An asterisk before "EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: 4-phospho-D-threonate 3-dehydrogenase
Reaction: 4-phospho-D-threonate + NAD+ = glycerone phosphate + CO2 + NADH + H+ (overall reaction)
(1a) 4-phospho-D-threonate + NAD+ = 3-dehydro-4-phospho-D-threonate + NADH + H+
(1b) 3-dehydro-4-phospho-D-threonate = glycerone phosphate + CO2 (spontaneous)
For diagram of reaction click here.
Glossary: D-threonate = (2S,3R)-2,3,4-trihydroxybutanoate
glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): pdxA2 (gene name) (ambiguous)
Systematic name: 4-phospho-D-threonate:NAD+ 3-oxidoreductase
Comments: The enzyme, characterized from bacteria, is involved in a pathway for D-threonate catabolism.
References:
1. Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl Acad. Sci. USA 113 (2016) E4161-E4169. [PMID: 27402745]
Accepted name: 4-phospho-D-erythronate 3-dehydrogenase
Reaction: 4-phospho-D-erythronate + NAD+ = glycerone phosphate + CO2 + NADH + H+ (overall reaction)
(1a) 4-phospho-D-erythronate + NAD+ = 3-dehydro-4-phospho-L-threonate + NADH + H+
(1b) 3-dehydro-4-phospho-L-threonate = glycerone phosphate + CO2 (spontaneous)
For diagram of reaction click here.
Glossary: D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
Other name(s): pdxA2 (gene name) (ambiguous)
Systematic name: 4-phospho-D-erythronate:NAD+ 3-oxidoreductase
Comments: The enzyme, characterized from bacteria, is involved in a pathway for D-erythronate catabolism.
References:
1. Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl Acad. Sci. USA 113 (2016) E4161-E4169. [PMID: 27402745]
Accepted name: D-erythronate 2-dehydrogenase
Reaction: D-erythronate + NAD+ = 2-dehydro-D-erythronate + NADH + H+
For diagram of reaction click here.
Glossary: D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
2-dehydro-D-erythronate = (3R)-3,4-dihydroxy-2-oxobutanoate
Other name(s): denD (gene name)
Systematic name: D-erythronate:NAD+ 2-oxidoreductase
Comments: The enzyme, characterized from bacteria, is involved in D-erythronate catabolism.
References:
1. Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl Acad. Sci. USA 113 (2016) E4161-E4169. [PMID: 27402745]
Accepted name: L-threonate 2-dehydrogenase
Reaction: L-threonate + NAD+ = 2-dehydro-L-erythronate + NADH + H+
For diagram of reaction click here.
Glossary: L-threonate = (2R,3S)-2,3,4-trihydroxybutanoate
2-dehydro-L-erythronate = (3R)-3,4-dihydroxy-2-oxobutanoate
Other name(s): ltnD (gene name)
Systematic name: L-threonate:NAD+ 2-oxidoreductase
Comments: The enzyme, characterized from bacteria, is involved in L-threonate catabolism.
References:
1. Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl Acad. Sci. USA 113 (2016) E4161-E4169. [PMID: 27402745]
Accepted name: 4-(γ-glutamylamino)butanal dehydrogenase
Reaction: 4-(γ-L-glutamylamino)butanal + NAD(P)+ + H2O = 4-(γ-L-glutamylamino)butanoate + NAD(P)H + H+
Other name(s): puuC (gene name)
Systematic name: 4-(γ-L-glutamylamino)butanal:NAD(P)+ oxidoreductase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in a putrescine catabolic pathway. It has a broad substrate range, and can also catalyse the activities of EC 1.2.1.19, aminobutyraldehyde dehydrogenase, and EC 1.2.1.24, succinate-semialdehyde dehydrogenase (NAD+).
References:
1. Kurihara, S., Oda, S., Kato, K., Kim, H.G., Koyanagi, T., Kumagai, H. and Suzuki, H. A novel putrescine utilization pathway involves γ-glutamylated intermediates of Escherichia coli K-12. J. Biol. Chem. 280 (2005) 4602-4608. [PMID: 15590624]
2. Jo, J.E., Mohan Raj, S., Rathnasingh, C., Selvakumar, E., Jung, W.C. and Park, S. Cloning, expression, and characterization of an aldehyde dehydrogenase from Escherichia coli K-12 that utilizes 3-hydroxypropionaldehyde as a substrate. Appl. Microbiol. Biotechnol. 81 (2008) 51-60. [PMID: 18668238]
3. Schneider, B.L. and Reitzer, L. Pathway and enzyme redundancy in putrescine catabolism in Escherichia coli. J. Bacteriol. 194 (2012) 4080-4088. [PMID: 22636776]
Accepted name: formylmethanofuran dehydrogenase
Reaction: a formylmethanofuran + H2O + 2 oxidized ferredoxin [iron-sulfur] cluster = CO2 + a methanofuran + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
For diagram of reaction click here.
Glossary: methanofuran a = 4-[4-(2-{[(4R*,5S*)-4,5,7-tricarboxyheptanoyl]-γ-L-glutamyl-γ-L-glutamylamino}ethyl)phenoxymethyl]furan-2-ylmethanamine
Other name(s): formylmethanofuran:acceptor oxidoreductase
Systematic name: formylmethanofuran:ferredoxin oxidoreductase
Comments: Contains a molybdopterin cofactor. In some organisms an additional subunit enables the incorporation of tungsten when molybdenum availability is low. The enzyme catalyses a reversible reaction in methanogenic archaea, and is involved in methanogenesis from CO2 as well as the oxidation of coenzyme M to CO2. The reaction is endergonic, and is driven by coupling with the soluble CoB-CoM heterodisulfide reductase via electron bifurcation.
References:
1. Karrasch, M., Börner, G., Enssle, M. and Thauer, R.K. The molybdoenzyme formylmethanofuran dehydrogenase from Methanosarcina barkeri contains a pterin cofactor. Eur. J. Biochem. 194 (1990) 367-372. [PMID: 2125267]
2. Bertram, P.A., Schmitz, R.A., Linder, D. and Thauer, R.K. Tungstate can substitute for molybdate in sustaining growth of Methanobacterium thermoautotrophicum. Identification and characterization of a tungsten isoenzyme of formylmethanofuran dehydrogenase. Arch. Microbiol. 161 (1994) 220-228. [PMID: 8161283]
3. Bertram, P.A., Karrasch, M., Schmitz, R.A., Bocher, R., Albracht, S.P. and Thauer, R.K. Formylmethanofuran dehydrogenases from methanogenic Archaea. Substrate specificity, EPR properties and reversible inactivation by cyanide of the molybdenum or tungsten iron-sulfur proteins. Eur. J. Biochem. 220 (1994) 477-484. [PMID: 8125106]
4. Vorholt, J.A. and Thauer, R.K. The active species of ‘CO2’ utilized by formylmethanofuran dehydrogenase from methanogenic Archaea. Eur. J. Biochem. 248 (1997) 919-924. [PMID: 9342247]
5. Meuer, J., Kuettner, H.C., Zhang, J.K., Hedderich, R. and Metcalf, W.W. Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc. Natl Acad. Sci. USA 99 (2002) 5632-5637. [PMID: 11929975]
6. Kaster, A.K., Moll, J., Parey, K. and Thauer, R.K. Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc. Natl Acad. Sci. USA 108 (2011) 2981-2986. [PMID: 21262829]
[EC 1.2.99.5 Transferred entry: formylmethanofuran dehydrogenase. Now EC 1.2.7.12, formylmethanofuran dehydrogenase (EC 1.2.99.5 created 1992, deleted 2017)]
Accepted name: dimethylglycine dehydrogenase
Reaction: N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein = sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein
Glossary: sarcosine = N-methylglycine
Other name(s): N,N-dimethylglycine oxidase; N,N-dimethylglycine:(acceptor) oxidoreductase (demethylating); Me2GlyDH; N,N-dimethylglycine:electron-transfer flavoprotein oxidoreductase (demethylating)
Systematic name: N,N-dimethylglycine,5,6,7,8-tetrahydrofolate:electron-transferflavoprotein oxidoreductase (demethylating,5,10-methylenetetrahydrofolate-forming)
Comments: A flavoprotein, containing a histidyl(Nπ)-(8α)FAD linkage at position 91 in the human protein. An imine intermediate is channeled from the FAD binding site to the 5,6,7,8-tetrahydrofolate binding site through a 40 Å tunnel [5,8,9]. In the absence of 5,6,7,8-tetrahydrofolate the enzyme forms formaldehyde [5,9].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-30-7
References:
1. Frisell, W.R. and MacKenzie, C.G. Separation and purification of sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 237 (1962) 94-98. [PMID: 13895406]
2. Hoskins, D.D. and MacKenzie, C.G. Solubilization and electron transfer flavoprotein requirement of mitochondrial sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 236 (1961) 177-183. [PMID: 13716069]
3. Wittwer, A.J. and Wagner, C. Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Purification and folate-binding characteristics. J. Biol. Chem. 256 (1981) 4102-4108. [PMID: 6163777]
4. Wittwer, A.J. and Wagner, C. Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Flavoprotein nature and enzymatic properties of the purified proteins. J. Biol. Chem. 256 (1981) 4109-4115. [PMID: 6163778]
5. Porter, D.H., Cook, R.J. and Wagner, C. Enzymatic properties of dimethylglycine dehydrogenase and sarcosine dehydrogenase from rat liver. Arch. Biochem. Biophys. 243 (1985) 396-407. [PMID: 2417560]
6. Brizio, C., Brandsch, R., Bufano, D., Pochini, L., Indiveri, C. and Barile, M. Over-expression in Escherichia coli, functional characterization and refolding of rat dimethylglycine dehydrogenase. Protein Expr. Purif. 37 (2004) 434-442. [PMID: 15358367]
7. Brizio, C., Brandsch, R., Douka, M., Wait, R. and Barile, M. The purified recombinant precursor of rat mitochondrial dimethylglycine dehydrogenase binds FAD via an autocatalytic reaction. Int. J. Biol. Macromol. 42 (2008) 455-462. [PMID: 18423846]
8. Luka, Z., Pakhomova, S., Loukachevitch, L.V., Newcomer, M.E. and Wagner, C. Folate in demethylation: the crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate. Biochem. Biophys. Res. Commun. 449 (2014) 392-398. [PMID: 24858690]
9. Augustin, P., Hromic, A., Pavkov-Keller, T., Gruber, K. and Macheroux, P. Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant. FEBS J. 283 (2016) 3587-3603. [PMID: 27486859]
Accepted name: nitrobenzene nitroreductase
Reaction: N-phenylhydroxylamine + 2 NADP+ + H2O = nitrobenzene + 2 NADPH + 2 H+ (overall reaction)
(1a) N-phenylhydroxylamine + NADP+ = nitrosobenzene + NADPH + H+
(1b) nitrosobenzene + NADP+ + H2O = nitrobenzene + NADPH + H+
Other name(s): cnbA (gene name)
Systematic name: N-phenylhydroxylamine:NADP+ oxidoreductase
Comments: Contains FMN. The enzyme, characterized from Pseudomonas species, catalyses two successive reductions of nitrobenzene, via a nitrosobenzene intermediate. It is also active on 1-chloro-4-nitrobenzene.
References:
1. Somerville, C.C., Nishino, S.F. and Spain, J.C. Purification and characterization of nitrobenzene nitroreductase from Pseudomonas pseudoalcaligenes JS45. J. Bacteriol. 177 (1995) 3837-3842. [PMID: 7601851]
2. Wu, J.F., Jiang, C.Y., Wang, B.J., Ma, Y.F., Liu, Z.P. and Liu, S.J. Novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in Comamonas sp. strain CNB-1. Appl. Environ. Microbiol. 72 (2006) 1759-1765. [PMID: 16517619]
[EC 1.7.99.4 Transferred entry: nitrate reductase, Now EC 1.7.1.1, nitrate reductase (NADH), EC 1.7.1.2, nitrate reductase [NAD(P)H], EC 1.7.1.3, nitrate reductase (NADPH), EC 1.7.5.1, nitrate reductase (quinone), EC 1.7.7.2, nitrate reductase (ferredoxin), and EC 1.9.6.1, nitrate reductase (cytochrome) (EC 1.7.99.4 created 1972, modified 1976, deleted 2017)]
Accepted name: nitric-oxide synthase (NADPH)
Reaction: 2 L-arginine + 3 NADPH + 3 H+ + 4 O2 = 2 L-citrulline + 2 nitric oxide + 3 NADP+ + 4 H2O (overall reaction)
(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
Glossary: nitric oxide = NO = nitrogen(II) oxide
Other name(s): NOS (gene name); nitric oxide synthetase (ambiguous); endothelium-derived relaxation factor-forming enzyme; endothelium-derived relaxing factor synthase; NO synthase (ambiguous); NADPH-diaphorase (ambiguous)
Systematic name: L-arginine,NADPH:oxygen oxidoreductase (nitric-oxide-forming)
Comments: The enzyme consists of linked oxygenase and reductase domains. The eukaryotic enzyme binds FAD, FMN, heme (iron protoporphyrin IX) and tetrahydrobiopterin, and its two domains 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. The reductase domain of the enzyme from the bacterium Sorangium cellulosum utilizes a [2Fe-2S] cluster to transfer the electrons from NADPH to the active center. cf. EC 1.14.14.47, nitric-oxide synthase (flavodoxin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, 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. 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]
5. 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 1.14.13.165 Transferred entry: nitric-oxide synthase [NAD(P)H]. Now classified as EC 1.14.14.47, nitric-oxide synthase (flavodoxin) (EC 1.14.13.165 created 2012, deleted 2017)]
Accepted name: indole-3-acetate monooxygenase
Reaction: (indol-3-yl)acetate + NADH + H+ + O2 = (2-hydroxy-1H-indol-3-yl)acetate + NAD+ + H2O
Glossary: (indol-3-yl)acetate =(1H-indol-3-yl)acetate = indole-3-acetate
Other name(s): iacA (gene name)
Systematic name: (indol-3-yl)acetate,NADH:oxygen oxidoreductase (2-hydroxylating)
Comments: The enzyme, characterized from Pseudomonas putida strains, catalyses the first step in a pathway for degradation of the plant hormone indole-3-acetate. When acting on indole, the enzyme forms indoxyl, which reacts spontaneously with oxygen to form the blue dye indigo.
