The Enzyme Database

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EC 1.1.1.100     
Accepted name: 3-oxoacyl-[acyl-carrier-protein] reductase
Reaction: a (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ = a 3-oxoacyl-[acyl-carrier protein] + NADPH + H+
Other name(s): β-ketoacyl-[acyl-carrier protein](ACP) reductase; β-ketoacyl acyl carrier protein (ACP) reductase; β-ketoacyl reductase; β-ketoacyl thioester reductase; β-ketoacyl-ACP reductase; β-ketoacyl-acyl carrier protein reductase; 3-ketoacyl acyl carrier protein reductase; NADPH-specific 3-oxoacyl-[acylcarrier protein]reductase; 3-oxoacyl-[ACP]reductase; (3R)-3-hydroxyacyl-[acyl-carrier-protein]:NADP+ oxidoreductase
Systematic name: (3R)-3-hydroxyacyl-[acyl-carrier protein]:NADP+ oxidoreductase
Comments: Exhibits a marked preference for acyl-carrier-protein derivatives over CoA derivatives as substrates.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 37250-34-3
References:
1.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [DOI] [PMID: 4561013]
2.  Shimakata, T. and Stumpf, P.K. Purification and characterizations of β-ketoacyl-[acyl-carrier-protein] reductase, β-hydroxyacyl-[acylcarrier-protein] dehydrase, and enoyl-[acyl-carrier-protein] reductase from Spinacia oleracea leaves. Arch. Biochem. Biophys. 218 (1982) 77–91. [DOI] [PMID: 6756317]
3.  Toomey, R.E. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XV. Preparation and general properties of β-ketoacyl acyl carrier protein reductase from Escherichia coli. Biochim. Biophys. Acta 116 (1966) 189–197. [DOI] [PMID: 4381013]
[EC 1.1.1.100 created 1972, modified 1976]
 
 
EC 1.1.1.224     
Accepted name: mannose-6-phosphate 6-reductase
Reaction: D-mannitol 1-phosphate + NADP+ = D-mannose 6-phosphate + NADPH + H+
Other name(s): NADPH-dependent mannose 6-phosphate reductase; mannose-6-phosphate reductase; 6-phosphomannose reductase; NADP-dependent mannose-6-P:mannitol-1-P oxidoreductase; NADPH-dependent M6P reductase; NADPH-mannose-6-P reductase
Systematic name: D-mannitol-1-phosphate:NADP+ 6-oxidoreductase
Comments: Involved in the biosynthesis of mannitol in celery (Apium graveolens) leaves.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 88747-79-9
References:
1.  Rumpho, M.E., Edwards, G.E. and Loescher, W.H. A pathway for photosynthetic carbon flow to mannitol in celery leaves. Activity and localization of key enzymes. Plant Physiol. 73 (1983) 869–873. [PMID: 16663332]
[EC 1.1.1.224 created 1989]
 
 
EC 1.1.1.279     
Accepted name: (R)-3-hydroxyacid-ester dehydrogenase
Reaction: ethyl (R)-3-hydroxyhexanoate + NADP+ = ethyl 3-oxohexanoate + NADPH + H+
Other name(s): 3-oxo ester (R)-reductase
Systematic name: ethyl-(R)-3-hydroxyhexanoate:NADP+ 3-oxidoreductase
Comments: Also acts on ethyl (R)-3-oxobutanoate and some other (R)-3-hydroxy acid esters. The (R)- symbol is allotted on the assumption that no substituents change the order of priority from O-3 > C-2 > C-4. A subunit of yeast fatty acid synthase EC 2.3.1.86, fatty-acyl-CoA synthase system. cf. EC 1.1.1.280, (S)-3-hydroxyacid ester dehydrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 114705-02-1
References:
1.  Heidlas, J., Engel, K.-H. and Tressl, R. Purification and characterization of two oxidoreductases involved in the enantioselective reduction of 3-oxo, 4-oxo and 5-oxo esters in baker's yeast. Eur. J. Biochem. 172 (1988) 633–639. [DOI] [PMID: 3280313]
[EC 1.1.1.279 created 1990 as EC 1.2.1.55, transferred 2003 to EC 1.1.1.279, modified 2018]
 
 
EC 1.1.1.431     
Accepted name: D-xylose reductase (NADPH)
Reaction: xylitol + NADP+ = D-xylose + NADPH + H+
Other name(s): XYL1 (gene name, ambiguous); xyl1 (gene name, ambiguous); xyrA (gene name); xyrB (gene name)
Systematic name: xylitol:NADP+ oxidoreductase
Comments: Xylose reductases catalyse the reduction of xylose to xylitol, the initial reaction in the fungal D-xylose degradation pathway. Most of the enzymes exhibit a strict requirement for NADPH (e.g. the enzymes from Saccharomyces cerevisiae, Aspergillus niger, Trichoderma reesei, Candida tropicalis, Saitozyma flava, and Candida intermedia). Some D-xylose reductases have dual cosubstrate specificity, though they still prefer NADPH to NADH (cf. EC 1.1.1.307, D-xylose reductase [NAD(P)H]). Very rarely the enzyme prefers NADH (cf. EC 1.1.1.430, D-xylose reductase (NADH)).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bolen, P.L. and Detroy, R.W. Induction of NADPH-linked D-xylose reductase and NAD-linked xylitol dehydrogenase activities in Pachysolen tannophilus by D-xylose, L-arabinose, or D-galactose. Biotechnol. Bioeng. 27 (1985) 302–307. [DOI] [PMID: 18553673]
2.  Suzuki, T., Yokoyama, S., Kinoshita, Y., Yamada, H., Hatsu, M., Takamizawa, K. and Kawai, K. Expression of xyrA gene encoding for D-xylose reductase of Candida tropicalis and production of xylitol in Escherichia coli. J. Biosci. Bioeng. 87 (1999) 280–284. [DOI] [PMID: 16232468]
3.  Nidetzky, B., Mayr, P., Hadwiger, P. and Stutz, A.E. Binding energy and specificity in the catalytic mechanism of yeast aldose reductases. Biochem. J. 344 Pt 1 (1999) 101–107. [PMID: 10548539]
4.  Mayr, P., Bruggler, K., Kulbe, K.D. and Nidetzky, B. D-Xylose metabolism by Candida intermedia: isolation and characterisation of two forms of aldose reductase with different coenzyme specificities. J. Chromatogr. B Biomed. Sci. Appl. 737 (2000) 195–202. [DOI] [PMID: 10681056]
5.  Sene, L., Felipe, M.G., Silva, S.S. and Vitolo, M. Preliminary kinetic characterization of xylose reductase and xylitol dehydrogenase extracted from Candida guilliermondii FTI 20037 cultivated in sugarcane bagasse hydrolysate for xylitol production. Appl. Biochem. Biotechnol. 91-93 (2001) 671–680. [DOI] [PMID: 11963895]
6.  Jeong, E.Y., Sopher, C., Kim, I.S. and Lee, H. Mutational study of the role of tyrosine-49 in the Saccharomyces cerevisiae xylose reductase. Yeast 18 (2001) 1081–1089. [DOI] [PMID: 11481678]
7.  Chroumpi, T., Peng, M., Aguilar-Pontes, M.V., Muller, A., Wang, M., Yan, J., Lipzen, A., Ng, V., Grigoriev, I.V., Makela, M.R. and de Vries, R.P. Revisiting a ‘simple’ fungal metabolic pathway reveals redundancy, complexity and diversity. Microb. Biotechnol. 14 (2021) 2525–2537. [DOI] [PMID: 33666344]
8.  Terebieniec, A., Chroumpi, T., Dilokpimol, A., Aguilar-Pontes, M.V., Makela, M.R. and de Vries, R.P. Characterization of D-xylose reductase, XyrB, from Aspergillus niger. Biotechnol Rep (Amst) 30:e00610 (2021). [DOI] [PMID: 33842213]
[EC 1.1.1.431 created 2022]
 
 
EC 1.3.1.9     
Accepted name: enoyl-[acyl-carrier-protein] reductase (NADH)
Reaction: an acyl-[acyl-carrier protein] + NAD+ = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH + H+
Other name(s): enoyl-[acyl carrier protein] reductase; enoyl-ACP reductase; NADH-enoyl acyl carrier protein reductase; NADH-specific enoyl-ACP reductase; acyl-[acyl-carrier-protein]:NAD+ oxidoreductase; fabI (gene name)
Systematic name: acyl-[acyl-carrier protein]:NAD+ oxidoreductase
Comments: The enzyme catalyses an essential step in fatty acid biosynthesis, the reduction of the 2,3-double bond in enoyl-acyl-[acyl-carrier-protein] derivatives of the elongating fatty acid moiety. The enzyme from the bacterium Escherichia coli accepts substrates with carbon chain length from 4 to 18 [3]. The FAS-I enzyme from the bacterium Mycobacterium tuberculosis prefers substrates with carbon chain length from 12 to 24 carbons.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37251-08-4
References:
1.  Shimakata, T. and Stumpf, P.K. Purification and characterizations of β-ketoacyl-[acyl-carrier-protein] reductase, β-hydroxyacyl-[acylcarrier-protein] dehydrase, and enoyl-[acyl-carrier-protein] reductase from Spinacia oleracea leaves. Arch. Biochem. Biophys. 218 (1982) 77–91. [DOI] [PMID: 6756317]
2.  Weeks, G. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. 18. Preparation and general properties of the enoyl acyl carrier protein reductases from Escherichia coli. J. Biol. Chem. 243 (1968) 1180–1189. [PMID: 4384650]
3.  Yu, X., Liu, T., Zhu, F. and Khosla, C. In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli. Proc. Natl. Acad. Sci. USA 108 (2011) 18643–18648. [DOI] [PMID: 22042840]
[EC 1.3.1.9 created 1972, modified 2013]
 
 
EC 1.4.1.22      
Deleted entry: ornithine cyclodeaminase. It was pointed out during the public-review process that there is no overall consumption of NAD+ during the reaction. As a result, transfer of the enzyme from EC 4.3.1.12 was not necessary and EC 1.4.1.22 was withdrawn before being made official
[EC 1.4.1.22 created 2006, deleted 2006]
 
