2GMS

E coli GDP-4-keto-6-deoxy-D-mannose-3-dehydratase with bound hydrated PLP

Summary for 2GMS

• Entry DOI: 10.2210/pdb2gms/pdb
• Related: 2GMU
• Descriptor: Putative pyridoxamine 5-phosphate-dependent dehydrase, Wbdk, MAGNESIUM ION, [4-(DIHYDROXYMETHYL)-5-HYDROXY-6-METHYLPYRIDIN-3-YL]METHYL DIHYDROGEN PHOSPHATE, ... (4 entities in total)
• Functional Keywords: colitose, 0-antigen, aspartate aminotransferase, plp, deoxysugar, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 89259.46

Authors

Cook, P.D.,Thoden, J.B.,Holden, H.M. (deposition date: 2006-04-07, release date: 2006-09-05, Last modification date: 2023-08-30)

Primary citation

Cook, P.D.,Thoden, J.B.,Holden, H.M.
The structure of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: a unique coenzyme B6-dependent enzyme.
Protein Sci., 15:2093-2106, 2006

PubMed Abstract: L-colitose is a 3,6-dideoxysugar found in the O-antigens of some Gram-negative bacteria such as Escherichia coli and in marine bacteria such as Pseudoalteromonas tetraodonis. The focus of this investigation, GDP-4-keto-6-deoxy-D-mannose-3-dehydratase, catalyzes the third step in colitose production, which is the removal of the hydroxyl group at C3' of GDP-4-keto-6-deoxymannose. It is an especially intriguing PLP-dependent enzyme in that it acts as both a transaminase and a dehydratase. Here we present the first X-ray structure of this enzyme isolated from E. coli Strain 5a, type O55:H7. The two subunits of the protein form a tight dimer with a buried surface area of approximately 5000 A2. This is a characteristic feature of the aspartate aminotransferase superfamily. Although the PLP-binding pocket is formed primarily by one subunit, there is a loop, delineated by Phe 240 to Glu 253 in the second subunit, that completes the active site architecture. The hydrated form of PLP was observed in one of the enzyme/cofactor complexes described here. Amino acid residues involved in anchoring the cofactor to the protein include Gly 56, Ser 57, Asp 159, Glu 162, and Ser 183 from one subunit and Asn 248 from the second monomer. In the second enzyme/cofactor complex reported, a glutamate ketimine intermediate was found trapped in the active site. Taken together, these two structures, along with previously reported biochemical data, support the role of His 188 as the active site base required for catalysis.

PubMed: 16943443
DOI: 10.1110/ps.062328306

Experimental method

X-RAY DIFFRACTION (1.8 Å)