References:
1. Leveau, J.H. and Lindow, S.E. Utilization of the plant hormone indole-3-acetic acid for growth by Pseudomonas putida strain 1290. Appl. Environ. Microbiol. 71 (2005) 2365-2371. [PMID: 15870323]
2. Scott, J.C., Greenhut, I.V. and Leveau, J.H. Functional characterization of the bacterial iac genes for degradation of the plant hormone indole-3-acetic acid. J Chem Ecol 39 (2013) 942-951. [PMID: 23881445]
Accepted name: toluene 4-monooxygenase
Reaction: toluene + NADH + H+ + O2 = 4-methylphenol + NAD+ + H2O
Glossary: 4-methylphenol = p-cresol
Other name(s): TMO
Systematic name: toluene,NADH:oxygen oxidoreductase (4-hydroxylating)
Comments: This bacterial enzyme belongs to a family of soluble diiron hydroxylases that includes toluene-, benzene-, xylene- and methane monooxygenases, phenol hydroxylases, and alkene epoxidases. The enzyme comprises a four-component complex that includes a hydroxylase, NADH-ferredoxin oxidoreductase, a Rieske-type [2Fe-2S] ferredoxin, and an effector protein.
References:
1. Whited, G.M. and Gibson, D.T. Toluene-4-monooxygenase, a three-component enzyme system that catalyzes the oxidation of toluene to p-cresol in Pseudomonas mendocina KR1. J. Bacteriol. 173 (1991) 3010-3016. [PMID: 2019563]
2. Hemmi, H., Studts, J.M., Chae, Y.K., Song, J., Markley, J.L. and Fox, B.G. Solution structure of the toluene 4-monooxygenase effector protein (T4moD). Biochemistry 40 (2001) 3512-3524. [PMID: 11297417]
3. Schwartz, J.K., Wei, P.P., Mitchell, K.H., Fox, B.G. and Solomon, E.I. Geometric and electronic structure studies of the binuclear nonheme ferrous active site of toluene-4-monooxygenase: parallels with methane monooxygenase and insight into the role of the effector proteins in O2 activation. J. Am. Chem. Soc. 130 (2008) 7098-7109. [PMID: 18479085]
4. Bailey, L.J., Acheson, J.F., McCoy, J.G., Elsen, N.L., Phillips, G.N., Jr. and Fox, B.G. Crystallographic analysis of active site contributions to regiospecificity in the diiron enzyme toluene 4-monooxygenase. Biochemistry 51 (2012) 1101-1113. [PMID: 22264099]
5. Hosseini, A., Brouk, M., Lucas, M.F., Glaser, F., Fishman, A. and Guallar, V. Atomic picture of ligand migration in toluene 4-monooxygenase. J. Phys. Chem. B 119 (2015) 671-678. [PMID: 24798294]
Accepted name: isobutylamine N-monooxygenase
Reaction: (1) 2-methylpropan-1-amine + FADH2 + O2 = N-(2-methylpropyl)hydroxylamine + FAD + H2O
(2) 2-methylpropan-1-amine + FMNH2 + O2 = N-(2-methylpropyl)hydroxylamine + FMN + H2O
Glossary: 2-methylpropan-1-amine = isobutylamine
N-(2-methylpropyl)hydroxylamine = N-hydroxy-2-methylpropan-1-amine = isobutylhydroxylamine
Other name(s): vlmH (gene name)
Systematic name: 2-methylpropan-1-amine,FADH2:O2 N-oxidoreductase
Comments: The enzyme, characterized from the bacterium Streptomyces viridifaciens, is part of a two component system that also includes a flavin reductase, which provides reduced flavin mononucleotide for this enzyme. The enzyme, which is involved in the biosynthesis of the azoxy antibiotic valanimycin, has a similar activity with either FMNH2 or FADH2. It exhibits broad specificity, and also accepts propan-1-amine, butan-1-amine, butan-2-amine and benzylamine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Parry, R.J. and Li, W. Purification and characterization of isobutylamine N-hydroxylase from the valanimycin producer Streptomyces viridifaciens MG456-hF10. Arch. Biochem. Biophys. 339 (1997) 47-54. [PMID: 9056232]
2. Parry, R.J., Li, W. and Cooper, H.N. Cloning, analysis, and overexpression of the gene encoding isobutylamine N-hydroxylase from the valanimycin producer, Streptomyces viridifaciens. J. Bacteriol. 179 (1997) 409-416. [PMID: 8990292]
3. Parry, R.J. and Li, W. An NADPH:FAD oxidoreductase from the valanimycin producer, Streptomyces viridifaciens. Cloning, analysis, and overexpression. J. Biol. Chem. 272 (1997) 23303-23311. [PMID: 9287340]
Accepted name: phenylacetaldehyde oxime monooxygenase
Reaction: (E)-phenylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + O2 = (R)-mandelonitrile + [oxidized NADPH—hemoprotein reductase] + 2 H2O (overall reaction)
(1a) (E)-phenylacetaldehyde oxime = (Z)-phenylacetaldehyde oxime
(1b) (Z)-phenylacetaldehyde oxime = phenylacetonitrile + H2O
(1c) phenylacetonitrile + [reduced NADPH—hemoprotein reductase] + O2 = (R)-mandelonitrile + [oxidized NADPH—hemoprotein reductase] + H2O
Glossary: (R)-mandelonitrile = (2R)-hydroxy(phenyl)acetonitrile
Other name(s): CYP71AN24 (gene name)
Systematic name: (E)-phenylacetaldehyde oxime,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase
Comments: This cytochrome P-450 (heme-thiolate) enzyme is involved in the biosynthesis of the cyanogenic glucosides (R)-prunasin and (R)-amygdalin. It catalyses three different activities - isomerization of the (E) isomer to the (Z) isomer, dehydration, and C-hydroxylation.
References:
1. Yamaguchi, T., Yamamoto, K. and Asano, Y. Identification and characterization of CYP79D16 and CYP71AN24 catalyzing the first and second steps in L-phenylalanine-derived cyanogenic glycoside biosynthesis in the Japanese apricot, Prunus mume Sieb. et Zucc. Plant Mol. Biol. 86 (2014) 215-223. [PMID: 25015725]
Accepted name: aromatic aldoxime N-monooxygenase
Reaction: (1) (E)-indol-3-ylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + glutathione + O2 = S-[(E)-N-hydroxy(indol-3-yl)acetimidoyl]-L-glutathione + [oxidized NADPH—hemoprotein reductase] + 2 H2O (overall reaction)
(1a) (E)-indol-3-ylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + O2 = 1-(1H-indol-3-yl)-2-aci-nitroethane + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) 1-(1H-indol-3-yl)-2-aci-nitroethane + glutathione = S-[(E)-N-hydroxy(indol-3-yl)acetimidoyl]-L-glutathione + H2O (spontaneous)
(2) (E)-phenylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + glutathione + O2 = S-[(Z)-N-hydroxy(phenyl)acetimidoyl]-L-glutathione + [oxidized NADPH—hemoprotein reductase] + 2 H2O (overall reaction)
(2a) (E)-phenylacetaldehyde oxime + [reduced NADPH—hemoprotein reductase] + O2 = 1-aci-nitro-2-phenylethane + [oxidized NADPH—hemoprotein reductase] + H2O
(2b) 1-aci-nitro-2-phenylethane + glutathione = S-[(Z)-N-hydroxy(phenyl)acetimidoyl]-L-glutathione + H2O (spontaneous)
Other name(s): CYP83B1 (gene name)
Systematic name: (E)-indol-3-ylacetaldoxime,[reduced NADPH—hemoprotein reductase],glutathione:oxygen oxidoreductase (oxime-hydroxylating)
Comments: This cytochrome P-450 (heme thiolate) enzyme is involved in the biosynthesis of glucosinolates in plants. The enzyme catalyses the N-hydroxylation of aromatic aldoximes derived from L-tryptophan, L-phenylalanine, and L-tyrosine, forming an aci-nitro intermediate that reacts non-enzymically with glutathione to produce an N-alkyl-thiohydroximate adduct, the committed precursor of glucosinolates. In the absence of glutathione, the enzyme is suicidal, probably due to interaction of the reactive aci-nitro compound with catalytic residues in the active site.
References:
1. Bak, S., Tax, F.E., Feldmann, K.A., Galbraith, D.W. and Feyereisen, R. CYP83B1, a cytochrome P450 at the metabolic branch point in auxin and indole glucosinolate biosynthesis in Arabidopsis. Plant Cell 13 (2001) 101-111. [PMID: 11158532]
2. Naur, P., Petersen, B.L., Mikkelsen, M.D., Bak, S., Rasmussen, H., Olsen, C.E. and Halkier, B.A. CYP83A1 and CYP83B1, two nonredundant cytochrome P450 enzymes metabolizing oximes in the biosynthesis of glucosinolates in Arabidopsis. Plant Physiol. 133 (2003) 63-72. [PMID: 12970475]
3. Geu-Flores, F., Møldrup, M.E., Böttcher, C., Olsen, C.E., Scheel, D. and Halkier, B.A. Cytosolic γ-glutamyl peptidases process glutathione conjugates in the biosynthesis of glucosinolates and camalexin in Arabidopsis. Plant Cell 23 (2011) 2456-2469. [PMID: 21712415]
Accepted name: pimeloyl-[acyl-carrier protein] synthase
Reaction: a long-chain acyl-[acyl-carrier protein] + 2 reduced flavodoxin + 3 O2 = pimeloyl-[acyl-carrier protein] + an n-alkanal + 2 oxidized flavodoxin + 3 H2O (overall reaction)
(1a) a long-chain acyl-[acyl-carrier protein] + reduced flavodoxin + O2 = a (7S)-7-hydroxy-long-chain-acyl-[acyl-carrier protein] + oxidized flavodoxin + H2O
(1b) a (7S)-7-hydroxy-long-chain-acyl-[acyl-carrier protein] + reduced flavodoxin + O2 = a (7R,8R)-7,8-dihydroxy-long-chain-acyl-[acyl-carrier protein] + oxidized flavodoxin + H2O
(1c) a (7R,8R)-7,8-dihydroxy-long-chain-acyl-[acyl-carrier protein] + reduced flavodoxin + O2 = a 7-oxoheptanoyl-[acyl-carrier protein] + an n-alkanal + oxidized flavodoxin + 2 H2O
(1d) a 7-oxoheptanoyl-[acyl-carrier protein] + oxidized flavodoxin + H2O = a pimeloyl-[acyl-carrier protein] + reduced flavodoxin + H+
Glossary: a long-chain acyl-[acyl-carrier protein] = an acyl-[acyl-carrier protein] thioester where the acyl chain contains 13 to 22 carbon atoms.
palmitoyl-[acyl-carrier protein] = hexadecanoyl-[acyl-carrier protein]
pimeloyl-[acyl-carrier protein] = 6-carboxyhexanoyl-[acyl-carrier protein]
Other name(s): bioI (gene name); P450BioI; CYP107H1
Systematic name: acyl-[acyl-carrier protein],reduced-flavodoxin:oxygen oxidoreductase (pimeloyl-[acyl-carrier protein] forming)
Comments: A cytochrome P-450 (heme-thiolate) protein. The enzyme catalyses an oxidative C-C bond cleavage of long-chain acyl-[acyl-carrier protein]s of various lengths to generate pimeloyl-[acyl-carrier protein], an intermediate in the biosynthesis of biotin. The preferred substrate of the enzyme from the bacterium Bacillus subtilis is palmitoyl-[acyl-carrier protein] which then gives heptanal as the alkanal. The mechanism is similar to EC 1.14.15.6, cholesterol monooxygenase (side-chain-cleaving), followed by a hydroxylation step, which may occur spontaneously [2].