 
EC 1.5.98.3     
Accepted name: coenzyme F420:methanophenazine dehydrogenase
Reaction: reduced coenzyme F420 + methanophenazine = oxidized coenzyme F420 + dihydromethanophenazine
Glossary: methanophenazine = 2-{[(6E,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl]oxy}phenazine
dihydromethanophenazine = 2-{[(6E,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl]oxy}-5,10-dihydrophenazine
Other name(s): F420H2 dehydrogenase; fpoBCDIF (gene names)
Systematic name: reduced coenzyme F420:methanophenazine oxidoreductase
Comments: The enzyme, found in some methanogenic archaea, is responsible for the reoxidation of coenzyme F420, which is reduced during methanogenesis, and for the reduction of methanophenazine to dihydromethanophenazine, which is required by EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase. The enzyme is membrane-bound, and is coupled to proton translocation across the cytoplasmic membrane, generating a proton motive force that is used for ATP generation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Brodersen, J., Gottschalk, G. and Deppenmeier, U. Membrane-bound F420H2-dependent heterodisulfide reduction in Methanococcus volta. Arch. Microbiol. 171 (1999) 115–121. [PMID: 9914308]
2.  Baumer, S., Ide, T., Jacobi, C., Johann, A., Gottschalk, G. and Deppenmeier, U. The F420H2 dehydrogenase from Methanosarcina mazei is a Redox-driven proton pump closely related to NADH dehydrogenases. J. Biol. Chem. 275 (2000) 17968–17973. [DOI] [PMID: 10751389]
3.  Deppenmeier, U. The membrane-bound electron transport system of Methanosarcina species. J. Bioenerg. Biomembr. 36 (2004) 55–64. [PMID: 15168610]
4.  Abken H. J. and Deppenmeier, U. Purification and properties of an F420H2 dehydrogenase from Methanosarcina mazei Gö1. FEMS Microbiol. Lett. 154 (2006) 231–237.
[EC 1.5.98.3 created 2017]
 
 
EC 1.6.1.1     
Accepted name: NAD(P)+ transhydrogenase (Si-specific)
Reaction: NADPH + NAD+ = NADP+ + NADH
Other name(s): pyridine nucleotide transhydrogenase; transhydrogenase; NAD(P)+ transhydrogenase; nicotinamide adenine dinucleotide (phosphate) transhydrogenase; NAD+ transhydrogenase; NADH transhydrogenase; nicotinamide nucleotide transhydrogenase; NADPH-NAD+ transhydrogenase; pyridine nucleotide transferase; NADPH-NAD+ oxidoreductase; NADH-NADP+-transhydrogenase; NADPH:NAD+ transhydrogenase; H+-Thase; non-energy-linked transhydrogenase; NADPH:NAD+ oxidoreductase (B-specific); NAD(P)+ transhydrogenase (B-specific)
Systematic name: NADPH:NAD+ oxidoreductase (Si-specific)
Comments: The enzyme from Azotobacter vinelandii is a flavoprotein (FAD). It is Si-specific with respect to both NAD+ and NADP+. See EC 1.6.1.3, NAD(P)+ transhydrogenase, for enzymes whose stereo specificity is not known.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-18-0
References:
1.  Humphrey, G.F. The distribution and properties of transhydrogenase from animal tissues. Biochem. J. 65 (1957) 546–550. [PMID: 13412660]
2.  You, K.-S. Stereospecificity for nicotinamide nucleotides in enzymatic and chemical hydride transfer reactions. CRC Crit. Rev. Biochem. 17 (1985) 313–451. [PMID: 3157549]
[EC 1.6.1.1 created 1961, modified 1986, modified 2013]
 
 
EC 1.6.1.5      
Transferred entry: proton-translocating NAD(P)+ transhydrogenase. Now EC 7.1.1.1, proton-translocating NAD(P)+ transhydrogenase
[EC 1.6.1.5 created 2015, deleted 2018]
 
 
EC 1.6.5.9     
Accepted name: NADH:quinone reductase (non-electrogenic)
Reaction: NADH + H+ + a quinone = NAD+ + a quinol
Other name(s): type II NAD(P)H:quinone oxidoreductase; NDE2 (gene name); ndh (gene name); NDH-II; NDH-2; NADH dehydrogenase (quinone) (ambiguous); ubiquinone reductase (ambiguous); coenzyme Q reductase (ambiguous); dihydronicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); DPNH-coenzyme Q reductase (ambiguous); DPNH-ubiquinone reductase (ambiguous); NADH-coenzyme Q oxidoreductase (ambiguous); NADH-coenzyme Q reductase (ambiguous); NADH-CoQ oxidoreductase (ambiguous); NADH-CoQ reductase (ambiguous); NADH-ubiquinone reductase (ambiguous); NADH-ubiquinone oxidoreductase (ambiguous); reduced nicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); NADH-Q6 oxidoreductase (ambiguous); NADH2 dehydrogenase (ubiquinone) (ambiguous); NADH:ubiquinone oxidoreductase; NADH:ubiquinone reductase (non-electrogenic)
Systematic name: NADH:quinone oxidoreductase
Comments: A flavoprotein (FAD or FMN). Occurs in mitochondria of yeast and plants, and in aerobic bacteria. Has low activity with NADPH. Unlike EC 7.1.1.2, NADH:ubiquinone reductase (H+-translocating), this enzyme does not pump proteons of sodium ions across the membrane. It is also not sensitive to rotenone.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9028-04-0
References:
1.  Bergsma, J., Strijker, R., Alkema, J.Y., Seijen, H.G. and Konings, W.N. NADH dehydrogenase and NADH oxidation in membrane vesicle from Bacillus subtilis. Eur. J. Biochem. 120 (1981) 599–606. [PMID: 6800784]
2.  Møller, I.M, and Palmer, J.M. Direct evidence for the presence of a rotenone-resistant NADH dehydrogenase on the inner surface of plant mitochondria. Physiol. Plant. 54 (1982) 267–274. [DOI]
3.  de Vries, S. and Grivell, L.A. Purification and characterization of a rotenone-insensitive NADH:Q6 oxidoreductase from mitochondria of Saccharomyces cerevisiae. Eur. J. Biochem. 176 (1988) 377–384. [DOI] [PMID: 3138118]
4.  Kerscher, S.J., Okun, J.G. and Brandt, U. A single external enzyme confers alternative NADH:ubiquinone oxidoreductase activity in Yarrowia lipolytica. J. Cell Sci. 112 ( Pt 14) (1999) 2347–2354. [PMID: 10381390]
5.  Rasmusson, A.G., Soole, K.L. and Elthon, T.E. Alternative NAD(P)H dehydrogenases of plant mitochondria. Annu. Rev. Plant Biol. 55 (2004) 23–39. [DOI] [PMID: 15725055]
6.  Melo, A.M., Bandeiras, T.M. and Teixeira, M. New insights into type II NAD(P)H:quinone oxidoreductases. Microbiol. Mol. Biol. Rev. 68 (2004) 603–616. [PMID: 15590775]
[EC 1.6.5.9 created 2011 (EC 1.6.5.11 created 1972 as EC 1.6.99.5, transferred 2015 to EC 1.6.5.11, incorporated 2019), modified 2019]
 
 
EC 1.7.2.5     
Accepted name: nitric oxide reductase (cytochrome c)
Reaction: nitrous oxide + 2 ferricytochrome c + H2O = 2 nitric oxide + 2 ferrocytochrome c + 2 H+
Systematic name: nitrous oxide:ferricytochrome-c oxidoreductase
Comments: The enzyme from Pseudomonas aeruginosa contains a dinuclear centre comprising a non-heme iron centre and heme b3, plus heme c, heme b and calcium; the acceptor is cytochrome c551
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Hendriks, J., Warne, A., Gohlke, U., Haltia, T., Ludovici, C., Lubben, M. and Saraste, M. The active site of the bacterial nitric oxide reductase is a dinuclear iron center. Biochemistry 37 (1998) 13102–13109. [DOI] [PMID: 9748316]
2.  Hendriks, J., Gohlke, U. and Saraste, M. From NO to OO: nitric oxide and dioxygen in bacterial respiration. J. Bioenerg. Biomembr. 30 (1998) 15–24. [PMID: 9623801]
3.  Heiss, B., Frunzke, K. and Zumpft, W.G. Formation of the N-N bond from nitric oxide by a membrane-bound cytochrome bc complex of nitrate-respiring (denitrifying) Pseudomonas stutzeri. J. Bacteriol. 171 (1989) 3288–3297. [DOI] [PMID: 2542222]
4.  Cheesman, M.R., Zumft, W.G. and Thomson, A.J. The MCD and EPR of the heme centers of nitric oxide reductase from Pseudomonas stutzeri: evidence that the enzyme is structurally related to the heme-copper oxidases. Biochemistry 37 (1998) 3994–4000. [DOI] [PMID: 9521721]
5.  Kumita, H., Matsuura, K., Hino, T., Takahashi, S., Hori, H., Fukumori, Y., Morishima, I. and Shiro, Y. NO reduction by nitric-oxide reductase from denitrifying bacterium Pseudomonas aeruginosa: characterization of reaction intermediates that appear in the single turnover cycle. J. Biol. Chem. 279 (2004) 55247–55254. [DOI] [PMID: 15504726]
6.  Hino, T., Matsumoto, Y., Nagano, S., Sugimoto, H., Fukumori, Y., Murata, T., Iwata, S. and Shiro, Y. Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330 (2010) 1666–1670. [DOI] [PMID: 21109633]
[EC 1.7.2.5 created 1992 as EC 1.7.99.7, transferred 2011 to EC 1.7.2.5]
 
 
EC 1.7.99.7      
Transferred entry: nitric-oxide reductase. Now EC 1.7.2.5 nitric oxide reductase (cytochrome c)
[EC 1.7.99.7 created 1992, modified 1999, deleted 2011]
 
 
EC 1.10.3.10      
Transferred entry: ubiquinol oxidase (H+-transporting). Now EC 7.1.1.3, ubiquinol oxidase (H+-transporting)
[EC 1.10.3.10 created 2011, modified 2014, deleted 2018]
 
