3e81 | pdb_00003e81

Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily

spinqualitylabelsall models 3e81, resolution 1.63Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3e81 is a 4 chain structure with sequence from Bacteroides thetaiotaomicron. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.629Å Ligands: EDO, MG, PEG, SLB, VN4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function KDGGP_BACTN Involved in the biosynthesis of 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid used in cell-wall polysaccharides (PubMed:18804026). Catalyzes the hydrolysis of 2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic acid (KDN-9-P) to yield 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN) (PubMed:18804026, PubMed:18986982, PubMed:23848398). Also able to hydrolyze N-acetylneuraminate-9-phosphate (Neu5NAc-9-P), 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-P), phosphoenolpyruvate (PEP), gluconate 6-phosphate, tyrosine phosphate ester and glucose-6-P as substrate (PubMed:18804026, PubMed:18986982, PubMed:23848398). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed The phosphotransferases of the haloalkanoate dehalogenase superfamily (HADSF) act upon a wide range of metabolites in all eukaryotes and prokaryotes and thus constitute a significant force in cell function. The challenge posed for biochemical function assignment of HADSF members is the identification of the structural determinants that target a specific metabolite. The "8KDOP" subfamily of the HADSF is defined by the known structure and catalytic activity of 2-keto-3-deoxy-8-phospho-d-manno-octulosonic acid (KDO-8-P) phosphatase. Homologues of this enzyme have been uniformly annotated as KDO-8-P phosphatase. One such gene, BT1713, from the Bacteroides thetaiotaomicron genome was recently found to encode the enzyme 2-keto-3-deoxy-d-glycero-d-galacto-9-phosphonononic acid (KDN-9-P) phosphatase in the biosynthetic pathway of the 9-carbon alpha-keto acid, 2-keto-3-deoxy-d-glycero-d-galactonononic acid (KDN). To find the structural elements that provide substrate-specific interactions and to allow identification of genomic sequence markers, the x-ray crystal structures of BT1713 liganded to the cofactor Mg(2+)and complexed with tungstate or VO(3)(-)/Neu5Ac were determined to 1.1, 1.85, and 1.63 A resolution, respectively. The structures define the active site to be at the subunit interface and, as confirmed by steady-state kinetics and site-directed mutagenesis, reveal Arg-64(*), Lys-67(*), and Glu-56 to be the key residues involved in sugar binding that are essential for BT1713 catalytic function. Bioinformatic analyses of the differentially conserved residues between BT1713 and KDO-8-P phosphatase homologues guided by the knowledge of the structure-based specificity determinants define Glu-56 and Lys-67(*) to be the key residues that can be used in future annotations. Structure-function analysis of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphatase defines specificity elements in type C0 haloalkanoate dehalogenase family members.,Lu Z, Wang L, Dunaway-Mariano D, Allen KN J Biol Chem. 2009 Jan 9;284(2):1224-33. Epub 2008 Nov 5. PMID:18986982 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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