References:
1. Stok, J.E. and De Voss, J. Expression, purification, and characterization of BioI: a carbon-carbon bond cleaving cytochrome P450 involved in biotin biosynthesis in Bacillus subtilis. Arch. Biochem. Biophys. 384 (2000) 351-360. [PMID: 11368323]
2. Cryle, M.J. and De Voss, J.J. Carbon-carbon bond cleavage by cytochrome p450(BioI)(CYP107H1). Chem. Commun. (Camb.) (2004) 86-87. [PMID: 14737344]
3. Cryle, M.J. and Schlichting, I. Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex. Proc. Natl. Acad. Sci. USA 105 (2008) 15696-15701. [PMID: 18838690]
4. Cryle, M.J. Selectivity in a barren landscape: the P450(BioI)-ACP complex. Biochem. Soc. Trans. 38 (2010) 934-939. [PMID: 20658980]
Accepted name: nitric-oxide synthase (flavodoxin)
Reaction: 2 L-arginine + 3 reduced flavodoxin + 4 O2 = 2 L-citrulline + 2 nitric oxide + 3 oxidized flavodoxin + 4 H2O (overall reaction)
(1a) 2 L-arginine + 2 reduced flavodoxin + 2 O2 = 2 Nω-hydroxy-L-arginine + 2 oxidized flavodoxin + 2 H2O
(1b) 2 Nω-hydroxy-L-arginine + reduced flavodoxin + 2 O2 = 2 L-citrulline + 2 nitric oxide + oxidized flavodoxin + 2 H2O
Glossary: nitric oxide = NO = nitrogen(II) oxide
Other name(s): nitric oxide synthetase (ambiguous); NO synthase (ambiguous)
Systematic name: L-arginine,reduced-flavodoxin:oxygen oxidoreductase (nitric-oxide-forming)
Comments: Binds heme (iron protoporphyrin IX) and tetrahydrobiopterin. The enzyme, found in bacteria and archaea, consist of only an oxygenase domain and functions together with bacterial ferredoxins or flavodoxins. The orthologous enzymes from plants and animals also contain a reductase domain and use only NADPH as the electron donor (cf. EC 1.14.13.39).
References:
1. Pant, K., Bilwes, A.M., Adak, S., Stuehr, D.J. and Crane, B.R. Structure of a nitric oxide synthase heme protein from Bacillus subtilis. Biochemistry 41 (2002) 11071-11079. [PMID: 12220171]
2. Adak, S., Aulak, K.S. and Stuehr, D.J. Direct evidence for nitric oxide production by a nitric-oxide synthase-like protein from Bacillus subtilis. J. Biol. Chem. 277 (2002) 16167-16171. [PMID: 11856757]
3. 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]
4. 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]
5. Holden, J.K., Lim, N. and Poulos, T.L. Identification of redox partners and development of a novel chimeric bacterial nitric oxide synthase for structure activity analyses. J. Biol. Chem. 289 (2014) 29437-29445. [PMID: 25194416]
[EC 1.14.15.12 Transferred entry: pimeloyl-[acyl-carrier protein] synthase, now EC 1.14.14.46, pimeloyl-[acyl-carrier protein] synthase (EC 1.14.15.12 created 2013, deleted 2017)]
Accepted name: (S)-corytuberine synthase
Reaction: (S)-reticuline + [reduced NADPH—hemoprotein reductase] + O2 = (S)-corytuberine + [oxidized NADPH—hemoprotein reductase] + 2 H2O.
For diagram of reaction click here.
Other name(s): CYP80G2
Systematic name: (S)-reticuline,NADPH:oxygen oxidoreductase (C-C phenol-coupling; (S)-corytuberine-forming)
Comments: A cytochrome P-450 (heme-thiolate) protein. The enzyme is involved in the biosynthesis of the quaternary benzylisoquinoline alkaloid magnoflorine in the plant Coptis japonica. It is specific for (S)-reticuline.
References:
1. Ikezawa, N., Iwasa, K. and Sato, F. Molecular cloning and characterization of CYP80G2, a cytochrome P450 that catalyzes an intramolecular C-C phenol coupling of (S)-reticuline in magnoflorine biosynthesis, from cultured Coptis japonica cells. J. Biol. Chem. 283 (2008) 8810-8821. [PMID: 18230623]
Accepted name: lytic cellulose monooxygenase (C1-hydroxylating)
Reaction: [(1→4)-β-D-glucosyl]n+m + reduced acceptor + O2 = [(1→4)-β-D-glucosyl]m-1-(1→4)-D-glucono-1,5-lactone + [(1→4)-β-D-glucosyl]n + acceptor + H2O
Other name(s): lytic polysaccharide monooxygenase (ambiguous); LPMO (ambiguous); LPMO9A
Systematic name: cellulose, hydrogen-donor:oxygen oxidoreductase (D-glucosyl C1-hydroxylating)
Comments: This copper-containing enzyme, found in fungi and bacteria, cleaves cellulose in an oxidative manner. The cellulose fragments that are formed contain a D-glucono-1,5-lactone residue at the reducing end, which hydrolyses quickly and spontaneously to the aldonic acid. The electrons are provided in vivo by the cytochrome b domain of EC 1.1.99.18, cellobiose dehydrogenase (acceptor) [1]. Ascorbate can serve as the electron donor in vitro.
References:
1. Phillips, C.M., Beeson, W.T., Cate, J.H. and Marletta, M.A. Cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by Neurospora crassa. ACS Chem. Biol. 6 (2011) 1399-1406. [PMID: 22004347]
2. Beeson, W.T., Phillips, C.M., Cate, J.H. and Marletta, M.A. Oxidative cleavage of cellulose by fungal copper-dependent polysaccharide monooxygenases. J. Am. Chem. Soc. 134 (2012) 890-892. [PMID: 22188218]
3. Li, X., Beeson, W.T., 4th, Phillips, C.M., Marletta, M.A. and Cate, J.H. Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases. Structure 20 (2012) 1051-1061. [PMID: 22578542]
4. Bey, M., Zhou, S., Poidevin, L., Henrissat, B., Coutinho, P.M., Berrin, J.G. and Sigoillot, J.C. Cello-oligosaccharide oxidation reveals differences between two lytic polysaccharide monooxygenases (family GH61) from Podospora anserina. Appl. Environ. Microbiol. 79 (2013) 488-496. [PMID: 23124232]
5. Frommhagen, M., Sforza, S., Westphal, A.H., Visser, J., Hinz, S.W., Koetsier, M.J., van Berkel, W.J., Gruppen, H. and Kabel, M.A. Discovery of the combined oxidative cleavage of plant xylan and cellulose by a new fungal polysaccharide monooxygenase. Biotechnol. Biofuels 8 (2015) 101. [PMID: 26185526]
6. Patel, I., Kracher, D., Ma, S., Garajova, S., Haon, M., Faulds, C.B., Berrin, J.G., Ludwig, R. and Record, E. Salt-responsive lytic polysaccharide monooxygenases from the mangrove fungus Pestalotiopsis sp. NCi6. Biotechnol Biofuels 9 (2016) 108. [PMID: 27213015]
7. Courtade, G., Wimmer, R., Rohr, A.K., Preims, M., Felice, A.K., Dimarogona, M., Vaaje-Kolstad, G., Sorlie, M., Sandgren, M., Ludwig, R., Eijsink, V.G. and Aachmann, F.L. Interactions of a fungal lytic polysaccharide monooxygenase with β-glucan substrates and cellobiose dehydrogenase. Proc. Natl. Acad. Sci. USA 113 (2016) 5922-5927. [PMID: 27152023]
Accepted name: lytic starch monooxygenase
Reaction: starch + reduced acceptor + O2 = D-glucono-1,5-lactone-terminated malto-oligosaccharides + short-chain malto-oligosaccharides + acceptor + H2O
Other name(s): LPMO (ambiguous)
Systematic name: starch, hydrogen-donor:oxygen oxidoreductase (D-glucosyl C1-hydroxylating)
Comments: The enzyme cleaves starch in an oxidative manner. It releases fragments of starch with a D-glucono-1,5-lactone at the reducing end. The initially formed α-D-glucono-1,5-lactone at the reducing end of the shortend amylose chain quickly hydrolyses spontaneously to the aldonic acid. In vitro ascorbate has been found to be able to serve as reducing agent. The enzyme contains copper at the active site.
References:
1. Vu, V.V., Beeson, W.T., Span, E.A., Farquhar, E.R. and Marletta, M.A. A family of starch-active polysaccharide monooxygenases. Proc. Natl. Acad. Sci. USA 111 (2014) 13822-13827. [PMID: 25201969]
2. Gudmundsson, M., Kim, S., Wu, M., Ishida, T., Momeni, M.H., Vaaje-Kolstad, G., Lundberg, D., Royant, A., Stahlberg, J., Eijsink, V.G., Beckham, G.T. and Sandgren, M. Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-ray photoreduction. J. Biol. Chem. 289 (2014) 18782-18792. [PMID: 24828494]
3. Lo Leggio, L., Simmons, T.J., Poulsen, J.C., Frandsen, K.E., Hemsworth, G.R., Stringer, M.A., von Freiesleben, P., Tovborg, M., Johansen, K.S., De Maria, L., Harris, P.V., Soong, C.L., Dupree, P., Tryfona, T., Lenfant, N., Henrissat, B., Davies, G.J. and Walton, P.H. Structure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase. Nat. Commun. 6 (2015) 5961. [PMID: 25608804]
Accepted name: lytic cellulose monooxygenase (C4-dehydrogenating)
Reaction: [(1→4)-β-D-glucosyl]n+m + reduced acceptor + O2 = 4-dehydro-β-D-glucosyl-[(1→4)-β-D-glucosyl]n-1 + [(1→4)-β-D-glucosyl]m + acceptor + H2O
Systematic name: cellulose, hydrogen-donor:oxygen oxidoreductase (D-glucosyl 4-dehydrogenating)
Comments: This copper-containing enzyme, found in fungi and bacteria, cleaves cellulose in an oxidative manner. The cellulose fragments that are formed contain a 4-dehydro-D-glucose residue at the non-reducing end. Some enzymes also oxidize cellulose at the C-1 position of the reducing end forming a D-glucono-1,5-lactone residue [cf. EC 1.14.99.54, lytic cellulose monooxygenase (C1-hydroxylating)].
References:
1. Beeson, W.T., Phillips, C.M., Cate, J.H. and Marletta, M.A. Oxidative cleavage of cellulose by fungal copper-dependent polysaccharide monooxygenases. J. Am. Chem. Soc. 134 (2012) 890-892. [PMID: 22188218]
2. Li, X., Beeson, W.T., 4th, Phillips, C.M., Marletta, M.A. and Cate, J.H. Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases. Structure 20 (2012) 1051-1061. [PMID: 22578542]
3. Forsberg, Z., Mackenzie, A.K., Sorlie, M., Rohr, A.K., Helland, R., Arvai, A.S., Vaaje-Kolstad, G. and Eijsink, V.G. Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases. Proc. Natl. Acad. Sci. USA 111 (2014) 8446-8451. [PMID: 24912171]
4. Borisova, A.S., Isaksen, T., Dimarogona, M., Kognole, A.A., Mathiesen, G., Varnai, A., Rohr, A.K., Payne, C.M., Sorlie, M., Sandgren, M. and Eijsink, V.G. Structural and functional characterization of a lytic polysaccharide monooxygenase with broad substrate specificity. J. Biol. Chem. 290 (2015) 22955-22969. [PMID: 26178376]
5. Patel, I., Kracher, D., Ma, S., Garajova, S., Haon, M., Faulds, C.B., Berrin, J.G., Ludwig, R. and Record, E. Salt-responsive lytic polysaccharide monooxygenases from the mangrove fungus Pestalotiopsis sp. NCi6. Biotechnol Biofuels 9 (2016) 108. [PMID: 27213015]
Accepted name: heme oxygenase (mycobilin-producing)
Reaction: (1) protoheme + 3 reduced acceptor + 3 O2 = mycobilin a + Fe2+ + 3 acceptor + 3 H2O
(2) protoheme + 3 reduced acceptor + 3 O2 = mycobilin b + Fe2+ + 3 acceptor + 3 H2O
For diagram of reaction click here.
