The Enzyme Database

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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
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 created 2016]

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