 
EC 1.10.3.12      
Transferred entry: menaquinol oxidase (H+-transporting). Now EC 7.1.1.5, menaquinol oxidase (H+-transporting)
[EC 1.10.3.12 created 2011, deleted 2018]
 
 
EC 1.10.3.13      
Transferred entry: caldariellaquinol oxidase (H+-transporting). Now EC 7.1.1.4, caldariellaquinol oxidase (H+-transporting)
[EC 1.10.3.13 created 2013, deleted 2018]
 
 
EC 1.10.3.14      
Transferred entry: ubiquinol oxidase (electrogenic, non H+-transporting). Now EC 7.1.1.7, ubiquinol oxidase (electrogenic, proton-motive force generating)
[EC 1.10.3.14 created 2014, modified 2017, deleted 2018]
 
 
EC 1.11.1.3     
Accepted name: fatty-acid peroxidase
Reaction: palmitate + 2 H2O2 = pentadecanal + CO2 + 3 H2O
Other name(s): long chain fatty acid peroxidase
Systematic name: hexadecanoate:hydrogen-peroxide oxidoreductase
Comments: Acts on long-chain fatty acids from dodecanoic to octadecanoic acid.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9029-52-1
References:
1.  Martin, R.O. and Stumpf, P.K. Fat metabolism in higher plants. XII. α-Oxidation of long chain fatty acids. J. Biol. Chem. 234 (1959) 2548–2554. [PMID: 14421733]
[EC 1.11.1.3 created 1961]
 
 
EC 1.12.7.2     
Accepted name: ferredoxin hydrogenase
Reaction: H2 + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H+
Other name(s): H2 oxidizing hydrogenase; H2 producing hydrogenase [ambiguous]; bidirectional hydrogenase; hydrogen-lyase [ambiguous]; hydrogenase (ferredoxin); hydrogenase I; hydrogenase II; hydrogenlyase [ambiguous]; uptake hydrogenase [ambiguous]
Systematic name: hydrogen:ferredoxin oxidoreductase
Comments: Contains iron-sulfur clusters. The enzymes from some sources contains nickel. Can use molecular hydrogen for the reduction of a variety of substances.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-05-8
References:
1.  Shug, A.L., Wilson, P.W., Green, D.E. and Mahler, H.R. The role of molybdenum and flavin in hydrogenase. J. Am. Chem. Soc. 76 (1954) 3355–3356.
2.  Tagawa, K. and Arnon, D.I. Ferredoxin as electron carriers in photosynthesis and in the bioogical production and consumption of hydrogen gas. Nature (Lond.) 195 (1962) 537–543.
3.  Valentine, R.C., Mortenson, L.E. and Carnahan, J.E. The hydrogenase system of Clostridium pasteurianum. J. Biol. Chem. 238 (1963) 1141–1144.
4.  Zumft, W.G. and Mortenson, L.E. The nitrogen-fixing complex of bacteria. Biochim. Biophys. Acta 416 (1975) 1–52. [PMID: 164247]
5.  Adams, M.W.W. The structure and mechanism of iron-hydrogenases. Biochim. Biophys. Acta 1020 (1990) 115–145. [DOI] [PMID: 2173950]
6.  Peters, J.W., Lanzilotta, W.N., Lemon, B.J. and Seefeldt, L.C. X-ray crystal structure of the Fe-only hydrogenase (Cpl) from Clostridium pasteurianum to 1.8 Angstrom resolution. Science 282 (1998) 1853–1858. [DOI] [PMID: 9836629]
[EC 1.12.7.2 created 1961 as EC 1.98.1.1, transferred 1965 to EC 1.12.1.1, transferred 1972 to EC 1.12.7.1, transferred 1978 to EC 1.18.3.1, transferred 1984 to EC 1.18.99.1, transferred 2002 to EC 1.12.7.2]
 
 
EC 1.14.11.48     
Accepted name: xanthine dioxygenase
Reaction: xanthine + 2-oxoglutarate + O2 = urate + succinate + CO2
For diagram of AMP catabolism, click here
Other name(s): XanA; α-ketoglutarate-dependent xanthine hydroxylase
Systematic name: xanthine,2-oxoglutarate:oxygen oxidoreductase
Comments: Requires Fe2+ and L-ascorbate. The enzyme, which was characterized from fungi, is specific for xanthine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cultrone, A., Scazzocchio, C., Rochet, M., Montero-Moran, G., Drevet, C. and Fernandez-Martin, R. Convergent evolution of hydroxylation mechanisms in the fungal kingdom: molybdenum cofactor-independent hydroxylation of xanthine via α-ketoglutarate-dependent dioxygenases. Mol. Microbiol. 57 (2005) 276–290. [DOI] [PMID: 15948966]
2.  Montero-Moran, G.M., Li, M., Rendon-Huerta, E., Jourdan, F., Lowe, D.J., Stumpff-Kane, A.W., Feig, M., Scazzocchio, C. and Hausinger, R.P. Purification and characterization of the FeII- and α-ketoglutarate-dependent xanthine hydroxylase from Aspergillus nidulans. Biochemistry 46 (2007) 5293–5304. [DOI] [PMID: 17429948]
3.  Li, M., Muller, T.A., Fraser, B.A. and Hausinger, R.P. Characterization of active site variants of xanthine hydroxylase from Aspergillus nidulans. Arch. Biochem. Biophys. 470 (2008) 44–53. [DOI] [PMID: 18036331]
[EC 1.14.11.48 created 2015]
 
 
EC 1.14.11.49     
Accepted name: uridine-5′-phosphate dioxygenase
Reaction: UMP + 2-oxoglutarate + O2 = 5′-dehydrouridine + succinate + CO2 + phosphate
For diagram of pyrimidine biosynthesis, click here
Glossary: 5′-dehydrouridine = uridine-5′-aldehyde
Other name(s): lipL (gene name)
Systematic name: UMP,2-oxoglutarate:oxygen oxidoreductase
Comments: The enzyme catalyses a net dephosphorylation and oxidation of UMP to generate 5′-dehydrouridine, the first intermediate in the biosynthesis of the unusual aminoribosyl moiety found in several C7-furanosyl nucleosides such as A-90289s, caprazamycins, liposidomycins, muraymycins and FR-900453. Requires Fe2+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yang, Z., Chi, X., Funabashi, M., Baba, S., Nonaka, K., Pahari, P., Unrine, J., Jacobsen, J.M., Elliott, G.I., Rohr, J. and Van Lanen, S.G. Characterization of LipL as a non-heme, Fe(II)-dependent α-ketoglutarate:UMP dioxygenase that generates uridine-5′-aldehyde during A-90289 biosynthesis. J. Biol. Chem. 286 (2011) 7885–7892. [DOI] [PMID: 21216959]
2.  Yang, Z., Unrine, J., Nonaka, K. and Van Lanen, S.G. Fe(II)-dependent, uridine-5′-monophosphate α-ketoglutarate dioxygenases in the synthesis of 5′-modified nucleosides. Methods Enzymol. 516 (2012) 153–168. [DOI] [PMID: 23034228]
[EC 1.14.11.49 created 2015]
 
 
EC 1.14.13.26      
Transferred entry: phosphatidylcholine 12-monooxygenase. Now classified as EC 1.14.18.4, phosphatidylcholine 12-monooxygenase.
[EC 1.14.13.26 created 1984, deleted 2015]
 
 
EC 1.14.13.79      
Transferred entry: ent-kaurenoic acid oxidase. Now EC 1.14.14.107, ent-kaurenoic acid oxidase
[EC 1.14.13.79 created 2002, deleted 2018]
 
 
EC 1.14.14.96     
Accepted name: 5-O-(4-coumaroyl)-D-quinate 3′-monooxygenase
Reaction: trans-5-O-(4-coumaroyl)-D-quinate + [reduced NADPH—hemoprotein reductase] + O2 = trans-5-O-caffeoyl-D-quinate + [oxidized NADPH—hemoprotein reductase] + H2O
Other name(s): 5-O-(4-coumaroyl)-D-quinate/shikimate 3′-hydroxylase; coumaroylquinate(coumaroylshikimate) 3′-monooxygenase; CYP98A3 (gene name)
Systematic name: trans-5-O-(4-coumaroyl)-D-quinate,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (3′-hydroxylating)
Comments: A cytochrome P-450 (heme-thiolate) protein, found in plants. It also acts on trans-5-O-(4-coumaroyl)shikimate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 112131-08-5
References:
1.  Kühnl, T., Koch, U., Heller, W. and Wellman, E. Chlorogenic acid biosynthesis: characterization of a light-induced microsomal 5-O-(4-coumaroyl)-D-quinate/shikimate 3′-hydroxylase from carrot (Daucus carota L.) cell suspension cultures. Arch. Biochem. Biophys. 258 (1987) 226–232. [DOI] [PMID: 2821918]
2.  Schoch, G., Goepfert, S., Morant, M., Hehn, A., Meyer, D., Ullmann, P. and Werck-Reichhart, D. CYP98A3 from Arabidopsis thaliana is a 3′-hydroxylase of phenolic esters, a missing link in the phenylpropanoid pathway. J. Biol. Chem. 276 (2001) 36566–36574. [PMID: 11429408]
3.  Franke, R., Humphreys, J.M., Hemm, M.R., Denault, J.W., Ruegger, M.O., Cusumano, J.C. and Chapple, C. The Arabidopsis REF8 gene encodes the 3-hydroxylase of phenylpropanoid metabolism. Plant J. 30 (2002) 33–45. [PMID: 11967091]
4.  Matsuno, M., Compagnon, V., Schoch, G.A., Schmitt, M., Debayle, D., Bassard, J.E., Pollet, B., Hehn, A., Heintz, D., Ullmann, P., Lapierre, C., Bernier, F., Ehlting, J. and Werck-Reichhart, D. Evolution of a novel phenolic pathway for pollen development. Science 325 (2009) 1688–1692. [PMID: 19779199]
[EC 1.14.14.96 created 1990 as EC 1.14.13.36, transferred 2018 to EC 1.14.14.96]
 
