The Enzyme Database

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EC 1.1.1.135     
Accepted name: GDP-6-deoxy-D-talose 4-dehydrogenase
Reaction: GDP-6-deoxy-α-D-talose + NAD(P)+ = GDP-4-dehydro-α-D-rhamnose + NAD(P)H + H+
For diagram of gdp-l-fucose and GDP-mannose biosynthesis, click here
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
GDP-6-deoxy-α-D-talose = GDP-α-D-pneumose
Other name(s): guanosine diphospho-6-deoxy-D-talose dehydrogenase; GDP-6-deoxy-D-talose:NAD(P)+ 4-oxidoreductase
Systematic name: GDP-6-deoxy-α-D-talose:NAD(P)+ 4-oxidoreductase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37250-66-1
References:
1.  Markovitz, A. Biosynthesis of guanosine diphosphate D-rhamnose and guanosine diphosphate D-talomethylose from guanosine diphosphate α-D-mannose. J. Biol. Chem. 239 (1964) 2091–2098. [PMID: 14209931]
[EC 1.1.1.135 created 1972, modified 1976]
 
 
EC 1.1.1.187     
Accepted name: GDP-4-dehydro-D-rhamnose reductase
Reaction: (1) GDP-α-D-rhamnose + NAD(P)+ = GDP-4-dehydro-α-D-rhamnose + NAD(P)H + H+
(2) GDP-6-deoxy-α-D-talose + NAD(P)+ = GDP-4-dehydro-α-D-rhamnose + NAD(P)H + H+
For diagram of gdp-l-fucose and GDP-mannose biosynthesis, click here
Glossary: GDP-α-D-rhamnose = GDP-6-deoxy-α-D-mannose
GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
GDP-6-deoxy-α-D-talose = GDP-α-D-pneumose
Other name(s): GDP-4-keto-6-deoxy-D-mannose reductase; GDP-4-keto-D-rhamnose reductase; guanosine diphosphate-4-keto-D-rhamnose reductase; GDP-6-deoxy-D-mannose:NAD(P)+ 4-oxidoreductase; GDP-6-deoxy-α-D-mannose:NAD(P)+ 4-oxidoreductase
Systematic name: GDP-4-dehydro-α-D-rhamnose:NAD(P)+ 4-oxidoreductase
Comments: The enzyme, which operates in the opposite direction to that shown, forms a mixture of GDP-α-D-rhamnose and its C-4 epimer, GDP-6-deoxy-α-D-talose. cf. EC 1.1.1.281, GDP-4-dehydro-6-deoxy-D-mannose reductase and EC 1.1.1.135, GDP-6-deoxy-D-talose 4-dehydrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9075-56-3
References:
1.  Barber, G.A. The synthesis of guanosine 5′-diphosphate D-rhamnose by enzymes of a higher plant. Biochim. Biophys. Acta 165 (1968) 68–75. [DOI] [PMID: 4386238]
2.  Winkler, N.W. and Markovitz, A. Guanosine diphosphate-4-keto-D-rhamnose reductase. A non-stereoselective enzyme. J. Biol. Chem. 246 (1971) 5868–5876. [PMID: 4398966]
[EC 1.1.1.187 created 1984]
 
