1KEW

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with thymidine diphosphate bound

Summary for 1KEW

• Entry DOI: 10.2210/pdb1kew/pdb
• Related: 1G1A 1KEP 1KER 1KET 1KEU
• Descriptor: dTDP-D-glucose 4,6-dehydratase, THYMIDINE-5'-DIPHOSPHATE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (5 entities in total)
• Functional Keywords: rossmann fold, lyase
• Biological source: Salmonella enterica subsp. enterica serovar Typhimurium
• Total number of polymer chains: 2
• Total formula weight: 83942.54

Authors

Allard, S.T.M.,Beis, K.,Giraud, M.-F.,Hegeman, A.D.,Gross, J.W.,Whitfield, C.,Graninger, M.,Messner, P.,Allen, A.G.,Naismith, J.H. (deposition date: 2001-11-17, release date: 2002-01-25, Last modification date: 2023-08-16)

Primary citation

Allard, S.T.,Beis, K.,Giraud, M.F.,Hegeman, A.D.,Gross, J.W.,Wilmouth, R.C.,Whitfield, C.,Graninger, M.,Messner, P.,Allen, A.G.,Maskell, D.J.,Naismith, J.H.
Toward a structural understanding of the dehydratase mechanism.
Structure, 10:81-92, 2002

PubMed Abstract: dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5'-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5'-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5'-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 A and 2.4 A. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily.

PubMed: 11796113
DOI: 10.1016/S0969-2126(01)00694-3

Experimental method

X-RAY DIFFRACTION (1.8 Å)