 
EC 1.14.14.107     
Accepted name: ent-kaurenoic acid monooxygenase
Reaction: ent-kaur-16-en-19-oate + 3 [reduced NADPH—hemoprotein reductase] + 3 O2 = gibberellin A12 + 3 [oxidized NADPH—hemoprotein reductase] + 4 H2O (overall reaction)
(1a) ent-kaur-16-en-19-oate + [reduced NADPH—hemoprotein reductase] + O2 = ent-7α-hydroxykaur-16-en-19-oate + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) ent-7α-hydroxykaur-16-en-19-oate + [reduced NADPH—hemoprotein reductase] + O2 = gibberellin A12 aldehyde + [oxidized NADPH—hemoprotein reductase] + 2 H2O
(1c) gibberellin A12 aldehyde + [reduced NADPH—hemoprotein reductase] + O2 = gibberellin A12 + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of gibberellin A12 biosynthesis, click here
Other name(s): KAO1 (gene name); CYP88A3 (gene name); ent-kaurenoic acid oxidase
Systematic name: ent-kaur-16-en-19-oate,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (hydroxylating)
Comments: A cytochrome P-450 (heme-thiolate) protein from plants. Catalyses three sucessive oxidations of ent-kaurenoic acid. The second step includes a ring-B contraction giving the gibbane skeleton. In pumpkin (Cucurbita maxima) ent-6α,7α-dihydroxykaur-16-en-19-oate is also formed.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 337507-95-6
References:
1.  Helliwell, C.A., Chandler, P.M., Poole, A., Dennis, E.S. and Peacock, W.J. The CYP88A cytochrome P450, ent-kaurenoic acid oxidase, catalyzes three steps of the gibberellin biosynthesis pathway. Proc. Natl. Acad. Sci. USA 98 (2001) 2065–2070. [DOI] [PMID: 11172076]
[EC 1.14.14.107 created 2002 as EC 1.14.13.79, transferred 2018 to EC 1.14.14.107]
 
 
EC 1.14.15.6     
Accepted name: cholesterol monooxygenase (side-chain-cleaving)
Reaction: cholesterol + 6 reduced adrenodoxin + 3 O2 + 6 H+ = pregnenolone + 4-methylpentanal + 6 oxidized adrenodoxin + 4 H2O (overall reaction)
(1a) cholesterol + 2 reduced adrenodoxin + O2 + 2 H+ = (22R)-22-hydroxycholesterol + 2 oxidized adrenodoxin + H2O
(1b) (22R)-22-hydroxycholesterol + 2 reduced adrenodoxin + O2 + 2 H+ = (20R,22R)-20,22-dihydroxycholesterol + 2 oxidized adrenodoxin + H2O
(1c) (20R,22R)-20,22-dihydroxy-cholesterol + 2 reduced adrenodoxin + O2 + 2 H+ = pregnenolone + 4-methylpentanal + 2 oxidized adrenodoxin + 2 H2O
Other name(s): cholesterol desmolase; cytochrome P-450scc; C27-side chain cleavage enzyme; cholesterol 20-22-desmolase; cholesterol C20-22 desmolase; cholesterol side-chain cleavage enzyme; cholesterol side-chain-cleaving enzyme; steroid 20-22 desmolase; steroid 20-22-lyase; CYP11A1 (gene name)
Systematic name: cholesterol,reduced-adrenodoxin:oxygen oxidoreductase (side-chain-cleaving)
Comments: A heme-thiolate protein (cytochrome P-450). The reaction proceeds in three stages, with two hydroxylations at C-22 and C-20 preceding scission of the side-chain between carbons 20 and 22. The initial source of the electrons is NADPH, which transfers the electrons to the adrenodoxin via EC 1.18.1.6, adrenodoxin-NADP+ reductase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37292-81-2, 440354-98-3
References:
1.  Burstein, S., Middleditch, B.S. and Gut, M. Mass spectrometric study of the enzymatic conversion of cholesterol to (22R)-22-hydroxycholesterol, (20R,22R)-20,22-dihydroxycholesterol, and pregnenolone, and of (22R)-22-hydroxycholesterol to the lgycol and pregnenolone in bovine adrenocortical preparations. Mode of oxygen incorporation. J. Biol. Chem. 250 (1975) 9028–9037. [PMID: 1238395]
2.  Hanukoglu, I., Spitsberg, V., Bumpus, J.A., Dus, K.M. and Jefcoate, C.R. Adrenal mitochondrial cytochrome P-450scc. Cholesterol and adrenodoxin interactions at equilibrium and during turnover. J. Biol. Chem. 256 (1981) 4321–4328. [PMID: 7217084]
3.  Hanukoglu, I. and Hanukoglu, Z. Stoichiometry of mitochondrial cytochromes P-450, adrenodoxin and adrenodoxin reductase in adrenal cortex and corpus luteum. Implications for membrane organization and gene regulation. Eur. J. Biochem. 157 (1986) 27–31. [DOI] [PMID: 3011431]
4.  Strushkevich, N., MacKenzie, F., Cherkesova, T., Grabovec, I., Usanov, S. and Park, H.W. Structural basis for pregnenolone biosynthesis by the mitochondrial monooxygenase system. Proc. Natl. Acad. Sci. USA 108 (2011) 10139–10143. [DOI] [PMID: 21636783]
5.  Mast, N., Annalora, A.J., Lodowski, D.T., Palczewski, K., Stout, C.D. and Pikuleva, I.A. Structural basis for three-step sequential catalysis by the cholesterol side chain cleavage enzyme CYP11A1. J. Biol. Chem. 286 (2011) 5607–5613. [DOI] [PMID: 21159775]
[EC 1.14.15.6 created 1983, modified 2013, modified 2014]
 
 
EC 1.14.18.4     
Accepted name: phosphatidylcholine 12-monooxygenase
Reaction: a 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine + 2 ferrocytochrome b5 + O2 + 2 H+ = a 1-acyl-2-[(12R)-12-hydroxyoleoyl]-sn-glycero-3-phosphocholine + 2 ferricytochrome b5 + H2O
Glossary: ricinoleic acid = (9Z,12R)-12-hydroxyoctadec-9-enoic acid
Other name(s): ricinoleic acid synthase; oleate Δ12-hydroxylase; oleate Δ12-monooxygenase
Systematic name: 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine,ferrocytochrome-b5:oxygen oxidoreductase (12-hydroxylating)
Comments: The enzyme, characterized from the plant Ricinus communis (castor bean), is involved in production of the 12-hydroxylated fatty acid ricinoleate. The enzyme, which shares sequence similarity with fatty-acyl desaturases, requires a cytochrome b5 as the electron donor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 77950-95-9
References:
1.  Galliard, T. and Stumpf, P.K. Fat metabolism in higher plants. 30. Enzymatic synthesis of ricinoleic acid by a microsomal preparation from developing Ricinus communis seeds. J. Biol. Chem. 241 (1966) 5806–5812. [PMID: 4289003]
2.  Moreau, R.A. and Stumpf, P.K. Recent studies of the enzymic-synthesis of ricinoleic acid by developing castor beans. Plant Physiol. 67 (1981) 672–676. [PMID: 16661734]
3.  Smith, M.A., Jonsson, L., Stymne, S. and Stobart, K. Evidence for cytochrome b5 as an electron donor in ricinoleic acid biosynthesis in microsomal preparations from developing castor bean (Ricinus communis L.). Biochem. J. 287 (1992) 141–144. [PMID: 1417766]
4.  Lin, J.T., McKeon, T.A., Goodrich-Tanrikulu, M. and Stafford, A.E. Characterization of oleoyl-12-hydroxylase in castor microsomes using the putative substrate, 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine. Lipids 31 (1996) 571–577. [DOI] [PMID: 8784737]
5.  Broun, P. and Somerville, C. Accumulation of ricinoleic, lesquerolic, and densipolic acids in seeds of transgenic Arabidopsis plants that express a fatty acyl hydroxylase cDNA from castor bean. Plant Physiol. 113 (1997) 933–942. [PMID: 9085577]
[EC 1.14.18.4 created 1984 as EC 1.14.13.26, transferred 2015 to EC 1.14.18.4]
 
 
EC 1.14.19.2     
Accepted name: stearoyl-[acyl-carrier-protein] 9-desaturase
Reaction: stearoyl-[acyl-carrier protein] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = oleoyl-[acyl-carrier protein] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
Other name(s): stearyl acyl carrier protein desaturase; stearyl-ACP desaturase; acyl-[acyl-carrier-protein] desaturase; acyl-[acyl-carrier protein],hydrogen-donor:oxygen oxidoreductase
Systematic name: stearoyl-[acyl-carrier protein],reduced ferredoxin:oxygen oxidoreductase (9,10 cis-dehydrogenating)
Comments: The enzyme is found in the lumen of plastids, where de novo biosynthesis of fatty acids occurs, and acts on freshly synthesized saturated fatty acids that are still linked to acyl-carrier protein. The enzyme determines the position of the double bond by its distance from the carboxylic acid end of the fatty acid. It also acts on palmitoyl-[acyl-carrier-protein] [4,5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37256-86-3
References:
1.  Jaworski, J.G. and Stumpf, P.K. Fat metabolism in higher plants. Properties of a soluble stearyl-acyl carrier protein desaturase from maturing Carthamus tinctorius. Arch. Biochem. Biophys. 162 (1974) 158–165. [DOI] [PMID: 4831331]
2.  Nagai, J. and Bloch, K. Enzymatic desaturation of stearyl acyl carrier protein. J. Biol. Chem. 243 (1968) 4626–4633. [PMID: 4300868]
3.  Shanklin, J. and Somerville, C. Stearoyl-acyl-carrier-protein desaturase from higher plants is structurally unrelated to the animal and fungal homologs. Proc. Natl. Acad. Sci. USA 88 (1991) 2510–2514. [DOI] [PMID: 2006187]
4.  Cahoon, E.B., Lindqvist, Y., Schneider, G. and Shanklin, J. Redesign of soluble fatty acid desaturases from plants for altered substrate specificity and double bond position. Proc. Natl. Acad. Sci. USA 94 (1997) 4872–4877. [DOI] [PMID: 9144157]
5.  Cao, Y., Xian, M., Yang, J., Xu, X., Liu, W. and Li, L. Heterologous expression of stearoyl-acyl carrier protein desaturase (S-ACP-DES) from Arabidopsis thaliana in Escherichia coli. Protein Expr. Purif. 69 (2010) 209–214. [DOI] [PMID: 19716420]
[EC 1.14.19.2 created 1972 as EC 1.14.99.6, modified 2000, transferred 2000 to EC 1.14.19.2, modified 2015]
 