Glossary: mycobilin a = 8,12-bis(2-carboxyethyl)-19-formyl-3,7,13,18-tetramethyl-3,17-divinylbiladiene-ab-1,15(21H)-dione
mycobilin b = 8,12-bis(2-carboxyethyl)-19-formyl-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ab-1,15(21H)-dione
Other name(s): mhuD (gene name)
Systematic name: protoheme,donor:oxygen oxidoreductase (mycobilin-producing)
Comments: The enzyme, characterized from the bacterium Mycobacterium tuberculosis, is involved in heme degradation and iron utilization. The enzyme binds two stacked protoheme molecules per monomer. Unlike the canonical heme oxygenases, the enzyme does not release carbon monoxide or formaldehyde. Instead, it forms unique products, named mycobilins, that retain the α-meso-carbon at the ring cleavage site as an aldehyde group. EC 1.6.2.4, NADPH-hemoprotein reductase, can act as electron donor in vitro.
References:
1. Chim, N., Iniguez, A., Nguyen, T.Q. and Goulding, C.W. Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis. J. Mol. Biol. 395 (2010) 595-608. [PMID: 19917297]
2. Nambu, S., Matsui, T., Goulding, C.W., Takahashi, S. and Ikeda-Saito, M. A new way to degrade heme: the Mycobacterium tuberculosis enzyme MhuD catalyzes heme degradation without generating CO. J. Biol. Chem. 288 (2013) 10101-10109. [PMID: 23420845]
3. Graves, A.B., Morse, R.P., Chao, A., Iniguez, A., Goulding, C.W. and Liptak, M.D. Crystallographic and spectroscopic insights into heme degradation by Mycobacterium tuberculosis MhuD. Inorg. Chem. 53 (2014) 5931-5940. [PMID: 24901029]
Accepted name: bacteriochlorophyllide c C-71-hydroxylase
Reaction: 2 S-adenosyl-L-methionine + a bacteriochlorophyllide c + H2O = a bacteriochlorophyllide e + 2 5'-deoxyadenosine + 2 L-methionine (overall reaction)
(1a) S-adenosyl-L-methionine + a bacteriochlorophyllide c + H2O = a 71-hydroxybacteriochlorophyllide c + 5'-deoxyadenosine + L-methionine
(1b) S-adenosyl-L-methionine + a 71-hydroxybacteriochlorophyllide c + H2O = a 71,71-dihydroxybacteriochlorophyllide c + 5'-deoxyadenosine + L-methionine
(1c) a 71,71-dihydroxybacteriochlorophyllide c = a bacteriochlorophyllide e + H2O (spontaneous)
For diagram of reaction click here.
Other name(s): bciD (gene name)
Systematic name: bacteriochlorophyllide-c:S-adenosyl-L-methionine oxidoreductase (C-71-hydroxylating)
Comments: The enzyme, found in green sulfur bacteria (Chlorobiaceae), is a radical S-adenosyl-L-methionine (AdoMet) enzyme and contains a [4Fe-4S] cluster. It catalyses two consecutive hydroxylation reactions of the C-7 methyl group of bacteriochlorophyllide c to form a geminal diol intermediate that spontaneously dehydrates to produce the formyl group of bacteriochlorophyllide e.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Harada, J., Mizoguchi, T., Satoh, S., Tsukatani, Y., Yokono, M., Noguchi, M., Tanaka, A. and Tamiaki, H. Specific gene bciD for C7-methyl oxidation in bacteriochlorophyll e biosynthesis of brown-colored green sulfur bacteria. PLoS One 8 (2013) e60026. [PMID: 23560066]
2. Thweatt, J.L., Ferlez, B.H., Golbeck, J.H. and Bryant, D.A. BciD is a radical S-adenosyl-L-methionine (SAM) enzyme that completes bacteriochlorophyllide e biosynthesis by oxidizing a methyl group into a formyl group at C-7. J. Biol. Chem. 292 (2017) 1361-1373. [PMID: 27994052]
Accepted name: methylated-DNA—[protein]-cysteine S-methyltransferase
Reaction: (1) DNA (containing 6-O-methylguanine) + protein L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine
(2) DNA (containing 4-O-methylthymine) + protein L-cysteine = DNA (without 4-O-methylthymine) + protein S-methyl-L-cysteine
Other name(s): ada (gene name); ogt (gene name); MGT1 (gene name); MGMT (gene name)
Systematic name: DNA-6-O-methylguanine/DNA-4-O-methylthymine:[protein]-L-cysteine S-methyltransferase
Comments: This protein is involved in the repair of methylated DNA. Unlike EC 3.2.2.20, DNA-3-methyladenine glycosidase I and EC 3.2.2.21, DNA-3-methyladenine glycosidase II, which remove the methylated base leaving an apurinic/apyrimidinic site, this enzyme transfers the methyl group from the methylated DNA to an internal cysteine residue, leaving an intact nucleotide. Since the methyl transfer is irreversible, the enzyme can only catalyse a single turnover.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 77271-19-3
References:
1. Foote, R.S., Mitra, S. and Pal, B.C. Demethylation of O6-methylguanine in a synthetic DNA polymer by an inducible activity in Escherichia coli. Biochem. Biophys. Res. Commun. 97 (1980) 654-659. [PMID: 7008792]
2. Olsson, M. and Lindehl, T. Repair of alkylated DNA in Escherichia coli. Methyl group transfer from O6-methylguanine to a protein cysteine residue. J. Biol. Chem. 255 (1980) 10569-10571. [PMID: 7000780]
3. McCarthy, T.V. and Lindahl, T. Methyl phosphotriesters in alkylated DNA are repaired by the Ada regulatory protein of E. coli. Nucleic Acids Res. 13 (1985) 2683-2698. [PMID: 2987862]
4. Potter, P.M., Wilkinson, M.C., Fitton, J., Carr, F.J., Brennand, J., Cooper, D.P. and Margison, G.P. Characterisation and nucleotide sequence of ogt, the O6-alkylguanine-DNA-alkyltransferase gene of E. coli. Nucleic Acids Res. 15 (1987) 9177-9193. [PMID: 2825131]
5. Rebeck, G.W., Smith, C.M., Goad, D.L. and Samson, L. Characterization of the major DNA repair methyltransferase activity in unadapted Escherichia coli and identification of a similar activity in Salmonella typhimurium. J. Bacteriol. 171 (1989) 4563-4568. [PMID: 2670886]
6. Koike, G., Maki, H., Takeya, H., Hayakawa, H. and Sekiguchi, M. Purification, structure, and biochemical properties of human O6-methylguanine-DNA methyltransferase. J. Biol. Chem. 265 (1990) 14754-14762. [PMID: 2394694]
7. Sassanfar, M., Dosanjh, M.K., Essigmann, J.M. and Samson, L. Relative efficiencies of the bacterial, yeast, and human DNA methyltransferases for the repair of O6-methylguanine and O4-methylthymine. Suggestive evidence for O4-methylthymine repair by eukaryotic methyltransferases. J. Biol. Chem. 266 (1991) 2767-2771. [PMID: 1993655]
8. Xiao, W., Derfler, B., Chen, J. and Samson, L. Primary sequence and biological functions of a Saccharomyces cerevisiae O6-methylguanine/O4-methylthymine DNA repair methyltransferase gene. EMBO J. 10 (1991) 2179-2186. [PMID: 2065659]
Accepted name: tetrahydromethanopterin S-methyltransferase
Reaction: 5-methyl-5,6,7,8-tetrahydromethanopterin + coenzyme M + 2 Na+in = 5,6,7,8-tetrahydromethanopterin + 2-(methylsulfanyl)ethane-1-sulfonate + 2 Na+out
For diagram of reaction click here.
Glossary: coenzyme M (CoM) = 2-sulfanylethane-1-sulfonate
tetrahydromethanopterin = 1-(4-{(1R)-1-[(6S,7S)-2-amino-7-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]ethylamino}phenyl)-1-deoxy-5-O-{5-O-[(1S)-1,3-dicarboxypropylphosphonato]-α-D-ribofuranosyl}-D-ribitol
Other name(s): tetrahydromethanopterin methyltransferase; mtrA-H (gene names); cmtA (gene name)
Systematic name: 5-methyl-5,6,7,8-tetrahydromethanopterin:2-sulfanylethane-1-sulfonate 2-methyltransferase
Comments: Involved in the formation of methane from CO2 in methanogenic archaea. The reaction involves the export of one or two sodium ions. The enzyme from the archaeon Methanobacterium thermoautotrophicum is a membrane-associated multienzyme complex composed of eight different subunits, and contains a 5'-hydroxybenzimidazolyl-cobamide prosthetic group, to which the methyl group is attached during the transfer. A soluble enzyme that is induced by the presence of CO has been reported as well [6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 103406-60-6
References:
1. Sauer, F.D. Tetrahydromethanopterin methyltransferase, a component of the methane synthesizing complex of Methanobacterium thermoautotrophicum. Biochem. Biophys. Res. Commun. 136 (1986) 542-547. [PMID: 3085670]
2. Gartner, P., Ecker, A., Fischer, R., Linder, D., Fuchs, G. and Thauer, R.K. Purification and properties of N5-methyltetrahydromethanopterin:coenzyme M methyltransferase from Methanobacterium thermoautotrophicum. Eur. J. Biochem. 213 (1993) 537-545. [PMID: 8477726]
3. Weiss, D.S., Gartner, P. and Thauer, R.K. The energetics and sodium-ion dependence of N5-methyltetrahydromethanopterin:coenzyme M methyltransferase studied with cob(I)alamin as methyl acceptor and methylcob(III)alamin as methyl donor. Eur. J. Biochem. 226 (1994) 799-809. [PMID: 7813469]
4. Harms, U., Weiss, D.S., Gartner, P., Linder, D. and Thauer, R.K. The energy conserving N5-methyltetrahydromethanopterin:coenzyme M methyltransferase complex from Methanobacterium thermoautotrophicum is composed of eight different subunits. Eur. J. Biochem. 228 (1995) 640-648. [PMID: 7737157]
5. Gottschalk, G. and Thauer, R.K. The Na(+)-translocating methyltransferase complex from methanogenic archaea. Biochim. Biophys. Acta 1505 (2001) 28-36. [PMID: 11248186]
6. Vepachedu, V.R. and Ferry, J.G. Role of the fused corrinoid/methyl transfer protein CmtA during CO-dependent growth of Methanosarcina acetivorans. J. Bacteriol. 194 (2012) 4161-4168. [PMID: 22636775]
Accepted name: 3-aminomethylindole N-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + 3-(aminomethyl)indole = 2 S-adenosyl-L-homocysteine + gramine (overall reaction)
(1a) S-adenosyl-L-methionine + 3-(aminomethyl)indole = S-adenosyl-L-homocysteine + (1H-indol-3-yl)-N-methylmethanamine
(1b) S-adenosyl-L-methionine + (1H-indol-3-yl)-N-methylmethanamine = S-adenosyl-L-homocysteine + gramine
For diagram of reaction click here.
Glossary: 3-(aminomethyl)indole = (1H-indol-3-yl)methanamine
gramine = (1H-indol-3-ylmethyl)dimethylamine = (1H-indol-3-yl)-N,N-dimethylmethanamine
Other name(s): NMT (gene name)
Systematic name: S-adenosyl-L-methionine:3-(aminomethyl)indole N-methyltransferase (gramine-forming)
Comments: The enzyme, characterized from Hordeum vulgare (barley), catalyses two successive N-methylation reactions during the biosynthesis of gramine, a toxic indole alkaloid.
References:
1. Leland, T.J. and Hanson, A.D. Induction of a specific N-methyltransferase enzyme by long-term heat stress during barley leaf growth. Plant Physiol. 79 (1985) 451-457. [PMID: 16664431]
2. Larsson, K.A., Zetterlund, I., Delp, G. and Jonsson, L.M. N-Methyltransferase involved in gramine biosynthesis in barley: cloning and characterization. Phytochemistry 67 (2006) 2002-2008. [PMID: 16930646]
Accepted name: vanillate/3-O-methylgallate O-demethylase
Reaction: (1) vanillate + tetrahydrofolate = protocatechuate + 5-methyltetrahydrofolate
(2) 3-O-methylgallate + tetrahydrofolate = gallate + 5-methyltetrahydrofolate
Glossary: protocatechuate = 3,4-dihydroxybenzoate
vanillate = 4-hydroxy-3-methoxybenzoate
gallate = 3,4,5-trihydroxybenzoate
Other name(s): ligM (gene name)
Systematic name: vanillate:tetrahydrofolate O-methyltransferase
Comments: The enzyme, characterized from the bacterium Sphingomonas sp. SYK6, is involved in the degradation of lignin. The enzyme has similar activities with vanillate and 3-O-methylgallate.
