The Enzyme Database

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EC 1.2.1.72     
Accepted name: erythrose-4-phosphate dehydrogenase
Reaction: D-erythrose 4-phosphate + NAD+ + H2O = 4-phosphoerythronate + NADH + 2 H+
For diagram of pyridoxal biosynthesis, click here
Other name(s): erythrose 4-phosphate dehydrogenase; E4PDH; GapB; Epd dehydrogenase; E4P dehydrogenase
Systematic name: D-erythrose 4-phosphate:NAD+ oxidoreductase
Comments: This enzyme was originally thought to be a glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12), but this has since been disproved, as glyceraldehyde 3-phosphate is not a substrate [1,2]. Forms part of the pyridoxal-5′-phosphate coenzyme biosynthesis pathway in Escherichia coli, along with EC 1.1.1.290 (4-phosphoerythronate dehydrogenase), EC 2.6.1.52 (phosphoserine transaminase), EC 1.1.1.262 (4-hydroxythreonine-4-phosphate dehydrogenase), EC 2.6.99.2 (pyridoxine 5′-phosphate synthase) and EC 1.4.3.5 (pyridoxamine-phosphate oxidase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 131554-04-6
References:
1.  Zhao, G., Pease, A.J., Bharani, N. and Winkler, M.E. Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5′-phosphate biosynthesis. J. Bacteriol. 177 (1995) 2804–2812. [DOI] [PMID: 7751290]
2.  Boschi-Muller, S., Azza, S., Pollastro, D., Corbier, C. and Branlant, G. Comparative enzymatic properties of GapB-encoded erythrose-4-phosphate dehydrogenase of Escherichia coli and phosphorylating glyceraldehyde-3-phosphate dehydrogenase. J. Biol. Chem. 272 (1997) 15106–15112. [DOI] [PMID: 9182530]
3.  Yang, Y., Zhao, G., Man, T.K. and Winkler, M.E. Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5′-phosphate coenzyme biosynthesis in Escherichia coli K-12. J. Bacteriol. 180 (1998) 4294–4299. [PMID: 9696782]
[EC 1.2.1.72 created 2006]
 
 
EC 1.4.3.5     
Accepted name: pyridoxal 5′-phosphate synthase
Reaction: (1) pyridoxamine 5′-phosphate + H2O + O2 = pyridoxal 5′-phosphate + NH3 + H2O2
(2) pyridoxine 5′-phosphate + O2 = pyridoxal 5′-phosphate + H2O2
For diagram of pyridoxal biosynthesis, click here
Glossary: pyridoxamine = 4-aminomethyl-3-hydroxy-5-hydroxymethyl-2-methylpyridine
Other name(s): pyridoxamine 5′-phosphate oxidase; pyridoxamine phosphate oxidase; pyridoxine (pyridoxamine)phosphate oxidase; pyridoxine (pyridoxamine) 5′-phosphate oxidase; pyridoxaminephosphate oxidase (EC 1.4.3.5: deaminating); PMP oxidase; pyridoxol-5′-phosphate:oxygen oxidoreductase (deaminating) (incorrect); pyridoxamine-phosphate oxidase; PdxH
Systematic name: pyridoxamine-5′-phosphate:oxygen oxidoreductase (deaminating)
Comments: A flavoprotein (FMN). In Escherichia coli, the coenzyme pyridoxal 5′-phosphate is synthesized de novo by a pathway that involves EC 1.2.1.72 (erythrose-4-phosphate dehydrogenase), EC 1.1.1.290 (4-phosphoerythronate dehydrogenase), EC 2.6.1.52 (phosphoserine transaminase), EC 1.1.1.262 (4-hydroxythreonine-4-phosphate dehydrogenase), EC 2.6.99.2 (pyridoxine 5′-phosphate synthase) and EC 1.4.3.5 (with pyridoxine 5′-phosphate as substrate). N4′-Substituted pyridoxamine derivatives are also oxidized in reaction (1) to form pyridoxal 5-phosphate and the corresponding primary amine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9029-21-4
References:
1.  Choi, J.-D., Bowers-Komro, D.M., Davis, M.D., Edmondson, D.E. and McCormick, D.B. Kinetic properties of pyridoxamine (pyridoxine)-5′-phosphate oxidase from rabbit liver. J. Biol. Chem. 258 (1983) 840–845. [PMID: 6822512]
2.  Wada, H. and Snell, E.E. The enzymatic oxidation of pyridoxine and pyridoxamine phosphates. J. Biol. Chem. 236 (1961) 2089–2095. [PMID: 13782387]
3.  Notheis, C., Drewke, C. and Leistner, E. Purification and characterization of the pyridoxol-5′-phosphate:oxygen oxidoreductase (deaminating) from Escherichia coli. Biochim. Biophys. Acta 1247 (1995) 265–271. [DOI] [PMID: 7696318]
4.  Laber, B., Maurer, W., Scharf, S., Stepusin, K. and Schmidt, F.S. Vitamin B6 biosynthesis: formation of pyridoxine 5′-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein. FEBS Lett. 449 (1999) 45–48. [DOI] [PMID: 10225425]
5.  Musayev, F.N., Di Salvo, M.L., Ko, T.P., Schirch, V. and Safo, M.K. Structure and properties of recombinant human pyridoxine 5′-phosphate oxidase. Protein Sci. 12 (2003) 1455–1463. [DOI] [PMID: 12824491]
6.  Safo, M.K., Musayev, F.N. and Schirch, V. Structure of Escherichia coli pyridoxine 5′-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme. Acta Crystallogr. D Biol. Crystallogr. 61 (2005) 599–604. [DOI] [PMID: 15858270]
7.  Zhang, Z. and McCormick, D.B. Uptake and metabolism of N-(4′-pyridoxyl)amines by isolated rat liver cells. Arch. Biochem. Biophys. 294 (1992) 394–397. [DOI] [PMID: 1567194]
[EC 1.4.3.5 created 1961, modified 2006]
 