 
EC 1.18.1.8      
Transferred entry: ferredoxin-NAD+ oxidoreductase (Na+-transporting). Now EC 7.2.1.2, ferredoxin—NAD+ oxidoreductase (Na+-transporting)
[EC 1.18.1.8 created 2015, deleted 2018]
 
 
EC 2.1.1.45     
Accepted name: thymidylate synthase
Reaction: 5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
For diagram of C1 metabolism, click here
Other name(s): dTMP synthase; thymidylate synthetase; methylenetetrahydrofolate:dUMP C-methyltransferase; TMP synthetase
Systematic name: 5,10-methylenetetrahydrofolate:dUMP C-methyltransferase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9031-61-2
References:
1.  Blakley, R.L. The biosynthesis of thymidylic acid. IV. Further studies on thymidylate synthase. J. Biol. Chem. 238 (1963) 2113–2118.
2.  Lockshin, A., Moran, R.G. and Danenberg, P.V. Thymidylate synthetase purified to homogeneity from human leukemic cells. Proc. Natl. Acad. Sci. USA 76 (1979) 750–754. [DOI] [PMID: 34155]
3.  Slavik, K. and Slavikova, V. Purification of thymidylate synthetase from enzyme-poor sources by affinity chromatography. Methods Enzymol. 66 (1980) 709–723. [PMID: 6990200]
4.  Wahba, A.J. and Friedkin, M. The enzymatic synthesis of thymidylate. I. Early steps in the purification of thymidylate synthetase of Escherichia coli. J. Biol. Chem. 237 (1962) 3794–3801. [PMID: 13998281]
[EC 2.1.1.45 created 1976]
 
 
EC 2.1.1.148     
Accepted name: thymidylate synthase (FAD)
Reaction: 5,10-methylenetetrahydrofolate + dUMP + NADPH + H+ = dTMP + tetrahydrofolate + NADP+
For diagram of C1 metabolism, click here
Other name(s): Thy1; ThyX
Systematic name: 5,10-methylenetetrahydrofolate,FADH2:dUMP C-methyltransferase
Comments: Contains FAD. All thymidylate synthases catalyse a reductive methylation involving the transfer of the methylene group of 5,10-methylenetetrahydrofolate to the C5 position of dUMP and a two electron reduction of the methylene group to a methyl group. Unlike the classical thymidylate synthase, ThyA (EC 2.1.1.45), which uses folate as both a 1-carbon donor and a source of reducing equivalents, this enzyme uses a flavin cofactor as a source of reducing equivalents, which are derived from NADPH.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 850167-13-4
References:
1.  Myllykallio, H., Lipowski, G., Leduc, D., Filee, J., Forterre, P. and Liebl, U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science 297 (2002) 105–107. [DOI] [PMID: 12029065]
2.  Griffin, J., Roshick, C., Iliffe-Lee, E. and McClarty, G. Catalytic mechanism of Chlamydia trachomatis flavin-dependent thymidylate synthase. J. Biol. Chem. 280 (2005) 5456–5467. [DOI] [PMID: 15591067]
3.  Graziani, S., Bernauer, J., Skouloubris, S., Graille, M., Zhou, C.Z., Marchand, C., Decottignies, P., van Tilbeurgh, H., Myllykallio, H. and Liebl, U. Catalytic mechanism and structure of viral flavin-dependent thymidylate synthase ThyX. J. Biol. Chem. 281 (2006) 24048–24057. [DOI] [PMID: 16707489]
4.  Koehn, E.M., Fleischmann, T., Conrad, J.A., Palfey, B.A., Lesley, S.A., Mathews, I.I. and Kohen, A. An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene. Nature 458 (2009) 919–923. [DOI] [PMID: 19370033]
5.  Koehn, E.M. and Kohen, A. Flavin-dependent thymidylate synthase: a novel pathway towards thymine. Arch. Biochem. Biophys. 493 (2010) 96–102. [DOI] [PMID: 19643076]
6.  Mishanina, T.V., Yu, L., Karunaratne, K., Mondal, D., Corcoran, J.M., Choi, M.A. and Kohen, A. An unprecedented mechanism of nucleotide methylation in organisms containing thyX. Science 351 (2016) 507–510. [DOI] [PMID: 26823429]
[EC 2.1.1.148 created 2003, modified 2010]
 
 
EC 2.1.1.213     
Accepted name: tRNA (guanine10-N2)-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + guanine10 in tRNA = 2 S-adenosyl-L-homocysteine + N2-dimethylguanine10 in tRNA (overall reaction)
(1a) S-adenosyl-L-methionine + guanine10 in tRNA = S-adenosyl-L-homocysteine + N2-methylguanine10 in tRNA
(1b) S-adenosyl-L-methionine + N2-methylguanine10 in tRNA = S-adenosyl-L-homocysteine + N2-dimethylguanine10 in tRNA
Other name(s): PAB1283; N(2),N(2)-dimethylguanosine tRNA methyltransferase; Trm-G10; PabTrm-G10; PabTrm-m2 2G10 enzyme
Systematic name: S-adenosyl-L-methionine:tRNA (guanine10-N2)-dimethyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Armengaud, J., Urbonavicius, J., Fernandez, B., Chaussinand, G., Bujnicki, J.M. and Grosjean, H. N2-Methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota. J. Biol. Chem. 279 (2004) 37142–37152. [DOI] [PMID: 15210688]
[EC 2.1.1.213 created 2011 (EC 2.1.1.32 created 1972, part transferred 2011 to EC 2.1.1.213)]
 
 
EC 2.1.1.373     
Accepted name: 2-hydroxy-4-(methylsulfanyl)butanoate S-methyltransferase
Reaction: S-adenosyl-L-methionine + (2R)-2-hydroxy-4-(methylsulfanyl)butanoate = S-adenosyl-L-homocysteine + (2R)-4-(dimethylsulfaniumyl)-2-hydroxybutanoate
Other name(s): dsyB (gene name); methylthiohydroxybutyrate methyltransferase; MTHB methyltransferase
Systematic name: S-adenosyl-L-methionine:(2R)-2-hydroxy-4-(methylsulfanyl)butanoate S-methyltransferase
Comments: The enzyme, characterized from the marine bacterium Labrenzia aggregata, participates in the biosynthesis of dimethylsulfoniopropanoate (DMSP). A eukaryotic enzyme that shares little sequence similarity with the bacterial enzyme was identified in many marine phytoplankton species.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Summers, P.S., Nolte, K.D., Cooper, A.J.L., Borgeas, H., Leustek, T., Rhodes, D. and Hanson, A.D. Identification and stereospecificity of the first three enzymes of 3-dimethylsulfoniopropionate biosynthesis in a chlorophyte alga. Plant Physiol. 116 (1998) 369–378. [DOI]
2.  Curson, A.R., Liu, J., Bermejo Martinez, A., Green, R.T., Chan, Y., Carrion, O., Williams, B.T., Zhang, S.H., Yang, G.P., Bulman Page, P.C., Zhang, X.H. and Todd, J.D. Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process. Nat. Microbiol. 2:17009 (2017). [DOI] [PMID: 28191900]
3.  Kageyama, H., Tanaka, Y., Shibata, A., Waditee-Sirisattha, R. and Takabe, T. Dimethylsulfoniopropionate biosynthesis in a diatom Thalassiosira pseudonana: Identification of a gene encoding MTHB-methyltransferase. Arch. Biochem. Biophys. 645 (2018) 100–106. [DOI] [PMID: 29574051]
4.  Curson, A.RJ., Williams, B.T., Pinchbeck, B.J., Sims, L.P., Martinez, A.B., Rivera, P.PL., Kumaresan, D., Mercade, E., Spurgin, L.G., Carrion, O., Moxon, S., Cattolico, R.A., Kuzhiumparambil, U., Guagliardo, P., Clode, P.L., Raina, J.B. and Todd, J.D. DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton. Nat. Microbiol. 3 (2018) 430–439. [DOI] [PMID: 29483657]
[EC 2.1.1.373 created 2020]
 
 
EC 2.1.3.10     
Accepted name: malonyl-S-ACP:biotin-protein carboxyltransferase
Reaction: a malonyl-[acyl-carrier protein] + a biotinyl-[protein] = an acetyl-[acyl-carrier protein] + a carboxybiotinyl-[protein]
For diagram of malonate decarboxylase, click here
Other name(s): malonyl-S-acyl-carrier protein:biotin-protein carboxyltransferase; MadC/MadD; MadC,D; malonyl-[acyl-carrier protein]:biotinyl-[protein] carboxyltransferase
Systematic name: malonyl-[acyl-carrier protein]:biotinyl-[protein] carboxytransferase
Comments: Derived from the components MadC and MadD of the anaerobic bacterium Malonomonas rubra, this enzyme is a component of EC 7.2.4.4, biotin-dependent malonate decarboxylase. The carboxy group is transferred from malonate to the cofactor of the biotin protein (MadF) with retention of configuration [2]. Similar to EC 4.1.1.87, malonyl-S-ACP decarboxylase, which forms part of the biotin-independent malonate decarboxylase (EC 4.1.1.88), this enzyme also follows on from EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase, and results in the regeneration of the acetyl-[acyl-carrier protein] [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [DOI] [PMID: 9128730]
2.  Micklefield, J., Harris, K.J., Gröger, S., Mocek, U., Hilbi, H., Dimroth, P. and Floss, H.G. Stereochemical course of malonate decarboxylase in Malonomonas rubra has biotin decarboxylation with retention. J. Am. Chem. Soc. 117 (1995) 1153–1154. [DOI]
3.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 2.1.3.10 created 2008, modified 2018]
 