 
EC 1.1.1.271     
Accepted name: GDP-L-fucose synthase
Reaction: GDP-β-L-fucose + NADP+ = GDP-4-dehydro-α-D-rhamnose + NADPH + H+
For diagram of GDP-L-Fucose and GDP-mannose biosynthesis, click here
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase; GDP-L-fucose:NADP+ 4-oxidoreductase (3,5-epimerizing)
Systematic name: GDP-β-L-fucose:NADP+ 4-oxidoreductase (3,5-epimerizing)
Comments: Both human and Escherichia coli enzymes can use NADH in place of NADPH to a slight extent.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 113756-18-6
References:
1.  Chang, S., Duerr, B. and Serif, G. An epimerase-reductase in L-fucose synthesis. J. Biol. Chem. 263 (1988) 1693–1697. [PMID: 3338988]
2.  Mattila, P., Räbinä, J, Hortling, S., Jelin, J. and Renkonen, R. Functional expression of Escherichia coli enzymes synthesizing GDP-L-fucose from inherent GDP-D-mannose in Saccharomyces cerevisiae. Glycobiology 10 (2000) 1041–1047. [DOI] [PMID: 11030750]
3.  Menon, S., Stahl, M., Kumar, R., Xu, G.-Y. and Sullivan, F. Stereochemical course and steady state mechanism of the reaction catalyzed by the GDP-fucose synthetase from Escherichia coli. J. Biol. Chem. 274 (1999) 26743–26750. [DOI] [PMID: 10480878]
4.  Somers, W.S., Stahl, M.L. and Sullivan, F.X. GDP-fucose synthetase from Escherichia coli: Structure of a unique member of the short-chain dehydrogenase/reductase family that catalyzes two distinct reactions at the same active site. Structure 6 (1998) 1601–1612. [DOI] [PMID: 9862812]
[EC 1.1.1.271 created 2002, modified 2003]
 
 
EC 1.1.1.281     
Accepted name: GDP-4-dehydro-6-deoxy-D-mannose reductase
Reaction: GDP-α-D-rhamnose + NAD(P)+ = GDP-4-dehydro-α-D-rhamnose + NAD(P)H + H+
For diagram of gdp-l-fucose and GDP-mannose biosynthesis, click here
Glossary: GDP-α-D-rhamnose = GDP-6-deoxy-α-D-mannose
GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): GDP-4-keto-6-deoxy-D-mannose reductase [ambiguous]; GDP-6-deoxy-D-lyxo-4-hexulose reductase; Rmd; GDP-6-deoxy-D-mannose:NAD(P)+ 4-oxidoreductase (D-rhamnose-forming); GDP-6-deoxy-α-D-mannose:NAD(P)+ 4-oxidoreductase (D-rhamnose-forming)
Systematic name: GDP-α-D-rhamnose:NAD(P)+ 4-oxidoreductase
Comments: This enzyme differs from EC 1.1.1.187, GDP-4-dehydro-D-rhamnose reductase, in that the only product formed is GDP-α-D-rhamnose. D-Rhamnose is a constituent of lipopolysaccharides of Gram-negative plant and human pathogenic bacteria.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kneidinger, B., Graninger, M., Adam, G., Puchberger, M., Kosma, P., Zayni, S. and Messner, P. Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 276 (2001) 5577–5583. [DOI] [PMID: 11096116]
2.  Mäki, M., Järvinen, N., Räbinä, J., Roos, C., Maaheimo, H., Mattila, P. and Renkonen, R. Functional expression of Pseudomonas aeruginosa GDP-4-keto-6-deoxy-D-mannose reductase which synthesizes GDP-rhamnose. Eur. J. Biochem. 269 (2002) 593–601. [DOI] [PMID: 11856318]
[EC 1.1.1.281 created 2004]
 
 
EC 2.6.1.102     
Accepted name: GDP-perosamine synthase
Reaction: GDP-α-D-perosamine + 2-oxoglutarate = GDP-4-dehydro-α-D-rhamnose + L-glutamate
Glossary: GDP-α-D-perosamine = GDP-4-amino-4,6-dideoxy-α-D-mannose
GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): RfbE; GDP-4-keto-6-deoxy-D-mannose-4-aminotransferase; GDP-perosamine synthetase; PerA; GDP-4-amino-4,6-dideoxy-α-D-mannose:2-oxoglutarate aminotransferase
Systematic name: GDP-α-D-perosamine:2-oxoglutarate aminotransferase
Comments: A pyridoxal 5′-phosphate enzyme. D-Perosamine is one of several dideoxy sugars found in the O-specific polysaccharide of the lipopolysaccharide component of the outer membrane of Gram-negative bacteria. The enzyme catalyses the final step in GDP-α-D-perosamine synthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Albermann, C. and Piepersberg, W. Expression and identification of the RfbE protein from Vibrio cholerae O1 and its use for the enzymatic synthesis of GDP-D-perosamine. Glycobiology 11 (2001) 655–661. [DOI] [PMID: 11479276]
2.  Zhao, G., Liu, J., Liu, X., Chen, M., Zhang, H. and Wang, P.G. Cloning and characterization of GDP-perosamine synthetase (Per) from Escherichia coli O157:H7 and synthesis of GDP-perosamine in vitro. Biochem. Biophys. Res. Commun. 363 (2007) 525–530. [DOI] [PMID: 17888872]
3.  Albermann, C. and Beuttler, H. Identification of the GDP-N-acetyl-d-perosamine producing enzymes from Escherichia coli O157:H7. FEBS Lett. 582 (2008) 479–484. [DOI] [PMID: 18201574]
4.  Cook, P.D., Carney, A.E. and Holden, H.M. Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase. Biochemistry 47 (2008) 10685–10693. [DOI] [PMID: 18795799]
[EC 2.6.1.102 created 2013]
 
