Center for Structural Genomics of Infectious Diseases

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Structure of IDP02274

CSGID target: IDP02274
PDB Id: 3IJ5 (NCBI MMDB)
Authors: 'G.Minasov,A.Halavaty,L.Shuvalova,I.Dubrovska,J.Winsor,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid)'
Responsible person: George Minasov
Responsible lab: Northwestern University
Deposition Date: Aug 03, 2009
Release Date: Aug 11, 2009

Description: 3-Deoxy-D-manno-octulosonate (KDO) is a carbohydrate molecule required for integrity of Gram-negative bacterial outer membrane, therefore its biosynthesis is a potential antibiotic target. In addition to serving as a linker molecule in the lipopolysaccharide layer on the outer membrane, KDO is also found as a building block of the capsular polysaccharide. Four enzymes encoded by the kds genes are required for the biosynthesis of the activated form of KDO. The third enzyme, 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) phosphatase (KdsC), catalyzes the hydrolysis of KDO8P to form KDO and inorganic phosphate. Subsequently, KDO is activated to cytidine monophosphate-KDO by the cytidylyltransferase (KdsB). KDO8P synthase is a homotetramer with the eight strand intramolecular beta barrel. Presented crystal structure of the KdsC from Yersinia pestis is homolog (about 75% homology) of the YrbI from Escherichia coli. To gain mechanistic insights in order to design inhibitors, more structures of the proteins and their complexes from different organisms are necessary.
Functional assignment: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

Ligand code	Name	Ligand type
175	3,5-dihydro-5-methylidene-4h-imidazol-4-on