 
EC 2.2.1.12     
Accepted name: 3-acetyloctanal synthase
Reaction: pyruvate + (E)-oct-2-enal = (S)-3-acetyloctanal + CO2
Other name(s): pigD (gene name)
Systematic name: pyruvate:(E)-oct-2-enal acetaldehydetransferase (decarboxylating)
Comments: Requires thiamine diphosphate. The enzyme, characterized from the bacterium Serratia marcescens, participates in the biosynthesis of the antibiotic prodigiosin. The enzyme decarboxylates pyruvate, followed by attack of the resulting two-carbon fragment on (E)-oct-2-enal, resulting in a Stetter reaction. In vitro the enzyme can act on a number of α,β-unsaturated carbonyl compounds, including aldehydes and ketones, and can catalyse both 1-2 and 1-4 carboligations depending on the substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Williamson, N.R., Simonsen, H.T., Ahmed, R.A., Goldet, G., Slater, H., Woodley, L., Leeper, F.J. and Salmond, G.P. Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces. Mol. Microbiol. 56 (2005) 971–989. [DOI] [PMID: 15853884]
2.  Dresen, C., Richter, M., Pohl, M., Ludeke, S. and Müller, M. The enzymatic asymmetric conjugate umpolung reaction. Angew. Chem. Int. Ed. Engl. 49 (2010) 6600–6603. [DOI] [PMID: 20669204]
3.  Kasparyan, E., Richter, M., Dresen, C., Walter, L.S., Fuchs, G., Leeper, F.J., Wacker, T., Andrade, S.L., Kolter, G., Pohl, M. and Müller, M. Asymmetric Stetter reactions catalyzed by thiamine diphosphate-dependent enzymes. Appl. Microbiol. Biotechnol. 98 (2014) 9681–9690. [DOI] [PMID: 24957249]
[EC 2.2.1.12 created 2014]
 
 
EC 2.3.1.15     
Accepted name: glycerol-3-phosphate 1-O-acyltransferase
Reaction: acyl-CoA + sn-glycerol 3-phosphate = CoA + 1-acyl-sn-glycerol 3-phosphate
Other name(s): α-glycerophosphate acyltransferase; 3-glycerophosphate acyltransferase; ACP:sn-glycerol-3-phosphate acyltransferase; glycerol 3-phosphate acyltransferase; glycerol phosphate acyltransferase; glycerol phosphate transacylase; glycerophosphate acyltransferase; glycerophosphate transacylase; sn-glycerol 3-phosphate acyltransferase; sn-glycerol-3-phosphate acyltransferase; glycerol-3-phosphate O-acyltransferase (ambiguous)
Systematic name: acyl-CoA:sn-glycerol-3-phosphate 1-O-acyltransferase
Comments: Acyl-[acyl-carrier protein] can also act as acyl donor. The enzyme acts only on derivatives of fatty acids of chain length larger than C10.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9029-96-3
References:
1.  Bertrams, M. and Heinz, E. Positional specificity and fatty-acid selectivity of purified sn-glycerol 3-phosphate acyltransferases from chloroplasts. Plant Physiol. 68 (1981) 653–657. [PMID: 16661974]
2.  Frentzen, M., Heinz, E., McKeon, T.A. and Stumpf, P.K. Specificities and selectivities of glycerol-3-phosphate acyltransferase and monoacylglycerol-3-phosphate acyltransferase from pea and spinach chloroplasts. Eur. J. Biochem. 129 (1983) 629–636. [DOI] [PMID: 6825679]
3.  Green, P.R., Merrill, A.H. and Bell, R.M. Membrane phospholipid synthesis in Escherichia coli. Purification, reconstitution, and characterization of sn-glycerol-3-phosphate acyltransferase. J. Biol. Chem. 256 (1981) 11151–11159. [PMID: 6350296]
4.  Yamashita, S. and Numa, N. Partial purification and properties of glycerophosphate acyltransferase from rat liver. Formation of 1-acylglycerol 3-phosphate from sn-glycerol 3-phosphate and palmityl coenzyme A. Eur. J. Biochem. 31 (1972) 565–573. [DOI] [PMID: 4650158]
[EC 2.3.1.15 created 1961, modified 1976, modified 1990]
 
 
EC 2.3.1.51     
Accepted name: 1-acylglycerol-3-phosphate O-acyltransferase
Reaction: acyl-CoA + 1-acyl-sn-glycerol 3-phosphate = CoA + 1,2-diacyl-sn-glycerol 3-phosphate
Other name(s): 1-acyl-sn-glycero-3-phosphate acyltransferase; 1-acyl-sn-glycerol 3-phosphate acyltransferase; 1-acylglycero-3-phosphate acyltransferase; 1-acylglycerolphosphate acyltransferase; 1-acylglycerophosphate acyltransferase; lysophosphatidic acid-acyltransferase
Systematic name: acyl-CoA:1-acyl-sn-glycerol-3-phosphate 2-O-acyltransferase
Comments: Acyl-[acyl-carrier protein] can also act as an acyl donor. The animal enzyme is specific for the transfer of unsaturated fatty acyl groups.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 51901-16-7
References:
1.  Frentzen, M., Heinz, E., McKeon, T.A. and Stumpf, P.K. Specificities and selectivities of glycerol-3-phosphate acyltransferase and monoacylglycerol-3-phosphate acyltransferase from pea and spinach chloroplasts. Eur. J. Biochem. 129 (1983) 629–636. [DOI] [PMID: 6825679]
2.  Hill, E.E. and Lands, W.E.M. Incorporation of long-chain and polyunsaturated acids into phosphatidate and phosphatidylcholine. Biochim. Biophys. Acta 152 (1968) 645–648. [DOI] [PMID: 5661029]
3.  Yamashita, S., Hosaka, K. and Numa, S. Acyl-donor specificities of partially purified 1-acylglycerophosphate acyltransferase, 2-acylglycerophosphate acyltransferase and 1-acylglycerophosphorylcholine acyltransferase from rat-liver microsomes. Eur. J. Biochem. 38 (1973) 25–31. [DOI] [PMID: 4774123]
[EC 2.3.1.51 created 1976, modified 1990]
 
 
EC 2.3.1.75     
Accepted name: long-chain-alcohol O-fatty-acyltransferase
Reaction: acyl-CoA + a long-chain alcohol = CoA + a long-chain ester
Other name(s): wax synthase; wax-ester synthase
Systematic name: acyl-CoA:long-chain-alcohol O-acyltransferase
Comments: Transfers saturated or unsaturated acyl residues of chain-length C18 to C20 to long-chain alcohols, forming waxes. The best acceptor is cis-icos-11-en-1-ol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 64060-40-8
References:
1.  Wu, X.-Y., Moreau, R.A. and Stumpf, P.K. Studies of biosynthesis of waxes by developing jojoba seed. 3. Biosynthesis of wax esters from acyl-CoA and long-chain alcohols. Lipids 16 (1981) 897–902.
[EC 2.3.1.75 created 1984]
 
 
EC 2.4.1.16     
Accepted name: chitin synthase
Reaction: UDP-N-acetyl-α-D-glucosamine + [(1→4)-N-acetyl-β-D-glucosaminyl]n = UDP + [(1→4)-N-acetyl-β-D-glucosaminyl]n+1
Glossary: chitin = [(1→4)-N-acetyl-β-D-glucosaminyl]n
Other name(s): chitin-UDP N-acetylglucosaminyltransferase; chitin-uridine diphosphate acetylglucosaminyltransferase; chitin synthetase; trans-N-acetylglucosaminosylase; UDP-N-acetyl-D-glucosamine:chitin 4-β-N-acetylglucosaminyl-transferase; UDP-N-acetyl-α-D-glucosamine:chitin 4-β-N-acetylglucosaminyltransferase
Systematic name: UDP-N-acetyl-α-D-glucosamine:chitin 4-β-N-acetylglucosaminyltransferase (configuration-inverting)
Comments: Converts UDP-N-acetyl-α-D-glucosamine into chitin and UDP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9030-18-6
References:
1.  Glaser, L. and Brown, D.H. The synthesis of chitin in cell-free extracts of Neurospora crassa. J. Biol. Chem. 228 (1957) 729–742. [PMID: 13475355]
2.  Sburlati, A. and Cabib, E. Chitin synthetase 2, a presumptive participant in septum formation in Saccharomyces cerevisiae. J. Biol. Chem. 261 (1986) 15147–15152. [PMID: 2945823]
[EC 2.4.1.16 created 1961]
 
 
EC 2.4.1.90     
Accepted name: N-acetyllactosamine synthase
Reaction: UDP-α-D-galactose + N-acetyl-D-glucosamine = UDP + N-acetyllactosamine
Other name(s): UDP-galactose—N-acetylglucosamine β-D-galactosyltransferase; uridine diphosphogalactose-acetylglucosamine galactosyltransferase; β-1,4-galactosyltransferase; acetyllactosamine synthetase; lactosamine synthase; lactosamine synthetase; lactose synthetase A protein; N-acetyllactosamine synthetase; UDP-galactose N-acetylglucosamine β-4-galactosyltransferase; UDP-galactose-acetylglucosamine galactosyltransferase; UDP-galactose-N-acetylglucosamine β-1,4-galactosyltransferase; UDP-galactose-N-acetylglucosamine galactosyltransferase; β1-4-galactosyltransferase; UDP-Gal:N-acetylglucosamine β1-4-galactosyltransferase; β1-4GalT; NAL synthetase; UDP-β-1,4-galactosyltransferase; Gal-T; UDP-galactose:N-acetylglucosaminide β1-4-galactosyltransferase; UDPgalactose:N-acetylglucosaminyl(β1-4)galactosyltransferase; β-N-acetylglucosaminide β1-4-galactosyltransferase; UDP-galactose:N-acetyl-D-glucosamine 4-β-D-galactosyltransferase
Systematic name: UDP-α-D-galactose:N-acetyl-D-glucosamine 4-β-D-galactosyltransferase
Comments: The reaction is catalysed by a component of EC 2.4.1.22 (lactose synthase), which is identical with EC 2.4.1.38 (β-N-acetylglucosaminyl-glycopeptide β-1,4-galactosyltransferase), and by an enzyme from the Golgi apparatus of animal tissues. Formerly listed also as EC 2.4.1.98.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9054-94-8
References:
1.  Deshmukh, D.S., Bear, W.D. and Soifer, D. Isolation and characterization of an enriched Golgi fraction from rat brain. Biochim. Biophys. Acta 542 (1978) 284–295. [DOI] [PMID: 99178]
2.  Helting, T. and Erbing, B. Galactosyl transfer in mouse mastocytoma: purification and properties of N-acetyllactosamine synthetase. Biochim. Biophys. Acta 293 (1973) 94–104. [DOI] [PMID: 4631039]
3.  Hill, R.L. and Brew, K. Lactose synthetase. Adv. Enzymol. Relat. Areas Mol. Biol. 43 (1975) 411–490. [PMID: 812340]
4.  Humphreys-Beher, M.G. Isolation and characterization of UDP-galactose:N-acetylglucosamine 4 β-galactosyltransferase activity induced in rat parotid glands treated with isoproterenol. J. Biol. Chem. 259 (1984) 5797–5802. [PMID: 6201486]
5.  Schachter, H., Jabbal, I., Hudgin, R.L., Pinteric, L., McGuire, E.J. and Roseman, S. Intracellular localization of liver sugar nucleotide glycoprotein glycosyltransferases in a Golgi-rich fraction. J. Biol. Chem. 245 (1970) 1090–1100. [PMID: 4392041]
[EC 2.4.1.90 created 1976 (EC 2.4.1.98 created 1980, incorporated 1984)]
 