 
EC 4.2.1.47     
Accepted name: GDP-mannose 4,6-dehydratase
Reaction: GDP-α-D-mannose = GDP-4-dehydro-α-D-rhamnose + H2O
For diagram of gdp-l-fucose and GDP-mannose biosynthesis, click here
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): guanosine 5′-diphosphate-D-mannose oxidoreductase; guanosine diphosphomannose oxidoreductase; guanosine diphosphomannose 4,6-dehydratase; GDP-D-mannose dehydratase; GDP-D-mannose 4,6-dehydratase; Gmd; GDP-mannose 4,6-hydro-lyase; GDP-mannose 4,6-hydro-lyase (GDP-4-dehydro-6-deoxy-D-mannose-forming)
Systematic name: GDP-α-D-mannose 4,6-hydro-lyase (GDP-4-dehydro-α-D-rhamnose-forming)
Comments: The bacterial enzyme requires bound NAD+. This enzyme forms the first step in the biosynthesis of GDP-α-D-rhamnose and GDP-β-L-fucose. In Aneurinibacillus thermoaerophilus L420-91T, this enzyme acts as a bifunctional enzyme, catalysing the above reaction as well as the reaction catalysed by EC 1.1.1.281, GDP-4-dehydro-6-deoxy-D-mannose reductase [5]. Belongs to the short-chain dehydrogenase/reductase enzyme family, having homologous structures and a conserved catalytic triad of Lys, Tyr and Ser/Thr residues [6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37211-59-9
References:
1.  Elbein, A.D. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. II. Guanosine diphosphate 4-keto-6-deoxy-D-mannose, an intermediate in the biosynthesis of guanosine diphosphate colitose. J. Biol. Chem. 240 (1965) 1926–1931. [PMID: 14299611]
2.  Liao, T.-H. and Barber, G.A. Purification of guanosine 5′-diphosphate D-mannose oxidoreductase from Phaseolus vulgaris. Biochim. Biophys. Acta 276 (1972) 85–93. [DOI] [PMID: 5047712]
3.  Melo, A., Elliott, H. and Glaser, L. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 243 (1968) 1467–1474. [PMID: 4869560]
4.  Sullivan, F.X., Kumar, R., Kriz, R., Stahl, M., Xu, G.Y., Rouse, J., Chang, X.J., Boodhoo, A., Potvin, B. and Cumming, D.A. Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro. J. Biol. Chem. 273 (1988) 8193–8202. [DOI] [PMID: 9525924]
5.  Kneidinger, B., Graninger, M., Adam, G., Puchberger, M., Kosma, P., Zayni, S. and Messner, P. Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 276 (2001) 5577–5583. [DOI] [PMID: 11096116]
6.  Mulichak, A.M., Bonin, C.P., Reiter, W.D. and Garavito, R.M. Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: implications for ligand binding and specificity. Biochemistry 41 (2000) 15578–15589. [DOI] [PMID: 12501186]
[EC 4.2.1.47 created 1972, modified 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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