References:
1. Nishikawa, S., Sonoki, T., Kasahara, T., Obi, T., Kubota, S., Kawai, S., Morohoshi, N. and Katayama, Y. Cloning and sequencing of the Sphingomonas (Pseudomonas) paucimobilis gene essential for the O demethylation of vanillate and syringate. Appl. Environ. Microbiol. 64 (1998) 836-842. [PMID: 9501423]
2. Masai, E., Sasaki, M., Minakawa, Y., Abe, T., Sonoki, T., Miyauchi, K., Katayama, Y. and Fukuda, M. A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate. J. Bacteriol. 186 (2004) 2757-2765. [PMID: 15090517]
3. Abe, T., Masai, E., Miyauchi, K., Katayama, Y. and Fukuda, M. A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6. J. Bacteriol. 187 (2005) 2030-2037. [PMID: 15743951]
Accepted name: anaerobilin synthase
Reaction: 2 S-adenosyl-L-methionine + protoheme + 2 reduced flavodoxin = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + anaerobilin + Fe2+ + 2 oxidized flavodoxin
For diagram of reaction click here.
Glossary: anaerobilin = (4Z,10Z,14E)-8,12-bis(2-carboxyethyl)-3,7,13,18-tetramethyl-1,2,17-trivinyl-23,24-dihydrobilin
Other name(s): chuW (gene name)
Systematic name: S-adenosyl-L-methionine:protoheme C-methyltransferase (anaerobilin-producing)
Comments: The enzyme, studied from the bacterium Escherichia coli O157:H7, is a radical SAM (AdoMet) enzyme that is involved in heme degradation and iron utilization under anaerobic conditions. The enzyme uses two SAM molecules for the reaction. The first molecule is used to generate a 5'-deoxyadenosyl radical, which abstracts a hydrogen atom from the methyl group of the second SAM molecule. The newly formed methylene radical attacks the substrate, causing a rearrangement of the porphyrin ring that results in the liberation of iron.
References:
1. LaMattina, J.W., Nix, D.B. and Lanzilotta, W.N. Radical new paradigm for heme degradation in Escherichia coli O157:H7. Proc. Natl. Acad. Sci. USA 113 (2016) 12138-12143. [PMID: 27791000]
2. LaMattina, J.W., Delrossi, M., Uy, K.G., Keul, N.D., Nix, D.B., Neelam, A.R. and Lanzilotta, W.N. Anaerobic heme degradation: ChuY Is an anaerobilin reductase that exhibits kinetic cooperativity. Biochemistry 56 (2017) 845-855. [PMID: 28045510]
Accepted name: mycocerosate synthase
Reaction: (1) a long-chain acyl-[mycocerosic acid synthase] + 3 methylmalonyl-CoA + 6 NADPH + 6 H+ = a trimethylated-mycocerosoyl-[mycocerosate synthase] + 3 CoA + 3 CO2 + 6 NADP+ + 3 H2O
(2) a long-chain acyl-[mycocerosic acid synthase] + 4 methylmalonyl-CoA + 8 NADPH + 8 H+ = a tetramethylated-mycocerosoyl-[mycocerosate synthase] + 4 CoA + 4 CO2 + 8 NADP+ + 4 H2O
Glossary: mycocerosic acid = a long-chain fatty acid with 3 or 4 methyl branches at positions 2,4,6 or 2,4,6,8, respectively. The carbon atoms bearing the methyl groups have the (R)-configuration.
Other name(s): mas (gene name); mycocerosic acid synthase; acyl-CoA:methylmalonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing); long-chain acyl-CoA:methylmalonyl-CoA C-acyltransferase (mycocerosate-forming)
Systematic name: long-chain acyl-[mycocerosic acid synthase]:methylmalonyl-CoA C-acyltransferase (mycocerosate-forming)
Comments: The enzyme, characterized from mycobacteria, is loaded with a long-chain acyl moiety by EC 6.2.1.49, long-chain fatty acid adenylyltransferase FadD28, and elongates it by incorporation of three or four methylmalonyl (but not malonyl) residues, to form tri- or tetramethyl-branched fatty-acids, respectively, such as 2,4,6,8-tetramethyloctacosanoate (C32-mycocerosate). Since the enzyme lacks a thioesterase domain, the product remains bound and requires additional enzyme(s) for removal. Even though the enzyme can accept C6 to C20 substrates in vitro, it prefers to act on C14-C20 substrates in vivo.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 95229-19-9
References:
1. Rainwater, D.L. and Kollattukudy, P.E. Fatty acid biosynthesis in Mycobacterium tuberculosis var. bovis Bacillus Calmette-Guérin. Purification and characterization of a novel fatty acid synthase, mycocerosic acid synthase, which elongates n-fatty acyl-CoA with methylmalonyl-CoA. J. Biol. Chem. 260 (1985) 616-623. [PMID: 3880746]
2. Mathur, M. and Kolattukudy, P.E. Molecular cloning and sequencing of the gene for mycocerosic acid synthase, a novel fatty acid elongating multifunctional enzyme, from Mycobacterium tuberculosis var. bovis Bacillus Calmette-Guerin. J. Biol. Chem. 267 (1992) 19388-19395. [PMID: 1527058]
3. Trivedi, O.A., Arora, P., Vats, A., Ansari, M.Z., Tickoo, R., Sridharan, V., Mohanty, D. and Gokhale, R.S. Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid. Mol. Cell 17 (2005) 631-643. [PMID: 15749014]
4. Menendez-Bravo, S., Comba, S., Sabatini, M., Arabolaza, A. and Gramajo, H. Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli. Metab. Eng. 24 (2014) 97-106. [PMID: 24831705]
Accepted name: β-lysine N6-acetyltransferase
Reaction: acetyl-CoA + (3S)-3,6-diaminohexanoate = CoA + (3S)-6-acetamido-3-aminohexanoate
Glossary: (3S)-3,6-diaminohexanoate = β-L-lysine
(3S)-6-acetamido-3-aminohexanoate = N6-acetyl-β-L-lysine
Other name(s): ablB (gene name)
Systematic name: acetyl-CoA:(3S)-3,6-diaminohexanoate N6-acetyltransferase
Comments: The enzyme is found in some methanogenic archaea and bacteria. In archaea it is induced under salt stress. The product, N6-acetyl-β-L-lysine, serves as a compatible solute, conferring high salt resistance on the producing organisms.
References:
1. Pfluger, K., Baumann, S., Gottschalk, G., Lin, W., Santos, H. and Muller, V. Lysine-2,3-aminomutase and β-lysine acetyltransferase genes of methanogenic archaea are salt induced and are essential for the biosynthesis of Nε-acetyl-β-lysine and growth at high salinity. Appl. Environ. Microbiol. 69 (2003) 6047-6055. [PMID: 14532061]
2. Muller, S., Hoffmann, T., Santos, H., Saum, S.H., Bremer, E. and Muller, V. Bacterial abl-like genes: production of the archaeal osmolyte N(ε)-acetyl-β-lysine by homologous overexpression of the yodP-kamA genes in Bacillus subtilis. Appl. Microbiol. Biotechnol. 91 (2011) 689-697. [PMID: 21538109]
Accepted name: 2-phosphonomethylmalate synthase
Reaction: acetyl-CoA + H2O + 3-phosphonopyruvate = (R)-2-(phosphonomethyl)malate + CoA
Other name(s): 2-phosphinomethylmalic acid synthase; PMM synthase
Systematic name: acetyl-CoA:3-phosphonopyruvate C-acetyltransferase
Comments: The enzyme, isolated from several Streptomyces species, participate in the biosynthesis of certain phosphonate antibiotics. The enzyme is analogous to EC 2.3.3.1 (Si)-citrate synthase.
References:
1. Shimotohno, K., Seto, H., Otake, N., Imai, S. and Satoh, A. Studies on the biosynthesis of bialaphos (SE-1293). 7. The absolute configuration of 2-phosphinomethylmalic acid, a biosynthetic intermediate of bialaphos. J. Antibiot. (Tokyo) 39 (1986) 1356-1359. [PMID: 3781934]
2. Shimotohno, K.W., Seto, H., Otake, N., Imai, S. and Murakami, T. Studies on the biosynthesis of bialaphos (SF-1293). 8. Purification and characterization of 2-phosphinomethylmalic acid synthase from Streptomyces hygroscopicus SF-1293. J. Antibiot. (Tokyo) 41 (1988) 1057-1065. [PMID: 3170341]
3. Eliot, A.C., Griffin, B.M., Thomas, P.M., Johannes, T.W., Kelleher, N.L., Zhao, H. and Metcalf, W.W. Cloning, expression, and biochemical characterization of Streptomyces rubellomurinus genes required for biosynthesis of antimalarial compound FR900098. Chem. Biol. 15 (2008) 765-770. [PMID: 18721747]
[EC 2.4.1.57 Deleted entry: phosphatidylinositol α-mannosyltransferase. Newer studies have shown that this is catalysed by two independent activities now covered by EC 2.4.1.345, phosphatidyl-myo-inositol α-mannosyl transferase, and EC 2.4.1.346, phosphatidyl-myo-inositol dimannoside synthase (EC 2.4.1.57 created 1972, modified 2003, deleted 2017)]
Accepted name: N-acetyl-β-D-glucosaminide β-(1,3)-galactosyltransferase
Reaction: UDP-α-D-galactose + N-acetyl-β-D-glucosaminyl-R = UDP + β-D-galactosyl-(1→3)-N-acetyl-β-D-glucosaminyl-R
For diagram of reaction click here.
Other name(s): B3GALT1 (gene name); uridine diphosphogalactose-acetyl-glucosaminylgalactosylglucosylceramide galactosyltransferase; GalT-4; UDP-galactose:N-acetyl-D-glucosaminyl-1,3-D-galactosyl-1,4-D-glucosylceramide β-D-galactosyltransferase; UDP-galactose:N-acetyl-D-glucosaminyl-(1→3)-D-galactosyl-(1→4)-D-glucosylceramide 3-β-D-galactosyltransferase; UDP-galactose:N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosylceramide 3-β-D-galactosyltransferase; UDP-galactose:N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosyl(1↔1)ceramide 3-β-D-galactosyltransferase; UDP-galactose:N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide 3-β-D-galactosyltransferase; glucosaminylgalactosylglucosylceramide β-galactosyltransferase
Systematic name: UDP-α-D-galactose:N-acetyl-β-D-glucosaminyl-R 3-β-D-galactosyltransferase
Comments: The enzyme transfers galactose from UDP-galactose to the 3-position of substrates with a non-reducing terminal N-acetyl-β-D-glucosamine (β-GlcNAc) residue. It can act on both glycolipids and glycoproteins, generating a structure known as the type 1 histo-blood group antigen precursor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9073-46-5
References:
1. Basu, M. and Basu, S. Enzymatic synthesis of a tetraglycosylceramide by a galactosyltransferase from rabbit bone marrow. J. Biol. Chem. 247 (1972) 1489-1495. [PMID: 4335001]
2. Basu, M., Presper, K.A., Basu, S., Hoffman, L.M. and Brooks, S.E. Differential activities of glycolipid glycosyltransferases in Tay-Sachs disease: studies in cultured cells from cerebrum. Proc. Natl. Acad. Sci. USA 76 (1979) 4270-4274. [PMID: 291963]
3. Amado, M., Almeida, R., Carneiro, F., Levery, S.B., Holmes, E.H., Nomoto, M., Hollingsworth, M.A., Hassan, H., Schwientek, T., Nielsen, P.A., Bennett, E.P. and Clausen, H. A family of human β3-galactosyltransferases. Characterization of four members of a UDP-galactose:β-N-acetyl-glucosamine/β-nacetyl-galactosamine β-1,3-galactosyltransferase family. J. Biol. Chem. 273 (1998) 12770-12778. [PMID: 9582303]
4. Amado, M., Almeida, R., Schwientek, T. and Clausen, H. Identification and characterization of large galactosyltransferase gene families: galactosyltransferases for all functions. Biochim. Biophys. Acta 1473 (1999) 35-53. [PMID: 10580128]
5. Bardoni, A., Valli, M. and Trinchera, M. Differential expression of β1,3galactosyltransferases in human colon cells derived from adenocarcinomas or normal mucosa. FEBS Lett. 451 (1999) 75-80. [PMID: 10356986]
Accepted name: phosphatidyl-myo-inositol α-mannosyltransferase
Reaction: GDP-α-D-mannose + 1-phosphatidyl-1D-myo-inositol = GDP + 2-O-(α-D-mannosyl)-1-phosphatidyl-1D-myo-inositol
Glossary: 1-phosphatidyl-1D-myo-inositol = PtdIns
Other name(s): mannosyltransferase PimA; PimA; guanosine diphosphomannose-phosphatidyl-inositol α-mannosyltransferase (ambiguous)
Systematic name: GDP-α-D-mannose:1-phosphatidyl-1D-myo-inositol 2-α-D-mannosyltransferase (configuration-retaining)
Comments: Requires Mg2+. The enzyme, found in Corynebacteriales, is involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs).
