synthesis in a cell-free system of Aerobacter aerogenes 62-1. Biochim. Biophys. Acta 801 (1984) 437-443.
2. Gibson, F. and Magrath, D.I. The isolation and characterization of a hydroxamic acid (aerobactin) formed by Aerobacter aerogenes 62-I. Biochim. Biophys. Acta 192 (1969) 175-184. [PMID: 4313071]
3. Maurer, P.J. and Miller, M. Microbial iron chelators: total synthesis of aerobactin and its constituent amino acid, N6-acetyl-N6-hydroxylysine. J. Am. Chem. Soc. 104 (1982) 3096-3101.
4. de Lorenzo, V., Bindereif, A., Paw, B.H. and Neilands, J.B. Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12. J. Bacteriol. 165 (1986) 570-578. [PMID: 2935523]
5. de Lorenzo, V. and Neilands, J.B. Characterization of iucA and iucC genes of the aerobactin system of plasmid ColV-K30 in Escherichia coli. J. Bacteriol. 167 (1986) 350-355. [PMID: 3087960]
6. Challis, G.L. A widely distributed bacterial pathway for siderophore biosynthesis independent of nonribosomal peptide synthetases. ChemBioChem 6 (2005) 601-611. [PMID: 15719346]
(E)-2,2',5,5'-tetrahydroxy-6H,6'H-[3,3'-bipyridinylidene]-6,6'-dione = nicotine blue
chanoclavine-I aldehyde = (1E)-2-methyl-3-[(4R,5R)-4-(methylamino)-1,3,4,5-tetrahydrobenz[cd]indol-5-yl]prop-2-enal
ecgonone methyl ester = 2β-carbomethoxy-3-tropinone = methyl (1R,2R,5S)-8-methyl-3-oxo-8-azabicyclo[3.2.1]octane-2-carboxylate
4-oxo-4-(3-pyridyl)-butanoate = 3-succinoyl-pyridine
4-oxo-4-(pyridin-3-yl)butanal = 3-succinoylsemialdehyde-pyridine
1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one = 2,6-dihydroxypseudooxynicotine
(2) (2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate + O2 = (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioate
(1a) 5-nitrosalicylate + O2 = 4-nitro-6-oxohepta-2,4-dienedioate
(1b) 4-nitro-6-oxohepta-2,4-dienedioate = 2-oxo-3-(5-oxofuran-2-ylidene)propanoate + nitrite (spontaneous)
(1a) 2 L-arginine + 2 NADPH + 2 H+ + 2 O2 = 2 Nω-hydroxy-L-arginine + 2 NADP+ + 2 H2O
(1b) 2 Nω-hydroxy-L-arginine + NADPH + H+ + 2 O2 = 2 L-citrulline + 2 nitric oxide + NADP+ + 2 H2O
(1a) 2 L-arginine + 2 NAD(P)H + 2 H+ + 2 O2 = 2 Nω-hydroxy-L-arginine + 2 NAD(P)+ + 2 H2O
(1b) 2 Nω-hydroxy-L-arginine + NAD(P)H + H+ + 2 O2 = 2 L-citrulline + 2 nitric oxide + NAD(P)+ + 2 H2O
(1a) L-tyrosine + ½ O2 = L-dopa
(1b) L-dopa + ½ O2 = dopaquinone + H2O
(2) 2 L-dopa + O2 = 2 dopaquinone + 2 H2O
(2) 2',3,4,4',6'-pentahydroxychalcone 4'-O-β-D-glucoside + ½ O2 = aureusidin 6-O-β-D-glucoside + H2O
(3) 2',3,4,4',6'-pentahydroxychalcone 4'-O-β-D-glucoside + O2 = bracteatin 6-O-β-D-glucoside + H2O
aureusidin = 4,6-dihydroxy-2-[(3,4-dihydroxyphenyl)methylidene]benzofuran-3(2H)-one
bracteatin = 4,6-dihydroxy-2-[(3,4,5-trihydroxyphenyl)methylidene]benzofuran-3(2H)-one
(2) UDP-α-D-glucose + 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one = UDP + (2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside
2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one = DIMBOA
(2R)-4-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = DIBOA β-D-glucoside
(2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = DIMBOA β-D-glucoside
(2) UDP-α-D-glucose + 2',3,4,4',6'-pentahydroxychalcone = UDP + 2',3,4,4',6'-pentahydroxychalcone 4'-O-β-D-glucoside
(1a) UDP-α-D-galactofuranose + α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol = UDP + β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol
(1b) UDP-α-D-galactofuranose + β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol = UDP + β-D-galactofuranosyl-(1→5)-β-D-galactofuranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-N-acetyl-α-D-glucosaminyl-diphospho-trans-octacis-decaprenol
epoxyqueosine = oQ
maleylacetate = (2Z)-4-oxohex-2-enedioate
mycophenolic acid O-acyl-glucuronide = 1-O-[(4E)-6-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)-4-methylhex-4-enoyl]-β-D-glucopyranuronic acid
(2) (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + fumarate
(2) carboxyspermidine = spermidine + CO2
(2) 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = oxaloacetate + pyruvate
(1a) (2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H2O
(1b) 2-isopropylmaleate + H2O = (2S)-2-isopropylmalate
β-isopropylmalate = (2R,3S)-3-isopropylmalate
For diagram of the structures of α-copaene and β-copaene, click here
(2) ATP + L-glutamate + 4-amino butanoyl-[BtrI acyl-carrier protein] = ADP + phosphate + 4-(L-γ-glutamylamino)butanoyl-[BtrI acyl-carrier protein]
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