 
EC 1.17.1.1     
Accepted name: CDP-4-dehydro-6-deoxyglucose reductase
Reaction: CDP-4-dehydro-3,6-dideoxy-D-glucose + NAD(P)+ + H2O = CDP-4-dehydro-6-deoxy-D-glucose + NAD(P)H + H+
For diagram of the biosynthesis of CDP-abequose, CDP-ascarylose, CDP-paratose and CDP-tyvelose, click here
Other name(s): CDP-4-keto-6-deoxyglucose reductase; cytidine diphospho-4-keto-6-deoxy-D-glucose reductase; cytidine diphosphate 4-keto-6-deoxy-D-glucose-3-dehydrogenase; CDP-4-keto-deoxy-glucose reductase; CDP-4-keto-6-deoxy-D-glucose-3-dehydrogenase system; NAD(P)H:CDP-4-keto-6-deoxy-D-glucose oxidoreductase
Systematic name: CDP-4-dehydro-3,6-dideoxy-D-glucose:NAD(P)+ 3-oxidoreductase
Comments: The enzyme consists of two proteins. One forms an enzyme-bound adduct of the CDP-4-dehydro-6-deoxyglucose with pyridoxamine phosphate, in which the 3-hydroxy group has been removed. The second catalyses the reduction of this adduct by NAD(P)H and release of the CDP-4-dehydro-3,6-dideoxy-D-glucose and pyridoxamine phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-87-4
References:
1.  Pape, H. and Strominger, J.L. Enzymatic synthesis of cytidine diphosphate 3,6-dideoxyhexoses. V. Partial purification of the two protein components required for introduction of the 3-deoxy group. J. Biol. Chem. 244 (1969) 3598–3604. [PMID: 4389672]
2.  Rubenstein, P.A. and Strominger, J.L. Enzymatic synthesis of cytidine diphosphate 3,6-dideoxyhexoses. VII. Mechanistic roles of enzyme E1 and pyridoxamine 5′-phosphate in the formation of cytidine diphosphate-4-keto-3,6-dideoxy-D-glucose from cytidine diphosphate-4-keto-6-deoxy-D-glucose. J. Biol. Chem. 249 (1974) 3776–3781. [PMID: 4152100]
3.  Liu, H.-W. and Thorson, J.S. Pathways and mechanisms in the biogenesis of novel deoxysugars by bacteria. Annu. Rev. Microbiol. 48 (1994) 223–256. [DOI] [PMID: 7826006]
[EC 1.17.1.1 created 1972, modified 2005]
 
