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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1e7q
Original Entry
Title:
Epimerase/reductase
Compound:
Gdp-fucose synthetase
Mutant:
Yes
UniProt/Swiss-Prot:
P32055-FCL_ECOLI
EC Class:
1.1.1.271
Other CSA Entries:
Overview of all sites for 1e7q
Homologues of 1e7q
Entries for UniProt/Swiss-Prot: P32055
Entries for EC: 1.1.1.271
Other Databases:
PDB entry: 1e7q
PDBsum entry: 1e7q
UniProt/Swiss-Prot: P32055
IntEnz entry: 1.1.1.271
Literature Report:
Introduction:
GDP-4-keto-6-deoxy-D-mannose epimerase/reductase (GMER) is a bifunctional enzyme, catalysing the last 2 steps, epimerisation and reduction, in the biosynthesis of GDP-L-fucose, the substrate of fucosyl transferases.

In bacteria, fucose is a component of the capsular polysaccharides and lipopolysaccharides which function as antigenic determinants. In human, fucose is a Lewis system antigen. It is a ligand to selectin and is involved in leukocytes and tumour cell adhesion to the endothelium. Human deficient in the biosynthesis of GDP fucose suffer from immune disorder adhesion deficiency type II, which cna lead to serious symptoms, for instance, immunodeficiency and psychomotor retardation
Mechanism:
Epimerisation of GDP-4-keto-6-deoxy-D-mannose occurs at C3 and C5 of the sugar. The mechanism involves the formation of a enolate intermediate from the keto substrate. Tyr136 acts as a general acid/base catalyst. With its pKa lowered by Lys140, it transiently protonates C4-keto group of the sugar to promote the formation of the enolate intermediate and also stabilise it. C3 or C5 of the enolate intermediate is then deprotonate by a base and reprotonate again from the opposite face of the sugar ring. Based on crystal structure and site-directed mutagenesis studies, both Cys109 and His179 can play the role of this base in abstracting a proton from C3 or C5 of the sugar ring.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CYSA 109 109Sidechain
Acid/baseSubstrate
It deprotonates C3 or C5 of the enolate intermediate and reprotonates it again from the opposite face of the sugar ring.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11021971 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 11021971 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
TYRA 136 136Sidechain
Acid/baseSubstrate
It transiently protonates the C4-keto group of the sugar to promote the formation of the enolate intermediate and also stabilise it.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11021971 Current protein Mutagenesis of residue
PubMed ID 11021971 Current protein Conservation of residue
PubMed ID 11021971 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 140 140Sidechain
ElectrostaticResidue
It lowers the pKa of Tyr 136 by electrostatic effects.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11021971 Current protein Mutagenesis of residue
PubMed ID 11021971 Current protein Conservation of residue
PubMed ID 9862812 Current protein Structural similarity to homologue of known mechanism
PubMed ID 9862812 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 179 179Sidechain
Acid/baseSubstrate
It deprotonates C3 or C5 of the enolate intermediate and reprotonates it again from the opposite face of the sugar ring.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11021971 Current protein Mutagenesis of residue
PubMed ID 11021971 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 9862812 Current protein Residue is positioned appropriately (ligand position hypothetical)
Notes:
The reductase activity is described in another csa entry under 1e7q.
References:
1
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.
W. S. Somers and M. L. Stahl and F. X. Sullivan
Structure 6, (12) 1601-12, (1998).
9862812
2
Probing the catalytic mechanism of GDP-4-keto-6-deoxy-d-mannose Epimerase/Reductase by kinetic and crystallographic characterization of site-specific mutants.
C. Rosano and A. Bisso and G. Izzo and M. Tonetti and L. Sturla and A. De Flora and M. Bolognesi
J Mol Biol 303, (1) 77-91, (2000).
11021971
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