 
EC 2.4.2.9     
Accepted name: uracil phosphoribosyltransferase
Reaction: UMP + diphosphate = uracil + 5-phospho-α-D-ribose 1-diphosphate
Other name(s): UMP pyrophosphorylase; UPRTase; UMP:pyrophosphate phosphoribosyltransferase; uridine 5′-phosphate pyrophosphorylase; uridine monophosphate pyrophosphorylase; uridylate pyrophosphorylase; uridylic pyrophosphorylase
Systematic name: UMP:diphosphate phospho-α-D-ribosyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9030-24-4
References:
1.  Crawford, I., Kornberg, A. and Simms, E.S. Conversion of uracil and orotate to uridine 5′-phosphate by enzymes in lactobacilli. J. Biol. Chem. 226 (1967) 1093–1101. [PMID: 13438895]
2.  Flaks, J.G. Nucleotide synthesis from 5-phosphoribosylpyrophosphate. Methods Enzymol. 6 (1963) 136–158.
[EC 2.4.2.9 created 1961]
 
 
EC 2.4.2.57     
Accepted name: AMP phosphorylase
Reaction: (1) AMP + phosphate = adenine + α-D-ribose 1,5-bisphosphate
(2) CMP + phosphate = cytosine + α-D-ribose 1,5-bisphosphate
(3) UMP + phosphate = uracil + α-D-ribose 1,5-bisphosphate
For diagram of AMP catabolism, click here
Other name(s): AMPpase; nucleoside monophosphate phosphorylase; deoA (gene name)
Systematic name: AMP:phosphate α-D-ribosyl 5′-phosphate-transferase
Comments: The enzyme from archaea is involved in AMP metabolism and CO2 fixation through type III RubisCO enzymes. The activity with CMP and UMP requires activation by cAMP [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Sato, T., Atomi, H. and Imanaka, T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 315 (2007) 1003–1006. [DOI] [PMID: 17303759]
2.  Aono, R., Sato, T., Yano, A., Yoshida, S., Nishitani, Y., Miki, K., Imanaka, T. and Atomi, H. Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. J. Bacteriol. 194 (2012) 6847–6855. [DOI] [PMID: 23065974]
3.  Nishitani, Y., Aono, R., Nakamura, A., Sato, T., Atomi, H., Imanaka, T. and Miki, K. Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization. J. Mol. Biol. 425 (2013) 2709–2721. [DOI] [PMID: 23659790]
[EC 2.4.2.57 created 2014]
 
 
EC 2.5.1.10     
Accepted name: (2E,6E)-farnesyl diphosphate synthase
Reaction: geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): farnesyl-diphosphate synthase; geranyl transferase I; prenyltransferase; farnesyl pyrophosphate synthetase; farnesylpyrophosphate synthetase; geranyltranstransferase
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate geranyltranstransferase
Comments: Some forms of this enzyme will also use dimethylallyl diphosphate as a substrate. The enzyme will not accept larger prenyl diphosphates as efficient donors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37277-79-5
References:
1.  Lynen, F., Agranoff, B.W., Eggerer, H., Henning, V. and Möslein, E.M. Zur Biosynthese der Terpene. VI. γ,γ-Dimethyl-allyl-pyrophosphat und Geranyl-pyrophosphat, biologische Vorstufen des Squalens. Angew. Chem. 71 (1959) 657–663.
2.  Ogura, K., Nishino, T. and Seto, S. The purification of prenyltransferase and isopentenyl pyrophosphate isomerase of pumpkin fruit and their some properties. J. Biochem. (Tokyo) 64 (1968) 197–203. [PMID: 4303505]
3.  Reed, B.C. and Rilling, H. Crystallization and partial characterization of prenyltransferase from avian liver. Biochemistry 14 (1975) 50–54. [PMID: 1109590]
4.  Takahashi, I. and Ogura, K. Farnesyl pyrophosphate synthetase from Bacillus subtilis. J. Biochem. (Tokyo) 89 (1981) 1581–1587. [PMID: 6792191]
5.  Takahashi, I. and Ogura, K. Prenyltransferases of Bacillus subtilis: undecaprenyl pyrophosphate synthetase and geranylgeranyl pyrophosphate synthetase. J. Biochem. (Tokyo) 92 (1982) 1527–1537. [PMID: 6818223]
[EC 2.5.1.10 created 1972, modified 2010]
 
 
EC 2.5.1.79     
Accepted name: thermospermine synthase
Reaction: S-adenosyl 3-(methylsulfanyl)propylamine + spermidine = S-methyl-5′-thioadenosine + thermospermine + H+
Glossary: thermospermine = N1-[3-(3-aminopropylamino)propyl]butane-1,4-diamine
S-adenosyl 3-(methylsulfanyl)propylamine = (3-aminopropyl){[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium
Other name(s): TSPMS; ACL5; SAC51; S-adenosyl 3-(methylthio)propylamine:spermidine 3-aminopropyltransferase (thermospermine synthesizing)
Systematic name: S-adenosyl 3-(methylsulfanyl)propylamine:spermidine 3-aminopropyltransferase (thermospermine-forming)
Comments: This plant enzyme is crucial for the proper functioning of xylem vessel elements in the vascular tissues of plants [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Romer, P., Faltermeier, A., Mertins, V., Gedrange, T., Mai, R. and Proff, P. Investigations about N-aminopropyl transferases probably involved in biomineralization. J. Physiol. Pharmacol. 59 Suppl 5 (2008) 27–37. [PMID: 19075322]
2.  Knott, J.M., Romer, P. and Sumper, M. Putative spermine synthases from Thalassiosira pseudonana and Arabidopsis thaliana synthesize thermospermine rather than spermine. FEBS Lett. 581 (2007) 3081–3086. [DOI] [PMID: 17560575]
3.  Muniz, L., Minguet, E.G., Singh, S.K., Pesquet, E., Vera-Sirera, F., Moreau-Courtois, C.L., Carbonell, J., Blazquez, M.A. and Tuominen, H. ACAULIS5 controls Arabidopsis xylem specification through the prevention of premature cell death. Development 135 (2008) 2573–2582. [DOI] [PMID: 18599510]
[EC 2.5.1.79 created 2010, modified 2013]
 
 
EC 2.5.1.145     
Accepted name: phosphatidylglycerol—prolipoprotein diacylglyceryl transferase
Reaction: L-1-phosphatidyl-sn-glycerol + a [prolipoprotein]-L-cysteine = sn-glycerol 1-phosphate + an [prolipoprotein]-S-1,2-diacyl-sn-glyceryl-L-cysteine
Other name(s): lgt (gene name)
Systematic name: L-1-phosphatidyl-sn-glycerol:[prolipoprotein]-L-cysteine diacyl-sn-glyceryltransferase
Comments: This bacterial enzyme, which is associated with the membrane, catalyses the transfer of an sn-1,2-diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the prospective N-terminal cysteine of a prolipoprotein, the first step in the formation of mature triacylated lipoproteins.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Sankaran, K. and Wu, H.C. Lipid modification of bacterial prolipoprotein. Transfer of diacylglyceryl moiety from phosphatidylglycerol. J. Biol. Chem. 269 (1994) 19701–19706. [PMID: 8051048]
2.  Qi, H.Y., Sankaran, K., Gan, K. and Wu, H.C. Structure-function relationship of bacterial prolipoprotein diacylglyceryl transferase: functionally significant conserved regions. J. Bacteriol. 177 (1995) 6820–6824. [PMID: 7592473]
3.  Gan, K., Sankaran, K., Williams, M.G., Aldea, M., Rudd, K.E., Kushner, S.R. and Wu, H.C. The umpA gene of Escherichia coli encodes phosphatidylglycerol:prolipoprotein diacylglyceryl transferase (lgt) and regulates thymidylate synthase levels through translational coupling. J. Bacteriol. 177 (1995) 1879–1882. [PMID: 7896715]
4.  Sankaran, K., Gan, K., Rash, B., Qi, H.Y., Wu, H.C. and Rick, P.D. Roles of histidine-103 and tyrosine-235 in the function of the prolipoprotein diacylglyceryl transferase of Escherichia coli. J. Bacteriol. 179 (1997) 2944–2948. [PMID: 9139912]
5.  Pailler, J., Aucher, W., Pires, M. and Buddelmeijer, N. Phosphatidylglycerol::prolipoprotein diacylglyceryl transferase (Lgt) of Escherichia coli has seven transmembrane segments, and its essential residues are embedded in the membrane. J. Bacteriol. 194 (2012) 2142–2151. [DOI] [PMID: 22287519]
[EC 2.5.1.145 created 2018]
 