References:
1. Kordulakova, J., Gilleron, M., Mikusova, K., Puzo, G., Brennan, P.J., Gicquel, B. and Jackson, M. Definition of the first mannosylation step in phosphatidylinositol mannoside synthesis. PimA is essential for growth of mycobacteria. J. Biol. Chem. 277 (2002) 31335-31344. [PMID: 12068013]
2. Gu, X., Chen, M., Wang, Q., Zhang, M., Wang, B. and Wang, H. Expression and purification of a functionally active recombinant GDP-mannosyltransferase (PimA) from Mycobacterium tuberculosis H37Rv. Protein Expr. Purif. 42 (2005) 47-53. [PMID: 15939292]
3. Giganti, D., Albesa-Jove, D., Urresti, S., Rodrigo-Unzueta, A., Martinez, M.A., Comino, N., Barilone, N., Bellinzoni, M., Chenal, A., Guerin, M.E. and Alzari, P.M. Secondary structure reshuffling modulates glycosyltransferase function at the membrane. Nat. Chem. Biol. 11 (2015) 16-18. [PMID: 25402770]
4. Rodrigo-Unzueta, A., Martinez, M.A., Comino, N., Alzari, P.M., Chenal, A. and Guerin, M.E. Molecular basis of membrane association by the phosphatidylinositol mannosyltransferase PimA enzyme from Mycobacteria. J. Biol. Chem. 291 (2016) 13955-13963. [PMID: 27189944]
Accepted name: phosphatidyl-myo-inositol dimannoside synthase
Reaction: (1) GDP-α-D-mannose + 2-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol = GDP + 2,6-di-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol
(2) GDP-α-D-mannose + 2-O-(6-O-acyl-α-D-mannosyl)-1-phosphatidyl-1D-myo-inositol = GDP + 2-O-(6-O-acyl-α-D-mannosyl)-6-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol
Glossary: 1-phosphatidyl-1D-myo-inositol = PtdIns
Other name(s): mannosyltransferase PimB; PimB; guanosine diphosphomannose-phosphatidyl-inositol α-mannosyltransferase (ambiguous)
Systematic name: GDP-α-D-mannose:2-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol 6-α-D-mannosyltransferase (configuration-retaining)
Comments: Requires Mg2+. The enzyme, found in Corynebacteriales, is involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs).
References:
1. Guerin, M.E., Kaur, D., Somashekar, B.S., Gibbs, S., Gest, P., Chatterjee, D., Brennan, P.J. and Jackson, M. New insights into the early steps of phosphatidylinositol mannoside biosynthesis in mycobacteria: PimB' is an essential enzyme of Mycobacterium smegmatis. J. Biol. Chem. 284 (2009) 25687-25696. [PMID: 19638342]
2. Mishra, A.K., Batt, S., Krumbach, K., Eggeling, L. and Besra, G.S. Characterization of the Corynebacterium glutamicum Δ pimB' Δ mgtA double deletion mutant and the role of Mycobacterium tuberculosis orthologues Rv2188c and Rv0557 in glycolipid biosynthesis. J. Bacteriol. 191 (2009) 4465-4472. [PMID: 19395496]
3. Batt, S.M., Jabeen, T., Mishra, A.K., Veerapen, N., Krumbach, K., Eggeling, L., Besra, G.S. and Futterer, K. Acceptor substrate discrimination in phosphatidyl-myo-inositol mannoside synthesis: structural and mutational analysis of mannosyltransferase Corynebacterium glutamicum PimB'. J. Biol. Chem. 285 (2010) 37741-37752. [PMID: 20843801]
Accepted name: β-D-galactosyl-(1→3)-N-acetyl-β-D-galactosaminide α-2,3-sialyltransferase
Reaction: CMP-N-acetyl-β-neuraminate + a β-D-galactosyl-(1→3)-N-acetyl-β-D-galactosaminyl-R = CMP + an N-acetyl-α-neuraminyl-(2→3)-β-D-galactosyl-(1→3)-N-acetyl-β-D-galactosaminyl-R
For diagram of reaction click here.
Glossary: a β-D-galactosyl-(1→3)-N-acetyl-β-D-galactosaminyl-(1→4)-[N-acetyl-α-neuraminyl-(2→3)]-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide = gangloside GM1a
an N-acetyl-α-neuraminyl-(2→3)-β-D-galactosyl-(1→3)-N-acetyl-β-D-galactosaminyl-(1→4)-[N-acetyl-α-neuraminyl-(2→3)]-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide = gangloside GD1a
Other name(s): CMP-N-acetylneuraminate:D-galactosyl-N-acetyl-D-galactosaminyl-(N-acetylneuraminyl)-D-galactosyl-D-glucosyl-(1↔1)-ceramide N-acetylneuraminyltransferase (ambiguous); monosialoganglioside sialyltransferase; CMP-N-acetylneuraminate:a β-D-galactosyl-(1→3)-N-acetyl-β-D-galactosaminyl-(1→4)-[α-N-acetylneuraminyl-(2→3)]-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide N-acetyl-β-neuraminyltransferase
Systematic name: CMP-N-acetyl-β-neuraminate:a β-D-galactosyl-(1→3)-N-acetyl-β-D-galactosaminyl-R α-(2→3)-N-acetylneuraminyltransferase (configuration-inverting)
Comments: The enzyme recognizes the sequence β-D-galactosyl-(1→3)-N-acetyl-D-galactosaminyl (known as type 1 histo-blood group precursor disaccharide) in non-reducing termini of glycan moieties in glycoproteins and glycolipids [1]. When acting on gangloside GM1a, it forms gangloside GD1a [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 60202-12-2
References:
1. Rearick, J.I., Sadler, J.E., Paulson, J.C. and Hill, R.L. Enzymatic characterization of β D-galactoside α2→3 sialyltransferase from porcine submaxillary gland. J. Biol. Chem. 254 (1979) 4444-4451. [PMID: 438198]
2. Yip, M.C.M. The enzymic synthesis of disialoganglioside: rat brain cytidine-5'-monophospho-N-acetylneuraminic acid: monosialoganglioside (GM1) sialyltransferase. Biochim. Biophys. Acta 306 (1973) 298-306. [PMID: 4351506]
Accepted name: N-(2-amino-2-carboxyethyl)-L-glutamate synthase
Reaction: O-phospho-L-serine + L-glutamate = N-[(2S)-2-amino-2-carboxyethyl]-L-glutamate + phosphate
Other name(s): SbnA; ACEGA synthase
Systematic name: O-phospho-L-serine:L-glutamate N-(2S)-2-amino-2-carboxyethyltransferase
Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of the siderophore staphyloferrin B.
References:
1. Beasley, F.C., Cheung, J. and Heinrichs, D.E. Mutation of L-2,3-diaminopropionic acid synthase genes blocks staphyloferrin B synthesis in Staphylococcus aureus. BMC Microbiol. 11 (2011) 199. [PMID: 21906287]
2. Kobylarz, M.J., Grigg, J.C., Takayama, S.J., Rai, D.K., Heinrichs, D.E. and Murphy, M.E. Synthesis of L-2,3-diaminopropionic acid, a siderophore and antibiotic precursor. Chem. Biol. 21 (2014) 379-388. [PMID: 24485762]
Accepted name: putrescine—2-oxoglutarate transaminase
Reaction: putrescine + 2-oxoglutarate = 1-pyrroline + L-glutamate + H2O (overall reaction)
(1a) putrescine + 2-oxoglutarate = 4-aminobutanal + L-glutamate
(1b) 4-aminobutanal = 1-pyrroline + H2O (spontaneous)
For diagram of reaction click here.
Glossary: putrescine = butane-1,4-diamine
1-pyrroline = 3,4-dihydro-2H-pyrrole
Other name(s): putrescine-α-ketoglutarate transaminase; YgjG; putrescine:α-ketoglutarate aminotransferase; PAT; putrescine:2-oxoglutarate aminotransferase; putrescine transaminase (ambiguous); putrescine aminotransferase (ambiguous)
Systematic name: butane-1,4-diamine:2-oxoglutarate aminotransferase
Comments: A pyridoxal-phosphate protein [3]. The product, 4-aminobutanal, spontaneously cyclizes to form 1-pyrroline, which is a substrate for EC 1.2.1.19, aminobutyraldehyde dehydrogenase. Cadaverine and spermidine can also act as substrates [3]. Forms part of the arginine-catabolism pathway [2]. cf. EC 2.6.1.113, putrescine—pyruvate transaminase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 98982-73-1
References:
1. Prieto-Santos, M.I., Martin-Checa, J., Balaña-Fouce, R. and Garrido-Pertierra, A. A pathway for putrescine catabolism in Escherichia coli. Biochim. Biophys. Acta 880 (1986) 242-244. [PMID: 3510672]
2. Samsonova, N.N., Smirnov, S.V., Novikova, A.E. and Ptitsyn, L.R. Identification of Escherichia coli K12 YdcW protein as a γ-aminobutyraldehyde dehydrogenase. FEBS Lett. 579 (2005) 4107-4112. [PMID: 16023116]
3. Samsonova, N.N., Smirnov, S.V., Altman, I.B. and Ptitsyn, L.R. Molecular cloning and characterization of Escherichia coli K12 ygjG gene. BMC Microbiol. 3 (2003) 2. [PMID: 12617754]
Accepted name: putrescine—pyruvate transaminase
Reaction: putrescine + pyruvate = 4-aminobutanal + alanine
Other name(s): spuC (gene name)
Systematic name: putrescine:pyruvate aminotransferase
Comments: A pyridoxal 5'-phosphate protein. The enzyme, studied in the bacterium Pseudomonas aeruginosa, participates in a putrescine degradation pathway. cf. EC 2.6.1.82, putrescine—2-oxoglutarate aminotransferase.
References:
1. Lu, C.D., Itoh, Y., Nakada, Y. and Jiang, Y. Functional analysis and regulation of the divergent spuABCDEFGH-spuI operons for polyamine uptake and utilization in Pseudomonas aeruginosa PAO1. J. Bacteriol. 184 (2002) 3765-3773. [PMID: 12081945]
Accepted name: 3-dehydrotetronate 4-kinase
Reaction: (1) ATP + 3-dehydro-L-erythronate = ADP + 3-dehydro-4-phospho-L-erythronate
(2) ATP + 3-dehydro-D-erythronate = ADP + 3-dehydro-4-phospho-D-erythronate
For diagram of reaction click here.
Glossary: L-erythronate = (2S,3S)-2,3,4-trihydroxybutanoate
D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
Other name(s): otnK (gene name)
Systematic name: ATP:3-dehydrotetronate 4-phosphotransferase
Comments: The enzyme, characterized from bacteria, is involved in D-erythronate and L-threonate catabolism.
References:
1. Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl Acad. Sci. USA 113 (2016) E4161-E4169. [PMID: 27402745]
[EC 2.7.7.95 Transferred entry: mycocerosic acid adenylyltransferase. Now EC 6.2.1.49, long-chain fatty acid adenylyltransferase FadD28 (EC 2.7.7.95 created 2016, deleted 2017)]
Accepted name: tRNA uracil 4-sulfurtransferase
Reaction: ATP + [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + uracil in tRNA + 2 reduced ferredoxin [iron-sulfur] cluster = AMP + diphosphate + 4-thiouracil in tRNA + [ThiI sulfur-carrier protein]-L-cysteine + 2 oxidized ferredoxin [iron-sulfur] cluster
Other name(s): thiI (gene name); transfer ribonucleate sulfurtransferase (ambiguous); RNA sulfurtransferase (ambiguous); ribonucleate sulfurtransferase (ambiguous); transfer RNA sulfurtransferase (ambiguous); transfer RNA thiolase (ambiguous); L-cysteine:tRNA sulfurtransferase (incorrect); tRNA sulfurtransferase (ambiguous)
Systematic name: [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine:uracil in tRNA sulfurtransferase
Comments: The enzyme, found in bacteria and archaea, is activated by EC 2.8.1.7, cysteine desulfurase, which transfers a sulfur atom to an internal L-cysteine residue, forming a cysteine persulfide. The activated enzyme then transfers the sulfur to a uridine in a tRNA chain in a reaction that requires ATP. The enzyme from the bacterium Escherichia coli forms 4-thiouridine only at position 8 of tRNA. The enzyme also participates in the biosynthesis of the thiazole moiety of thiamine, but different domains are involved in the two processes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9055-57-6
References:
1. Abrell, J.W., Kaufman, E.E. and Lipsett, M.N. The biosynthesis of 4-thiouridylate. Separation and purification of two enzymes in the transfer ribonucleic acid-sulfurtransferase system. J. Biol. Chem. 246 (1971) 294-301. [PMID: 5541999]
2. Hayward, R.S. and Weiss, S.B. RNA thiolase: the enzymatic transfer of sulfur from cysteine to sRNA in Escherichia coli extracts. Proc. Natl. Acad. Sci. USA 55 (1966) 1161-1168. [PMID: 5334200]
3. Lipsett, M.N. and Peterkofsky, A. Enzymatic thiolation of E. coli sRNA. Proc. Natl. Acad. Sci. USA 55 (1966) 1169-1174. [PMID: 5334201]
4. Wong, T., Weiss, S.B., Eliceiri, G.L. and Bryant, J. Ribonucleic acid sulfurtransferase from Bacillus subtilis W168. Sulfuration with β-mercaptopyruvate and properties of the enzyme system. Biochemistry 9 (1970) 2376-2386. [PMID: 4987417]
5. Kambampati, R. and Lauhon, C.T. Evidence for the transfer of sulfane sulfur from IscS to ThiI during the in vitro biosynthesis of 4-thiouridine in Escherichia coli tRNA. J. Biol. Chem. 275 (2000) 10727-10730. [PMID: 10753862]
6. Mueller, E.G., Palenchar, P.M. and Buck, C.J. The role of the cysteine residues of ThiI in the generation of 4-thiouridine in tRNA. J. Biol. Chem. 276 (2001) 33588-33595. [PMID: 11443125]
7. Lauhon, C.T., Erwin, W.M. and Ton, G.N. Substrate specificity for 4-thiouridine modification in Escherichia coli. J. Biol. Chem. 279 (2004) 23022-23029. [PMID: 15037613]
8. Neumann, P., Lakomek, K., Naumann, P.T., Erwin, W.M., Lauhon, C.T. and Ficner, R. Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification. Nucleic Acids Res. 42 (2014) 6673-6685. [PMID: 24705700]
9. Liu, Y., Vinyard, D.J., Reesbeck, M.E., Suzuki, T., Manakongtreecheep, K., Holland, P.L., Brudvig, G.W. and Soll, D. A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes. Proc. Natl Acad. Sci. USA 113 (2016) 12703-12708. [PMID: 27791189]
Accepted name: tRNA-5-methyluridine54 2-sulfurtransferase
Reaction: ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O = AMP + diphosphate + 5-methyl-2-thiouracil54 in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
Other name(s): TtuA
Systematic name: [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH:tRNA (5-methyluridine54-2-O)-sulfurtransferase
Comments: The enzyme, found in thermophilic bacteria such as Thermus thermophilus and archaea such as Pyrococcus horikoshii, modifies the ribothymidine (5-methyluridine) residue at position 54 of tRNAs. Contains zinc.
