The Enzyme Database

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EC 1.1.1.290     
Accepted name: 4-phosphoerythronate dehydrogenase
Reaction: 4-phospho-D-erythronate + NAD+ = (3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH + H+
For diagram of pyridoxal biosynthesis, click here
Other name(s): PdxB; PdxB 4PE dehydrogenase; 4-O-phosphoerythronate dehydrogenase; 4PE dehydrogenase; erythronate-4-phosphate dehydrogenase
Systematic name: 4-phospho-D-erythronate:NAD+ 2-oxidoreductase
Comments: This enzyme catalyses a step in a bacterial pathway for the biosynthesis of pyridoxal 5′-phosphate. The enzyme contains a tightly-bound NAD(H) cofactor that is not re-oxidized by free NAD+. In order to re-oxidize the cofactor and restore enzyme activity, the enzyme catalyses the reduction of a 2-oxo acid (such as 2-oxoglutarate, oxaloacetate, or pyruvate) to the respective (R)-hydroxy acid [6]. cf. EC 1.1.1.399, 2-oxoglutarate reductase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 125858-75-5
References:
1.  Lam, H.M. and Winkler, M.E. Metabolic relationships between pyridoxine (vitamin B6) and serine biosynthesis in Escherichia coli K-12. J. Bacteriol. 172 (1990) 6518–6528. [DOI] [PMID: 2121717]
2.  Pease, A.J., Roa, B.R., Luo, W. and Winkler, M.E. Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12. J. Bacteriol. 184 (2002) 1359–1369. [DOI] [PMID: 11844765]
3.  Zhao, G. and Winkler, M.E. A novel α-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria. J. Bacteriol. 178 (1996) 232–239. [DOI] [PMID: 8550422]
4.  Grant, G.A. A new family of 2-hydroxyacid dehydrogenases. Biochem. Biophys. Res. Commun. 165 (1989) 1371–1374. [DOI] [PMID: 2692566]
5.  Schoenlein, P.V., Roa, B.B. and Winkler, M.E. Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12. J. Bacteriol. 171 (1989) 6084–6092. [DOI] [PMID: 2681152]
6.  Rudolph, J., Kim, J. and Copley, S.D. Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates. Biochemistry 49 (2010) 9249–9255. [DOI] [PMID: 20831184]
[EC 1.1.1.290 created 2006, modified 2016]
 
 
EC 1.1.1.408     
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-erythronate + NADH + H+
(1b) 3-dehydro-4-phospho-D-erythronate = glycerone phosphate + CO2 (spontaneous)
For diagram of erythronate and threonate catabolism, 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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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. [DOI] [PMID: 27402745]
[EC 1.1.1.408 created 2017]
 
 
EC 1.1.1.409     
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 erythronate and threonate catabolism, 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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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. [DOI] [PMID: 27402745]
[EC 1.1.1.409 created 2017]
 
 
EC 1.1.1.410     
Accepted name: D-erythronate 2-dehydrogenase
Reaction: D-erythronate + NAD+ = 2-dehydro-D-erythronate + NADH + H+
For diagram of erythronate and threonate catabolism, 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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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. [DOI] [PMID: 27402745]
[EC 1.1.1.410 created 2017]
 
 
EC 2.7.1.217     
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 erythronate and threonate catabolism, 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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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. [DOI] [PMID: 27402745]
[EC 2.7.1.217 created 2017]
 
 
EC 2.7.1.220     
Accepted name: D-erythronate 4-kinase
Reaction: ATP + D-erythronate = ADP + 4-phospho-D-erythronate
Glossary: D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate
Other name(s): denK (gene name)
Systematic name: ATP:D-erythronate 4-phosphotransferase
Comments: The enzyme, characterized from bacteria, is involved in a pathway for D-erythronate catabolism.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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. [DOI] [PMID: 27402745]
[EC 2.7.1.220 created 2017]
 
 
EC 4.1.1.104     
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 erythronate and threonate catabolism, 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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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. [DOI] [PMID: 27402745]
[EC 4.1.1.104 created 2017]
 
 
EC 4.2.1.11     
Accepted name: phosphopyruvate hydratase
Reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O
For diagram of the Entner-Doudoroff pathway, click here
Other name(s): enolase; 2-phosphoglycerate dehydratase; 14-3-2-protein; nervous-system specific enolase; phosphoenolpyruvate hydratase; 2-phosphoglycerate dehydratase; 2-phosphoglyceric dehydratase; 2-phosphoglycerate enolase; γ-enolase; 2-phospho-D-glycerate hydro-lyase
Systematic name: 2-phospho-D-glycerate hydro-lyase (phosphoenolpyruvate-forming)
Comments: Also acts on 3-phospho-D-erythronate.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-08-8
References:
1.  Holt, A. and Wold, F. The isolation and characterization of rabbit muscle enolase. J. Biol. Chem. 236 (1961) 3227–3231. [PMID: 13908561]
2.  Malmström, B.G. Enolase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 5, Academic Press, New York, 1961, pp. 471–494.
3.  Westhead, E.W. and McLain, G. Purification of brewers’ and bakers’ yeast enolase yielding a single active component. J. Biol. Chem. 239 (1964) 2464–2468. [PMID: 14235523]
[EC 4.2.1.11 created 1961]
 
 
EC 5.3.1.35     
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 erythronate and threonate catabolism, 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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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. [DOI] [PMID: 27402745]
[EC 5.3.1.35 created 2017]
 
 


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