Information on EC 4.2.1.168 - GDP-4-dehydro-6-deoxy-alpha-D-mannose 3-dehydratase

colD

3 entries

GDP-4-keto-6-deoxy-D-mannose-3-dehydratase

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WbdK

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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]

(1b), spontaneous

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GDP-2-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] + H2O = GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + NH3

(1c), spontaneous

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GDP-4-dehydro-alpha-D-rhamnose + L-glutamate = 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] + 2-oxoglutarate + H2O

(1a)

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GDP-4-dehydro-alpha-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + 2-oxoglutarate + NH3

overall reaction

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KEGG

O-Antigen nucleotide sugar biosynthesis

GDP-4-dehydro-alpha-D-rhamnose 3-hydro-lyase

This enzyme, involved in beta-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.

GDP-4-dehydro-alpha-D-rhamnose + L-glutamate

GDP-4-dehydro-3,6-dideoxy-alpha-D-mannose + 2-oxoglutarate + ammonia

3 entries

GDP-D-perosamine + L-glutamate

GDP-4-dehydro-3,6-dideoxymannose + 2-oxoglutarate + ammonia

Escherichia coli

Q9F118

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738573

wild-type ColD is able to catalyze the production of GDP-4-keto-3,6-dideoxymannose using GDP-perosamine instead of GDP-4-keto-6-deoxymannose as a substrate

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?

additional information

?

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Yersinia pseudotuberculosis

G4WJD4

enzyme functions as GDP-4-keto-6-deoxy-D-mannose-3-dehydrase responsible for C-3 deoxygenation of GDP-4-keto-6-deoxy-D-mannose. The enzyme is coenzyme B6-dependent and catalysis is initiated by a transamination step in which pyridoxal 5'-phosphate is converted to pyridoxamine 5'-phosphate in the presene of L-glutamate. This coenzyme forms a Schiff base with the keto sugar substrate and the resulting adduct undergoes a pyridoxamine 5'-phosphate-mediated beta-dehydration reaction to give a sugar enamine intermediate, which after tautomerization and hydrolysis to release ammonia yields GDP-4-keto-3,6-dideoxy-D-mannose as the product

721596

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?

pyridoxamine 5'-phosphate

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737666, 738573, 739597

Q9F118

UniProt

Yersinia pseudotuberculosis

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721596

G4WJD4

UniProt

physiological function

Escherichia coli

Q9F118

enzyme catalyzes the third step in the pathway to colitose, namely the PLP-dependent removal of the C3'-hydroxyl group from GDP-4-keto-6-deoxymannose

737666

H188N mutant with bound GDP-perosamine, to 1.7 A resolution. The sugar analog is trapped in the active site as an external aldimine. The active site is positioned between the two subunits of the dimer. The diphosphoryl groups of the ligand are anchored to the protein via Arg219 and Arg331, the hydroxyl groups of the hexose only lie within hydrogen bonding distance to ordered water molecules. The hexose moiety of the ligand adopts a boat rather than the typically observed chair conformation

Escherichia coli

Q9F118

738573

mutant H188K in the presence of alpha-ketoglutarate and pyridoxal 5'-phosphate, to 1.9 A resolution. The observed electron density is consistent with the formation of a geminal diamine intermediate formed by the reaction of an internal aldimine with glutamate

Escherichia coli

Q9F118

737666

the two subunits of the protein form a tight dimer. The PLP-binding pocket is formed primarily by one subunit, with a loop from Phe 240 to Glu 253 in the second subunit, that completes the active site architecture. The hydrated form of PLP is observed. Amino acid residues involved in anchoring the cofactor to the protein include Gly56, Ser57, Asp159, Glu162, and Ser183 from one subunit and Asn248 from the second monomer. His188 is the active site base required for catalysis

H188K

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ExplorEnz (official portal for IUBMB Enzyme Nomenclature)

Expasy Enzyme Nomenclature Database

KEGG

MetaCyc

SABIO-RK

NCBI: PubMed, Protein, Nucleotide, Structure, Gene, OMIM

Enzyme Nomenclature (alternative site)

UniProt

PDB

PROSITE Database of protein families and domains

InterPro (database of protein families, domains and functional sites)