References:
1. Shigi, N., Sakaguchi, Y., Suzuki, T. and Watanabe, K. Identification of two tRNA thiolation genes required for cell growth at extremely high temperatures. J. Biol. Chem. 281 (2006) 14296-14306. [PMID: 16547008]
2. Shigi, N., Suzuki, T., Terada, T., Shirouzu, M., Yokoyama, S. and Watanabe, K. Temperature-dependent biosynthesis of 2-thioribothymidine of Thermus thermophilus tRNA. J. Biol. Chem. 281 (2006) 2104-2113. [PMID: 16317006]
3. Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Katsura, K., Terada, T., Shirouzu, M., Sekine, S., Shigi, N. and Yokoyama, S. Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA. Proteins 81 (2013) 1232-1244. [PMID: 23444054]
4. Chen, M., Narai, S., Omura, N., Shigi, N., Chimnaronk, S., Tanaka, Y. and Yao, M. Crystallographic study of the 2-thioribothymidine-synthetic complex TtuA-TtuB from Thermus thermophilus. Acta Crystallogr. F Struct. Biol. Commun. 72 (2016) 777-781. [PMID: 27710943]
Accepted name: carboxymethylcellulase
Reaction: Endohydrolysis of (1→4)-β-D-glucosidic linkages in (carboxymethyl)cellulose.
Other name(s): CMCase
Systematic name: 4-β-D-(carboxymethyl)glucan 4-(carboxymethyl)glucanohydrolase
Comments: The enzyme from the acidophilic bacterium Alicyclobacillus acidocaldarius is an endo-cleaving hydrolase that cleaves β(1→4)-linked residues. However, it is specific for (carboxymethyl)cellulose and does not act on cellulosic substrates such as avicel.
References:
1. Morana, A., Esposito, A., Maurelli, L., Ruggiero, G., Ionata, E., Rossi, M. and La Cara, F. A novel thermoacidophilic cellulase from Alicyclobacillus acidocaldarius. Protein Pept. Lett. 15 (2008) 1017-1021. [PMID: 18991780]
[EC 3.5.1.120 Transferred entry: 2-aminomuconate deaminase (2-hydroxymuconate-forming). Now EC 3.5.99.11, 2-aminomuconate deaminase (2-hydroxymuconate-forming) (EC 3.5.1.120 created 2016, deleted 2017)]
Accepted name: 2-aminomuconate deaminase (2-hydroxymuconate-forming)
Reaction: 2-aminomuconate + H2O = (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NH3
Glossary: 2-aminomuconate = (2Z,4E)-2-aminohexa-2,4-dienedioate
(2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (2Z,4E)-2-hydroxymuconate
Other name(s): cnbZ (gene name)
Systematic name: 2-aminomuconate aminohydrolase [(2Z,4E)-2-hydroxyhexa-2,4-dienedioate-forming]
Comments: The enzyme, characterized from the bacterium Comamonas testosteroni CNB-1, converts 2-aminomuconate to 2-hydroxyhexa-2,4-dienedioate, unlike the enzymes from Pseudomonas, which produce (3E)-2-oxohex-3-enedioate (see EC 3.5.99.5, 2-aminomuconate deaminase). The enzyme also acts on 2-amino-5-chloromuconate.
References:
1. Liu, L., Wu, J.F., Ma, Y.F., Wang, S.Y., Zhao, G.P. and Liu, S.J. A novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with Comamonas sp. strain CNB-1. J. Bacteriol. 189 (2007) 2677-2682. [PMID: 17259310]
Accepted name: carbon disulfide hydrolase
Reaction: carbon disulfide + 2 H2O = CO2 + 2 hydrogen sulfide (overall reaction)
(1a) carbon disulfide + H2O = carbonyl sulfide + hydrogen sulfide
(1b) carbonyl sulfide + H2O = CO2 + hydrogen sulfide
Other name(s): CS2 hydrolase (misleading); carbon disulfide lyase; CS2-converting enzyme; carbon disulphide-lyase (decarboxylating)
Systematic name: carbon-disulfide hydrogen-sulfide-lyase (decarboxylating)
Comments: The enzyme contains Zn2+. The hyperthermophilic archaeon Acidianus sp. A1-3 obtains energy by the conversion of carbon disulfide to hydrogen sulfide, with carbonyl sulfide as an intermediate.
References:
1. Smeulders, M.J., Barends, T.R., Pol, A., Scherer, A., Zandvoort, M.H., Udvarhelyi, A., Khadem, A.F., Menzel, A., Hermans, J., Shoeman, R.L., Wessels, H.J., van den Heuvel, L.P., Russ, L., Schlichting, I., Jetten, M.S. and Op den Camp, H.J. Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon. Nature 478 (2011) 412-416. [PMID: 22012399]
Accepted name: 3-dehydro-4-phosphotetronate decarboxylase
Reaction: (1) 3-dehydro-4-phospho-L-erythronate = glycerone phosphate + CO2
(2) 3-dehydro-4-phospho-D-erythronate = glycerone phosphate + CO2
For diagram of reaction click here.
Glossary: L-erythronate = (2S,3S)-2,3,4-trihydroxybutanoate
D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
Other name(s): otnC (gene name)
Systematic name: 3-dehydro-4-phosphotetronate carboxy-lyase
Comments: The enzyme, characterized from bacteria, is involved in D-erythronate and L-threonate catabolism.
References:
1. Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl Acad. Sci. USA 113 (2016) E4161-E4169. [PMID: 27402745]
Accepted name: dihydroneopterin phosphate aldolase
Reaction: 7,8-dihydroneopterin 3'-phosphate = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde phosphate
Other name(s): H2NMP aldolase
Systematic name: 7,8-dihydroneopterin 3'-phosphate glycolaldehyde phosphate-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]
Comments: The enzyme participates in methanopterin biosynthesis the archaeon Pyrococcus furiosus. The enzyme is specific for 7,8-dihydroneopterin 3'-phosphate. cf. EC 4.1.2.25, dihydroneopterin aldolase and EC 4.1.2.60, dihydroneopterin triphosphate aldolase.
References:
1. de Crecy-Lagard, V., Phillips, G., Grochowski, L.L., El Yacoubi, B., Jenney, F., Adams, M.W., Murzin, A.G. and White, R.H. Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate. ACS Chem. Biol. 7 (2012) 1807-1816. [PMID: 22931285]
Accepted name: dihydroneopterin triphosphate aldolase
Reaction: 7,8-dihydroneopterin 3'-triphosphate = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde triphosphate
Other name(s): PTPS-III
Systematic name: 7,8-dihydroneopterin 3'-triphosphate glycolaldehyde phosphate-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]
Comments: The enzyme, which participates in a pathway for folate biosynthesis, is found in the Stramenopiles, a large group that includes oomycetes, various microalgae and brown algae, as well as in several bacterial phyla. It provides a bypass mechanism compensating for the lack of EC 4.1.2.25, dihydroneopterin aldolase. In the malaria parasite Plasmodium falciparum the enzyme is bifunctional and also catalyses the activity of EC 4.2.3.12, 6-pyruvoyltetrahydropterin synthase. cf. EC 4.1.2.59, dihydroneopterin phosphate aldolase.
References:
1. Dittrich, S., Mitchell, S.L., Blagborough, A.M., Wang, Q., Wang, P., Sims, P.F. and Hyde, J.E. An atypical orthologue of 6-pyruvoyltetrahydropterin synthase can provide the missing link in the folate biosynthesis pathway of malaria parasites. Mol. Microbiol. 67 (2008) 609-618. [PMID: 18093090]
2. Hyde, J.E., Dittrich, S., Wang, P., Sims, P.F., de Crecy-Lagard, V. and Hanson, A.D. Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms. Trends Parasitol. 24 (2008) 502-508. [PMID: 18805734]
3. Pribat, A., Jeanguenin, L., Lara-Nunez, A., Ziemak, M.J., Hyde, J.E., de Crecy-Lagard, V. and Hanson, A.D. 6-Pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria. J. Bacteriol. 191 (2009) 4158-4165. [PMID: 19395485]
[EC 4.4.1.27 Transferred entry: carbon disulfide lyase. Now EC 3.13.1.5, carbon disulfide hydrolase (EC 4.4.1.27 created 2013, deleted 2017)]
Accepted name: magnesium dechelatase
Reaction: (1) chlorophyll a + 2 H+ = pheophytin a + Mg2+
(2) chlorophylide a + 2 H+ = pheophorbide a + Mg2+
For diagram of reaction click here.
Other name(s): SGR (gene name); SGRL (gene name); Mg-dechelatase
Systematic name: chlorophyll a magnesium lyase
Comments: Inhibited by Ca2+, Mg2+ and especially Hg2+. SGR has very low activity with chlorophyllide a and none with chlorophyll b. It acts on chlorophyll a both in its free form and in protein complex. SGRL, on the other hand, is more active with chlorophyllide a than with chlorophyll a. The magnesium formed is scavenged by MCS (metal-chelating substance).
References:
1. Tang, L., Okazawa, A., Fukusaki, E. and Kobayashi, A. Removal of magnesium by Mg-dechelatase is a major step in the chlorophyll-degrading pathway in Ginkgo biloba in the process of autumnal tints. Z. Naturforsch. C 55 (2000) 923-926. [PMID: 11204197]
2. Costa, M.A., Civello, P.M., Chaves, A.R. and Martínez, G.A. Characterization of Mg-dechelatase activity obtained from Fragaria x ananassa fruit. Plant Physiol. Biochem. 40 (2002) 111-118.
3. Wang, T., Quisenberry, S.S., Ni, X. and Tolmay, V. Enzymatic chlorophyll degradation in wheat near-isogenic lines elicited by cereal aphid (Homoptera: Aphididae) feeding. J. Econ. Entomol. 97 (2004) 661-667. [PMID: 15154496]
4. Suzuki, T., Kunieda, T., Murai, F., Morioka, S. and Shioi, Y. Mg-dechelation activity in radish cotyledons with artificial and native substrates, Mg-chlorophyllin a and chlorophyllide a. Plant Physiol. Biochem. 43 (2005) 459-464. [PMID: 15890522]
5. Kunieda, T., Amano, T. and Shioi, Y. Search for chlorophyll degradation enzyme, Mg-dechelatase, from extracts of Chenopodium album with native and artificial substrates. Plant Sci. 169 (2005) 177-183.
6. Shimoda, Y., Ito, H. and Tanaka, A. Arabidopsis STAY-GREEN, Mendel’s green cotyledon gene, encodes magnesium-dechelatase. Plant Cell 28 (2016) 2147-2160. [PMID: 27604697]
Accepted name: sirohydrochlorin nickelchelatase
Reaction: Ni-sirohydrochlorin + 2 H+ = sirohydrochlorin + Ni2+
For diagram of reaction click here.
