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1wvg
From Proteopedia
| 1wvg, resolution 1.80Å () | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||||
| Gene: | ddhB (Salmonella enterica subsp. enterica serovar Typhi) | ||||||||
| Activity: | CDP-glucose 4,6-dehydratase, with EC number 4.2.1.45 | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi
Tyvelose is a unique 3,6-dideoxyhexose found in the O antigens of some pathogenic species of Yersinia and Salmonella. It is produced via a complex biochemical pathway that employs CDP-D-glucose as the starting ligand. CDP-D-glucose 4,6-dehydratase catalyzes the first irreversible step in the synthesis of this 3,6-dideoxysugar by converting CDP-D-glucose to CDP-4-keto-6-deoxyglucose via an NAD+ -dependent intramolecular oxidation-reduction reaction. Here, the cloning, protein purification and X-ray crystallographic analysis of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with the substrate analog CDP-D-xylose are described. Each subunit of the tetrameric enzyme folds into two domains. The N-terminal region contains a Rossmann fold and provides the platform for NAD(H) binding. The C-terminal motif is primarily composed of alpha-helices and houses the binding pocket for the CDP portion of the CDP-D-xylose ligand. The xylose moiety extends into the active-site cleft that is located between the two domains. Key residues involved in anchoring the sugar group to the protein include Ser134, Tyr159, Asn197 and Arg208. Strikingly, Ser134 O gamma and Tyr159 O eta sit within 2.9 A of the 4'-hydroxyl group of xylose. Additionally, the side chains of Asp135 and Lys136 are located at 3.5 and 3.2 A, respectively, from C-5 of xylose. In the structurally related dTDP-D-glucose 4,6-dehydratase, the Asp/Lys pair is replaced with an Asp/Glu couple. On the basis of this investigation, it can be speculated that Tyr159 serves as the catalytic base to abstract the 4'-hydroxyl proton from the sugar and that Asp135 and Lys136 play critical roles in the subsequent dehydration step that leads to the final product.
Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose., Koropatkin NM, Holden HM, Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):365-73. Epub 2005, Mar 24. PMID:15805590
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
1wvg is a 2 chain structure with sequence from Salmonella enterica subsp. enterica serovar typhi. Full crystallographic information is available from OCA.
Reference
- Koropatkin NM, Holden HM. Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose. Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):365-73. Epub 2005, Mar 24. PMID:15805590 doi:10.1107/S0907444904033876
