3I6B

Crystal structure of YrbI lacking the last 8 residues, in complex with Kdo and inorganic phosphate

Summary for 3I6B

• Entry DOI: 10.2210/pdb3i6b/pdb
• Related: 2R8E 2R8X 2R8Y 2R8Z 3HYC
• Descriptor: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, MAGNESIUM ION, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: yrbi, kdsc, kdo, phosphatase, hydrolase, lipopolysaccharide biosynthesis, magnesium
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 77778.46

Authors

Biswas, T.,Tsodikov, O.V. (deposition date: 2009-07-06, release date: 2009-09-01, Last modification date: 2023-09-06)

Primary citation

Biswas, T.,Yi, L.,Aggarwal, P.,Wu, J.,Rubin, J.R.,Stuckey, J.A.,Woodard, R.W.,Tsodikov, O.V.
The Tail of KdsC: CONFORMATIONAL CHANGES CONTROL THE ACTIVITY OF A HALOACID DEHALOGENASE SUPERFAMILY PHOSPHATASE.
J.Biol.Chem., 284:30594-30603, 2009

PubMed Abstract: The phosphatase KdsC cleaves 3-deoxy-D-manno-octulosonate 8-phosphate to generate a molecule of inorganic phosphate and Kdo. Kdo is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. Because lipopolysaccharide is an important determinant of bacterial resistance and toxicity, KdsC is a potential target for novel antibacterial agents. KdsC belongs to the broad haloacid dehalogenase superfamily. In haloacid dehalogenase superfamily enzymes, substrate specificity and catalytic efficiency are generally dictated by a fold feature called the cap domain. It is therefore not clear why KdsC, which lacks a cap domain, is catalytically efficient and highly specific to 3-deoxy-D-manno-octulosonate 8-phosphate. Here, we present a set of seven structures of tetrameric Escherichia coli KdsC (ranging from 1.4 to 3.06 A in resolution) that model different intermediate states in its catalytic mechanism. A crystal structure of product-bound E. coli KdsC shows how the interface between adjacent monomers defines the active site pocket. Kdo is engaged in a network of polar and nonpolar interactions with residues at this interface, which explains substrate specificity. Furthermore, this structural and kinetic analysis strongly suggests that the binding of the flexible C-terminal region (tail) to the active site makes KdsC catalytically efficient by facilitating product release.

PubMed: 19726684
DOI: 10.1074/jbc.M109.012278

Experimental method

X-RAY DIFFRACTION (2.49 Å)