 
EC 2.7.1.17     
Accepted name: xylulokinase
Reaction: ATP + D-xylulose = ADP + D-xylulose 5-phosphate
Other name(s): xylulokinase (phosphorylating); D-xylulokinase
Systematic name: ATP:D-xylulose 5-phosphotransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9030-58-4
References:
1.  Hickman, J. and Ashwell, G. Purification and properties of D-xylulokinase in liver. J. Biol. Chem. 232 (1958) 737–748. [PMID: 13549459]
2.  Simpson, F.J. D-Xylulokinase. Methods Enzymol. 9 (1966) 454–458.
3.  Slein, M.W. Xylose isomerase from Pasteurella pestis, strain A-1122. J. Am. Chem. Soc. 77 (1955) 1663–1667. [DOI]
4.  Stumpf, P.K. and Horecker, B.L. The røole of xylulose 5-phosphate in xylose metabolism of Lactobacillus pentosus. J. Biol. Chem. 218 (1956) 753–768. [PMID: 13295228]
[EC 2.7.1.17 created 1961]
 
 
EC 2.7.1.48     
Accepted name: uridine/cytidine kinase
Reaction: (1) ATP + uridine = ADP + UMP
(2) ATP + cytidine = ADP + CMP
Other name(s): UCK (gene name); URK1 (gene name); pyrimidine ribonucleoside kinase; uridine-cytidine kinase; uridine kinase (phosphorylating); uridine phosphokinase; ATP:uridine 5′-phosphotransferase; uridine kinase
Systematic name: ATP:uridine/cytidine 5′-phosphotransferase
Comments: The enzyme, found in prokaryotes and eukaryotes, phosphorylates both uridine and cytidine to their monophosphate forms. The enzyme from Escherichia coli prefers GTP to ATP. The human enzyme also catalyses the phosphorylation of several cytotoxic ribonucleoside analogs. cf. EC 2.7.1.213, cytidine kinase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9026-39-5
References:
1.  Sköld, O. Uridine kinase from Erlich ascites tumor: purification and properties. J. Biol. Chem. 235 (1960) 3273–3279.
2.  Orengo, A. Regulation of enzymic activity by metabolites. I. Uridine-cytidine kinase of Novikoff ascites rat tumor. J. Biol. Chem. 244 (1969) 2204–2209. [PMID: 5782006]
3.  Valentin-Hansen, P. Uridine-cytidine kinase from Escherichia coli. Methods Enzymol. 51 (1978) 308–314. [PMID: 211379]
4.  Kern, L. The URK1 gene of Saccharomyces cerevisiae encoding uridine kinase. Nucleic Acids Res. 18:5279 (1990). [PMID: 2169608]
5.  Van Rompay, A.R., Norda, A., Linden, K., Johansson, M. and Karlsson, A. Phosphorylation of uridine and cytidine nucleoside analogs by two human uridine-cytidine kinases. Mol. Pharmacol. 59 (2001) 1181–1186. [PMID: 11306702]
6.  Ohler, L., Niopek-Witz, S., Mainguet, S.E. and Mohlmann, T. Pyrimidine salvage: physiological functions and interaction with chloroplast biogenesis. Plant Physiol. 180 (2019) 1816–1828. [PMID: 31101721]
[EC 2.7.1.48 created 1965, modified 2020]
 
 
EC 2.7.1.174     
Accepted name: diacylglycerol kinase (CTP)
Reaction: CTP + 1,2-diacyl-sn-glycerol = CDP + 1,2-diacyl-sn-glycerol 3-phosphate
Glossary: 1,2-diacyl-sn-glycerol 3-phosphate = phosphatidate
Other name(s): DAG kinase; CTP-dependent diacylglycerol kinase; diglyceride kinase (ambiguous); DGK1 (gene name); diacylglycerol kinase (CTP dependent)
Systematic name: CTP:1,2-diacyl-sn-glycerol 3-phosphotransferase
Comments: Requires Ca2+ or Mg2+ for activity. Involved in synthesis of membrane phospholipids and the neutral lipid triacylglycerol. Unlike the diacylglycerol kinases from bacteria, plants, and animals [cf. EC 2.7.1.107, diacylglycerol kinase (ATP)], the enzyme from Saccharomyces cerevisiae utilizes CTP. The enzyme can also use dCTP, but not ATP, GTP or UTP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Han, G.S., O'Hara, L., Carman, G.M. and Siniossoglou, S. An unconventional diacylglycerol kinase that regulates phospholipid synthesis and nuclear membrane growth. J. Biol. Chem. 283 (2008) 20433–20442. [DOI] [PMID: 18458075]
2.  Han, G.S., O'Hara, L., Siniossoglou, S. and Carman, G.M. Characterization of the yeast DGK1-encoded CTP-dependent diacylglycerol kinase. J. Biol. Chem. 283 (2008) 20443–20453. [DOI] [PMID: 18458076]
3.  Fakas, S., Konstantinou, C. and Carman, G.M. DGK1-encoded diacylglycerol kinase activity is required for phospholipid synthesis during growth resumption from stationary phase in Saccharomyces cerevisiae. J. Biol. Chem. 286 (2011) 1464–1474. [DOI] [PMID: 21071438]
[EC 2.7.1.174 created 2012, modified 2013]
 
 
EC 2.7.4.14     
Accepted name: UMP/CMP kinase
Reaction: (1) ATP + (d)CMP = ADP + (d)CDP
(2) ATP + UMP = ADP + UDP
Other name(s): cytidylate kinase (misleading); deoxycytidylate kinase (misleading); CTP:CMP phosphotransferase (misleading); dCMP kinase (misleading); deoxycytidine monophosphokinase (misleading); UMP-CMP kinase; ATP:UMP-CMP phosphotransferase; pyrimidine nucleoside monophosphate kinase; uridine monophosphate-cytidine monophosphate phosphotransferase
Systematic name: ATP:(d)CMP/UMP phosphotransferase
Comments: This eukaryotic enzyme is a bifunctional enzyme that catalyses the phosphorylation of both CMP and UMP with similar efficiency. dCMP can also act as acceptor. Different from the monofunctional prokaryotic enzymes EC 2.7.4.25, (d)CMP kinase and EC 2.7.4.22, UMP kinase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 37278-21-0
References:
1.  Hurwitz, J. The enzymatic incorporation of ribonucleotides into polydeoxynucleotide material. J. Biol. Chem. 234 (1959) 2351–2358. [PMID: 14405566]
2.  Ruffner, B.W., Jr. and Anderson, E.P. Adenosine triphosphate: uridine monophosphate-cytidine monophosphate phosphotransferase from Tetrahymena pyriformis. J. Biol. Chem. 244 (1969) 5994–6002. [PMID: 5350952]
3.  Scheffzek, K., Kliche, W., Wiesmuller, L. and Reinstein, J. Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5′-adenosyl) P5-(5′-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 Å: implications for water-mediated specificity. Biochemistry 35 (1996) 9716–9727. [DOI] [PMID: 8703943]
4.  Zhou, L., Lacroute, F. and Thornburg, R. Cloning, expression in Escherichia coli, and characterization of Arabidopsis thaliana UMP/CMP kinase. Plant Physiol. 117 (1998) 245–254. [PMID: 9576794]
5.  Van Rompay, A.R., Johansson, M. and Karlsson, A. Phosphorylation of deoxycytidine analog monophosphates by UMP-CMP kinase: molecular characterization of the human enzyme. Mol. Pharmacol. 56 (1999) 562–569. [PMID: 10462544]
[EC 2.7.4.14 created 1961 as EC 2.7.4.5, transferred 1972 to EC 2.7.4.14, modified 1980, modified 2011]
 
 
EC 2.7.4.22     
Accepted name: UMP kinase
Reaction: ATP + UMP = ADP + UDP
Other name(s): uridylate kinase; UMPK; uridine monophosphate kinase; PyrH; UMP-kinase; SmbA
Systematic name: ATP:UMP phosphotransferase
Comments: This enzyme is strictly specific for UMP as substrate and is used by prokaryotes in the de novo synthesis of pyrimidines, in contrast to eukaryotes, which use the dual-specificity enzyme UMP/CMP kinase (EC 2.7.4.14) for the same purpose [2]. This enzyme is the subject of feedback regulation, being inhibited by UTP and activated by GTP [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9036-23-1
References:
1.  Serina, L., Blondin, C., Krin, E., Sismeiro, O., Danchin, A., Sakamoto, H., Gilles, A.M. and Bârzu, O. Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry 34 (1995) 5066–5074. [PMID: 7711027]
2.  Marco-Marín, C., Gil-Ortiz, F. and Rubio, V. The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis. J. Mol. Biol. 352 (2005) 438–454. [DOI] [PMID: 16095620]
[EC 2.7.4.22 created 2006]
 
 
EC 2.7.4.25     
Accepted name: (d)CMP kinase
Reaction: ATP + (d)CMP = ADP + (d)CDP
Glossary: CMP = cytidine monophosphate
dCMP = deoxycytidine monophosphate
CDP = cytidine diphosphate
dCDP = deoxycytidine diphosphate
UMP = uridine monophosphate
UDP = uridine diphosphate
Other name(s): cmk (gene name); prokaryotic cytidylate kinase; deoxycytidylate kinase (misleading); dCMP kinase (misleading); deoxycytidine monophosphokinase (misleading)
Systematic name: ATP:(d)CMP phosphotransferase
Comments: The prokaryotic cytidine monophosphate kinase specifically phosphorylates CMP (or dCMP), using ATP as the preferred phosphoryl donor. Unlike EC 2.7.4.14, a eukaryotic enzyme that phosphorylates UMP and CMP with similar efficiency, the prokaryotic enzyme phosphorylates UMP with very low rates, and this function is catalysed in prokaryotes by EC 2.7.4.22, UMP kinase. The enzyme phosphorylates dCMP nearly as well as it does CMP [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Bertrand, T., Briozzo, P., Assairi, L., Ofiteru, A., Bucurenci, N., Munier-Lehmann, H., Golinelli-Pimpaneau, B., Barzu, O. and Gilles, A.M. Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme. J. Mol. Biol. 315 (2002) 1099–1110. [DOI] [PMID: 11827479]
2.  Thum, C., Schneider, C.Z., Palma, M.S., Santos, D.S. and Basso, L.A. The Rv1712 Locus from Mycobacterium tuberculosis H37Rv codes for a functional CMP kinase that preferentially phosphorylates dCMP. J. Bacteriol. 191 (2009) 2884–2887. [DOI] [PMID: 19181797]
[EC 2.7.4.25 created 2011]
 
 


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