 
EC 2.4.1.160     
Accepted name: pyridoxine 5′-O-β-D-glucosyltransferase
Reaction: UDP-glucose + pyridoxine = UDP + 5′-O-β-D-glucosylpyridoxine
Other name(s): UDP-glucose:pyridoxine 5′-O-β-glucosyltransferase; uridine diphosphoglucose-pyridoxine 5′-β-glucosyltransferase; UDP-glucose-pyridoxine glucosyltransferase
Systematic name: UDP-glucose:pyridoxine 5′-O-β-D-glucosyltransferase
Comments: 4′-Deoxypyridoxine and pyridoxamine can also act as acceptors, but more slowly.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 83744-97-2
References:
1.  Tadera, K., Fumio, Y. and Kobayashi, A. Specificity of a particulate glucosyltransferase in seedlings of Pisum sativum L. which catalyzes the formation of 5′-O-(β-D-glucopyranosyl)pyridoxine. J. Nutr. Sci. Vitaminol. 28 (1982) 359–366. [PMID: 6217302]
[EC 2.4.1.160 created 1986]
 
 
EC 2.6.1.30     
Accepted name: pyridoxamine—pyruvate transaminase
Reaction: pyridoxamine + pyruvate = pyridoxal + L-alanine
Other name(s): pyridoxamine-pyruvic transaminase
Systematic name: pyridoxamine:pyruvate aminotransferase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 9023-38-5
References:
1.  Wada, H. and Snell, E.E. Enzymatic transamination of pyridoxamine. II. Crystalline pyridoxamine-pyruvate transaminase. J. Biol. Chem. 237 (1962) 133–137. [PMID: 14004227]
[EC 2.6.1.30 created 1972]
 
 
EC 2.6.1.31     
Accepted name: pyridoxamine—oxaloacetate transaminase
Reaction: pyridoxamine + oxaloacetate = pyridoxal + L-aspartate
Systematic name: pyridoxamine:oxaloacetate aminotransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37277-88-6
References:
1.  Wada, H. and Snell, E.E. Enzymatic transamination of pyridoxamine. I. With oxaloacetate and α-ketoglutarate. J. Biol. Chem. 237 (1962) 127–132. [PMID: 14004226]
2.  Wu, H.L.C. and Mason, M. Pyridoxamine-oxaloacetic transaminase of rat kidney. J. Biol. Chem. 239 (1964) 1492–1497. [PMID: 14189882]
[EC 2.6.1.31 created 1972]
 
 
EC 2.6.1.54     
Accepted name: pyridoxamine-phosphate transaminase
Reaction: pyridoxamine 5′-phosphate + 2-oxoglutarate = pyridoxal 5′-phosphate + D-glutamate
Other name(s): pyridoxamine phosphate aminotransferase; pyridoxamine 5′-phosphate-α-ketoglutarate transaminase; pyridoxamine 5′-phosphate transaminase
Systematic name: pyridoxamine-5′-phosphate:2-oxoglutarate aminotransferase (D-glutamate-forming)
Comments: Also acts, more slowly, on pyridoxamine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9074-84-4
References:
1.  Tani, Y., Ukita, M. and Ogata, K. Studies on vitamin B6 metabolism in microorganisms. Part X. Further purification and characterization of pyridoxamine 5′-phosphate-α-ketoglutarate transaminase from Clostridium kainantoi. Agric. Biol. Chem. 36 (1972) 181–188.
[EC 2.6.1.54 created 1976]
 
 
EC 2.7.1.35     
Accepted name: pyridoxal kinase
Reaction: ATP + pyridoxal = ADP + pyridoxal 5′-phosphate
Other name(s): pyridoxal kinase (phosphorylating); pyridoxal 5-phosphate-kinase; pyridoxal phosphokinase; pyridoxine kinase
Systematic name: ATP:pyridoxal 5′-phosphotransferase
Comments: Pyridoxine, pyridoxamine and various derivatives can also act as acceptors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9026-42-0
References:
1.  McCormick, D.B., Gregory, M.E. and Snell, E.E. Pyridoxal phosphokinases. I. Assay, distribution, purification, and properties. J. Biol. Chem. 236 (1961) 2076–2084. [PMID: 13773826]
2.  Trufanov, A.F. and Krisanova, J.A. Biosynthesis of pyridoxal phosphate by liver sections of rat in vitro. Byull. Eksp. Biol. Med. 22(6) (1946) 40–43.
[EC 2.7.1.35 created 1961]
 
