8DAK

Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3-epimerase from Campylobacter jejuni, serotype HS:3

Summary for 8DAK

• Entry DOI: 10.2210/pdb8dak/pdb
• Descriptor: GDP-D-glycero-4-keto-d-lyxo-heptose-3-epimerase, GUANOSINE-5'-DIPHOSPHATE, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: 3-epimerase, campylobacter, capsular polysaccharide, isomerase
• Biological source: Campylobacter jejuni
• Total number of polymer chains: 2
• Total formula weight: 43480.63

Authors

Thoden, J.B.,Ghosh, M.K.,Xiang, D.F.,Raushel, F.M.,Holden, H.M. (deposition date: 2022-06-13, release date: 2022-06-22, Last modification date: 2023-10-18)

Primary citation

Ghosh, M.K.,Xiang, D.F.,Thoden, J.B.,Holden, H.M.,Raushel, F.M.
C3- and C3/C5-Epimerases Required for the Biosynthesis of the Capsular Polysaccharides from Campylobacter jejuni .
Biochemistry, 61:2036-2048, 2022

PubMed Abstract: is a human pathogen and one of the leading causes of food poisoning in Europe and the United States. The outside of the bacterium is coated with a capsular polysaccharide that assists in the evasion of the host immune system. Many of the serotyped strains of contain a 6-deoxy-heptose moiety that is biosynthesized from GDP-d--d--heptose by the successive actions of a 4,6-dehydratase, a C3/C5-epimerase, and a C4-reductase. We identified 18 different C3/C5-epimerases that could be clustered together into three groups at a sequence identity of >89%. Four of the enzymes from the largest cluster (from serotypes HS:3, HS:10, HS:23/36, and HS:41) were shown to only catalyze the epimerization at C3. Three enzymes from the second largest cluster (HS:2, HS:15, and HS:42) were shown to catalyze the epimerization at C3 and C5. Enzymes from the third cluster were not characterized. The three-dimensional structures of the epimerases from serotypes HS:3, HS:23/36, HS:15, and HS:41 were determined to resolutions of 1.5-1.9 Å. The overall subunit architecture places these enzymes into the diverse "cupin" superfamily. Within X-ray coordinate error, the immediate regions surrounding the active sites are identical, suggesting that factors extending farther out may influence product outcome. The X-ray crystal structures are consistent with His-67 and Tyr-134 acting as general acid/base catalysts for the epimerization of C3 and/or C5. Two amino acid changes (A76V/C136L) were enough to convert the C3-epimerase from serotype HS:3 to one that could now catalyze the epimerization at both C3 and C5.

PubMed: 36093987
DOI: 10.1021/acs.biochem.2c00364

Experimental method

X-RAY DIFFRACTION (1.5 Å)