The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase

J Biol Chem. 2009 Oct 30;284(44):30594-603. doi: 10.1074/jbc.M109.012278. Epub 2009 Sep 2.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents
  • Catalytic Domain
  • Crystallography, X-Ray
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Hydrolases / chemistry*
  • Hydrolases / metabolism
  • Lipopolysaccharides
  • Phosphoric Monoester Hydrolases / chemistry*
  • Phosphoric Monoester Hydrolases / metabolism
  • Protein Conformation
  • Substrate Specificity
  • Sugar Acids / metabolism
  • Sugar Phosphates / metabolism

Substances

  • 3-deoxyoctulosonate 8-phosphate
  • Anti-Bacterial Agents
  • Escherichia coli Proteins
  • Lipopolysaccharides
  • Sugar Acids
  • Sugar Phosphates
  • Hydrolases
  • Phosphoric Monoester Hydrolases
  • 3-deoxy-manno-octulosonate-8-phosphatase
  • 2-haloacid dehalogenase

Associated data

  • PDB/2R8
  • PDB/2R8E
  • PDB/2R8Y
  • PDB/2R8Z
  • PDB/3HYC
  • PDB/3I6B