3E8M

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

Summary for 3E8M

• Entry DOI: 10.2210/pdb3e8m/pdb
• Related: 3E81 3E84
• Descriptor: Acylneuraminate cytidylyltransferase, MAGNESIUM ION, CHLORIDE ION, ... (9 entities in total)
• Functional Keywords: 2-keto-3-deoxynononic acid 9-phosphate phosphohydrolase, nucleotidyltransferase, transferase
• Biological source: Bacteroides thetaiotaomicron
• Total number of polymer chains: 4
• Total formula weight: 75534.68

Authors

Lu, Z.,Wang, L.,Dunaway-Mariano, D.,Allen, K.N. (deposition date: 2008-08-20, release date: 2008-11-04, Last modification date: 2023-08-30)

Primary citation

Lu, Z.,Wang, L.,Dunaway-Mariano, D.,Allen, K.N.
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.
J.Biol.Chem., 284:1224-1233, 2009

PubMed Abstract: 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.

PubMed: 18986982
DOI: 10.1074/jbc.M807056200

Experimental method

X-RAY DIFFRACTION (1.1 Å)