The Enzyme Database

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EC 1.1.1.356     
Accepted name: GDP-L-colitose synthase
Reaction: GDP-β-L-colitose + NAD(P)+ = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + NAD(P)H + H+
For diagram of GDP-colitose biosynthesis, click here
Glossary: L-colitose = 3,6-dideoxy-L-xylo-hexopyranose
GDP-4-dehydro-3,6-dideoxy-α-D-mannose = GDP-3,6-dideoxy-α-D-threo-hexopyranos-4-ulose
Other name(s): ColC
Systematic name: GDP-β-L-colitose:NAD(P)+ 4-oxidoreductase (5-epimerizing)
Comments: The enzyme is involved in biosynthesis of L-colitose, a 3,6-dideoxyhexose found in the O-antigen of Gram-negative lipopolysaccharides, where it catalyses the reaction in the reverse direction. The enzyme also performs the NAD(P)H-dependent epimerisation at C-5 of the sugar. The enzyme from Yersinia pseudotuberculosis is Si-specific with respect to NAD(P)H [1].
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]
[EC 1.1.1.356 created 2013]
 
 
EC 2.4.1.341     
Accepted name: α-1,2-colitosyltransferase
Reaction: GDP-β-L-colitose + β-D-galactopyranosyl-(1→3)-N-acetyl-D-glucosamine = GDP + α-L-colitosyl-(1→2)-β-D-galactosyl-(1→3)-N-acetyl-D-glucosamine
Glossary: β-D-galactopyranosyl-(1→3)-N-acetyl-D-glucosamine = lacto-N-biose
Other name(s): wbgN (gene name)
Systematic name: GDP-β-L-colitose:β-D-galactopyranosyl-(1→3)-N-acetyl-D-glucosamine L-colitosyltransferase (configuration-inverting)
Comments: The enzyme, characterized from the bacterium Escherichia coli O55:H7, participates in the biosynthesis of an O-antigen. The reaction involves anomeric inversion, and does not require any metal ions. The enzyme is highly specific towards the acceptor, exclusively recognizing lacto-N-biose, but can accept GDP-L-fucose as the donor with almost the same activity as with GDP-β-L-colitose.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wu, Z., Zhao, G., Li, T., Qu, J., Guan, W., Wang, J., Ma, C., Li, X., Zhao, W., Wang, P.G. and Li, L. Biochemical characterization of an α1,2-colitosyltransferase from Escherichia coli O55:H7. Glycobiology (2015) . [DOI] [PMID: 26703456]
[EC 2.4.1.341 created 2016]
 
 
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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