Other name(s): cfbA (gene name)
Systematic name: Ni-sirohydrochlorin nickel-lyase (sirohydrochlorin-forming)
Comments: The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, participates in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F430, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase. It catalyses the insertion of the nickel ion into sirohydrochlorin.
References:
1. Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354 (2016) 339-342. [PMID: 27846569]
Accepted name: fructoselysine 3-epimerase
Reaction: N6-(D-fructosyl)-L-lysine = N6-(D-psicosyl)-L-lysine
Other name(s): frlC (gene name)
Systematic name: D-fructosyl-L-lysine 3-epimerase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the catabolism of fructoseamines, amino acid sugar complexes that are formed non-enzymically.
References:
1. Wiame, E. and Van Schaftingen, E. Fructoselysine 3-epimerase, an enzyme involved in the metabolism of the unusual Amadori compound psicoselysine in Escherichia coli. Biochem. J. 378 (2004) 1047-1052. [PMID: 14641112]
Accepted name: 2-dehydrotetronate isomerase
Reaction: (1) 2-dehydro-L-erythronate = 3-dehydro-L-erythronate
(2) 2-dehydro-D-erythronate = 3-dehydro-D-erythronate
For diagram of reaction click here.
Glossary: L-erythronate = (2S,3S)-2,3,4-trihydroxybutanoate
D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
Other name(s): otnI (gene name)
Systematic name: 2-dehydrotetronate isomerase
Comments: The enzyme, characterized from bacteria, is involved in D-erythronate and L-threonate catabolism.
References:
1. Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl Acad. Sci. USA 113 (2016) E4161-E4169. [PMID: 27402745]
Accepted name: lysine 5,6-aminomutase
Reaction: (1) (3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate
(2) D-lysine = 2,5-diaminohexanoate
For diagram of reaction click here.
Other name(s): β-lysine 5,6-aminomutase; β-lysine mutase; L-β-lysine 5,6-aminomutase; D-lysine 5,6-aminomutase; D-α-lysine mutase; adenosylcobalamin-dependent D-lysine 5,6-aminomutase
Systematic name: (3S)-3,6-diaminohexanoate 5,6-aminomutase
Comments: This enzyme is a member of the ‘AdoMet radical’ (radical SAM) family. It requires pyridoxal phosphate and adenosylcobalamin for activity. A 5'-deoxyadenosyl radical is generated during the reaction cycle by reductive cleavage of adenosylcobalamin, which is regenerated at the end of the reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9075-69-8
References:
1. Stadtman, T.C. and Tasi, L. A cobamide coenzyme dependent migration of the ε-amino group of D-lysine. Biochem. Biophys. Res. Commun. 28 (1967) 920-926. [PMID: 4229021]
2. Stadtman, T.C. and Renz, P. Anaerobic degradation of lysine. V. Some properties of the cobamide coenzyme-dependent β-lysine mutase of Clostridium sticklandii. Arch. Biochem. Biophys. 125 (1968) 226-239. [PMID: 5649516]
3. Morley, C.G.D. and Stadtman, T.C. Studies on the fermentation of D-α-lysine. Purification and properties of an adenosine triphosphate regulated B12-coenzyme-dependent D-α-lysine mutase complex from Clostridium sticklandii. Biochemistry 9 (1970) 4890-4900. [PMID: 5480154]
4. Retey, J., Kunz, F., Arigoni, D. and Stadtman, T.C. Zur Kenntnis der β-Lysin-Mutase-Reaktion: mechanismus und sterischer Verlauf. Helv. Chim. Acta 61 (1978) 2989-2998.
5. Chang, C.H. and Frey, P.A. Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-lysine 5, 6-aminomutase from Clostridium sticklandii. J. Biol. Chem. 275 (2000) 106-114. [PMID: 10617592]
6. Tang, K.H., Harms, A. and Frey, P.A. Identification of a novel pyridoxal 5'-phosphate binding site in adenosylcobalamin-dependent lysine 5,6-aminomutase from Porphyromonas gingivalis. Biochemistry 41 (2002) 8767-8776. [PMID: 12093296]
7. Tang, K.H., Mansoorabadi, S.O., Reed, G.H. and Frey, P.A. Radical triplets and suicide inhibition in reactions of 4-thia-D- and 4-thia-L-lysine with lysine 5,6-aminomutase. Biochemistry 48 (2009) 8151-8160. [PMID: 19634897]
8. Berkovitch, F., Behshad, E., Tang, K.H., Enns, E.A., Frey, P.A. and Drennan, C.L. A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase. Proc. Natl Acad. Sci. USA 101 (2004) 15870-15875. [PMID: 15514022]
[EC 5.4.3.4 Transferred entry: D-lysine 5,6-aminomutase. Now included in EC 5.4.3.3, lysine 5,6-aminomutase (EC 5.4.3.4 created 1972, modified 2003, deleted 2017)]
Accepted name: long-chain fatty acid adenylyltransferase FadD28
Reaction: ATP + a long-chain fatty acid + holo-[mycocerosate synthase] = AMP + diphosphate + a long-chain acyl-[mycocerosate synthase] (overall reaction)
(1a) ATP + a long-chain fatty acid = diphosphate + a long-chain acyl-adenylate ester
(1b) a long-chain acyl-adenylate ester + holo-[mycocerosate synthase] = AMP + a long-chain acyl-[mycocerosate synthase]
Other name(s): fadD28 (gene name)
Systematic name: long-chain fatty acid:holo-[mycocerosate synthase] ligase (AMP-forming)
Comments: The enzyme, found in certain mycobacteria, activates long-chain fatty acids by adenylation and transfers them to EC 2.3.1.111, mycocerosate synthase. The enzyme participates in the biosynthesis of the virulent lipids dimycocerosates (DIM) and dimycocerosyl triglycosyl phenolphthiocerol (PGL).
References:
1. Fitzmaurice, A.M. and Kolattukudy, P.E. Open reading frame 3, which is adjacent to the mycocerosic acid synthase gene, is expressed as an acyl coenzyme A synthase in Mycobacterium bovis BCG. J. Bacteriol. 179 (1997) 2608-2615. [PMID: 9098059]
2. Goyal, A., Yousuf, M., Rajakumara, E., Arora, P., Gokhale, R.S. and Sankaranarayanan, R. Crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of FadD28, a fatty-acyl AMP ligase from Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (2006) 350-352. [PMID: 16582482]
3. Arora, P., Goyal, A., Natarajan, V.T., Rajakumara, E., Verma, P., Gupta, R., Yousuf, M., Trivedi, O.A., Mohanty, D., Tyagi, A., Sankaranarayanan, R. and Gokhale, R.S. Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis. Nat. Chem. Biol. 5 (2009) 166-173. [PMID: 19182784]
4. Menendez-Bravo, S., Comba, S., Sabatini, M., Arabolaza, A. and Gramajo, H. Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli. Metab. Eng. 24 (2014) 97-106. [PMID: 24831705]
5. Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040-1050. [PMID: 25561717]
Accepted name: phosphopantothenate—cysteine ligase (CTP)
Reaction: CTP + (R)-4'-phosphopantothenate + L-cysteine = CMP + diphosphate + N-[(R)-4'-phosphopantothenoyl]-L-cysteine
For diagram of reaction click here.
Other name(s): phosphopantothenoylcysteine synthetase; phosphopantothenate—cysteine ligase
Systematic name: (R)-4'-phosphopantothenate:L-cysteine ligase
Comments: A key enzyme in the production of coenzyme A. The bacterial enzyme requires CTP, in contrast to the eukaryotic enzyme, EC 6.3.2.51, which requires ATP. Cysteine can be replaced by some of its derivatives.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-50-1
References:
1. Brown, G.M. The metabolism of pantothenic acid. J. Biol. Chem. 234 (1959) 370-378. [PMID: 13630913]
2. Strauss, E., Kinsland, C., Ge, Y., McLafferty, F.W. and Begley, T.P. Phosphopantothenoylcysteine synthetase from Escherichia coli. Identification and characterization of the last unidentified Coenzyme A biosynthetic enzymes in bacteria. J. Biol. Chem. 276 (2001) 13513-13516. [PMID: 11278255]
3. Kupke, T. Molecular characterization of the 4'-phosphopantothenoylcysteine synthetase domain of bacterial Dfp flavoproteins. J. Biol. Chem. 277 (2002) 36137-36145. [PMID: 12140293]
Accepted name: tenuazonic acid synthetase
Reaction: ATP + L-isoleucine + acetoacetyl-CoA = AMP + diphosphate + tenuazonic acid + CoA
Glossary: tenuazonic acid = (5S)-3-acetyl-5-[(2S)-butan-2-yl]-4-hydroxy-1,5-dihydro-2H-pyrrol-2-one
Other name(s): TAS1 (gene name)
Systematic name: L-isoleucine:acetoacetyl-CoA ligase (tenuazonic acid-forming)
Comments: This fungal enzyme, isolated from Magnaporthe oryzae, is an non-ribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) hybrid protein that consists of condensation (C), adenylation (A) and peptidyl-carrier protein (PCP) domains in the NRPS portion and a ketosynthase (KS) domain in the PKS portion. ATP is required for activation of isoleucine, which is then condensed with acetoacetyl-CoA. Cyclization and release from the enzyme are catalysed by the KS domain.
References:
1. Yun, C.S., Motoyama, T. and Osada, H. Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS-PKS hybrid enzyme. Nat Commun 6 (2015) 8758. [PMID: 26503170]
Accepted name: phosphopantothenate—cysteine ligase (ATP)
Reaction: ATP + (R)-4'-phosphopantothenate + L-cysteine = AMP + diphosphate + N-[(R)-4'-phosphopantothenoyl]-L-cysteine
For diagram of reaction click here.
Other name(s): phosphopantothenoylcysteine synthetase (ambiguous); PPCS (gene name)
Systematic name: (R)-4'-phosphopantothenate:L-cysteine ligase (ATP-utilizing)
Comments: A key enzyme in the production of coenzyme A. The eukaryotic enzyme requires ATP, in contrast to the bacterial enzyme, EC 6.3.2.5, phosphopantothenate—cysteine ligase, which requires CTP.
References:
1. Daugherty, M. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J. Biol. Chem. 277 (2002) 21431-21439. [PMID: 11923312]
2. Manoj, N., Strauss, E., Begley, T.P. and Ealick, S.E. Structure of human phosphopantothenoylcysteine synthetase at 2.3 Å Resolution. Structure 11 (2003) 927-936. [PMID: 12906824]
3. Kupke, T., Hernandez-Acosta, P. and Culianez-Macia, F.A. 4'-phosphopantetheine and coenzyme A biosynthesis in plants. J. Biol. Chem. 278 (2003) 38229-38237. [PMID: 12860978]
Accepted name: Ni-sirohydrochlorin a,c-diamide reductive cyclase
Reaction: ATP + Ni-sirohydrochlorin a,c-diamide + 3 reduced electron acceptor + H2O = ADP + phosphate + 15,173-seco-F430-173-acid + 3 electron acceptor
For diagram of reaction click here.
Other name(s): cfbC (gene name); cfbD (gene name)
Systematic name: Ni-sirohydrochlorin a,c-diamide reductive cyclo-ligase (ADP-forming)
Comments: The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, participates in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F430, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase.
References:
1. Pfaltz, A., Kobelt, A., Huster, R. and Thauer, R.K. Biosynthesis of coenzyme F430 in methanogenic bacteria. Identification of 15,173-seco-F430-173-acid as an intermediate. Eur. J. Biochem. 170 (1987) 459-467. [PMID: 3691535]
2. Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354 (2016) 339-342. [PMID: 27846569]
Accepted name: Ni-sirohydrochlorin a,c-diamide synthase
Reaction: 2 ATP + Ni-sirohydrochlorin + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + Ni-sirohydrochlorin a,c-diamide + 2 L-glutamate
For diagram of reaction click here.
Other name(s): cfbB (gene name)
Systematic name: Ni-sirohydrochlorin:L-glutamine amido-ligase (ADP-forming)
Comments: The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, participates in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F430, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase.
References:
1. Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354 (2016) 339-342. [PMID: 27846569]
Accepted name: coenzyme F430 synthetase
Reaction: ATP + 15,173-seco-F430-173-acid = ADP + phosphate + coenzyme F430
For diagram of reaction click here.
Other name(s): cfbE (gene name)
Systematic name: 15,173-seco-F430-173-acid cyclo-ligase (ADP-forming)
Comments: The enzyme, studied from the methanogenic archaeon Methanosarcina acetivorans, catalyses the last step in the biosynthesis of the nickel-containing tetrapyrrole cofactor coenzyme F430, which is required by EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase.
References:
1. Zheng, K., Ngo, P.D., Owens, V.L., Yang, X.P. and Mansoorabadi, S.O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354 (2016) 339-342. [PMID: 27846569]