 
EC 3.1.3.74     
Accepted name: pyridoxal phosphatase
Reaction: pyridoxal 5′-phosphate + H2O = pyridoxal + phosphate
Other name(s): vitamine B6 (pyridoxine) phosphatase; PLP phosphatase; vitamin B6-phosphate phosphatase; PNP phosphatase
Systematic name: pyridoxal-5′-phosphate phosphohydrolase
Comments: Requires Mg2+. This enzyme is specific for phosphorylated vitamin B6 compounds: it acts not only on pyridoxal phosphate (PLP), but also on pyridoxine phosphate (PNP), pyridoxamine phosphate (PMP), 4-pyridoxic acid phosphate and 4-deoxypyridoxine phosphate. This reaction can also be carried out by EC 3.1.3.1 (alkaline phosphatase) and EC 3.1.3.2 (acid phosphatase), but these enzymes have very broad substrate specificities.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9076-92-0
References:
1.  Fonda, M.L. Purification and characterization of vitamin B6-phosphate phosphatase from human erythrocytes. J. Biol. Chem. 267 (1992) 15978–15983. [PMID: 1322411]
2.  Fonda, M.L. and Zhang, Y.N. Kinetic mechanism and divalent metal activation of human erythrocyte pyridoxal phosphatase. Arch. Biochem. Biophys. 320 (1995) 345–352. [DOI] [PMID: 7625842]
3.  Jang, Y.M., Kim, D.W., Kang, T.C., Won, M.H., Baek, N.I., Moon, B.J., Choi, S.Y. and Kwon, O.S. Human pyridoxal phosphatase. Molecular cloning, functional expression, and tissue distribution. J. Biol. Chem. 278 (2003) 50040–50046. [DOI] [PMID: 14522954]
[EC 3.1.3.74 created 2004]
 
 
EC 4.2.1.168     
Accepted name: GDP-4-dehydro-6-deoxy-α-D-mannose 3-dehydratase
Reaction: GDP-4-dehydro-α-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + 2-oxoglutarate + NH3 (overall reaction)
(1a) GDP-4-dehydro-α-D-rhamnose + L-glutamate = 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] + 2-oxoglutarate + H2O
(1b) 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] = 2-GDP-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] (spontaneous)
(1c) GDP-2-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] + H2O = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + NH3 (spontaneous)
For diagram of GDP-colitose biosynthesis, click here
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): colD (gene name)
Systematic name: GDP-4-dehydro-α-D-rhamnose 3-hydro-lyase
Comments: This enzyme, involved in β-L-colitose biosynthesis, is a unique vitamin-B6-dependent enzyme. In the first step of catalysis, the bound pyridoxal phosphate (PLP) cafactor is transaminated to the pyridoxamine 5′-phosphate (PMP) form of vitamin B6, using L-glutamate as the amino group donor. The PMP cofactor then forms a Schiff base with the sugar substrate and the resulting adduct undergoes a 1,4-dehydration to eliminate the 3-OH group. Hydrolysis of the product from the enzyme restores the PLP cofactor and results in the release of an unstable enamine intermediate. This intermediate tautomerizes to form an imine form, which hydrolyses spontaneously, releasing ammonia and forming the final product.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Alam, J., Beyer, N. and Liu, H.W. Biosynthesis of colitose: expression, purification, and mechanistic characterization of GDP-4-keto-6-deoxy-D-mannose-3-dehydrase (ColD) and GDP-L-colitose synthase (ColC). Biochemistry 43 (2004) 16450–16460. [DOI] [PMID: 15610039]
2.  Cook, P.D. and Holden, H.M. A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation. Biochemistry 46 (2007) 14215–14224. [DOI] [PMID: 17997582]
[EC 4.2.1.168 created 2016]
 
 


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