8DAK image
Entry Detail
PDB ID:
8DAK
Keywords:
Title:
Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3-epimerase from Campylobacter jejuni, serotype HS:3
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-06-13
Release Date:
2022-06-22
Method Details:
Experimental Method:
Resolution:
1.50 Å
R-Value Free:
0.21
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:GDP-D-glycero-4-keto-d-lyxo-heptose-3-epimerase
Chain IDs:A, B
Chain Length:184
Number of Molecules:2
Biological Source:Campylobacter jejuni
Primary Citation
C3- and C3/C5-Epimerases Required for the Biosynthesis of the Capsular Polysaccharides from Campylobacter jejuni .
Biochemistry 61 2036 2048 (2022)
PMID: 36093987 DOI: 10.1021/acs.biochem.2c00364

Abstact

Campylobacter jejuni 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 C. jejuni contain a 6-deoxy-heptose moiety that is biosynthesized from GDP-d-glycero-d-manno-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.

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