Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism

EMBO J. 2000 Aug 1;19(15):3849-56. doi: 10.1093/emboj/19.15.3849.

Abstract

Carbon-carbon bond formation is an essential reaction in organic chemistry and the use of aldolase enzymes for the stereochemical control of such reactions is an attractive alternative to conventional chemical methods. Here we describe the crystal structures of a novel class II enzyme, 2-dehydro-3-deoxy-galactarate (DDG) aldolase from Escherichia coli, in the presence and absence of substrate. The crystal structure was determined by locating only four Se sites to obtain phases for 506 protein residues. The protomer displays a modified (alpha/beta)(8) barrel fold, in which the eighth alpha-helix points away from the beta-barrel instead of packing against it. Analysis of the DDG aldolase crystal structures suggests a novel aldolase mechanism in which a phosphate anion accepts the proton from the methyl group of pyruvate.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Aldehyde-Lyases / chemistry*
  • Aldehyde-Lyases / classification
  • Crystallography, X-Ray*
  • Escherichia coli / enzymology
  • Models, Molecular
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Pyruvic Acid / metabolism
  • Selenomethionine / chemistry
  • Sugar Acids / metabolism
  • Tartronates

Substances

  • 2-dehydro-3-deoxygalactaric acid
  • Sugar Acids
  • Tartronates
  • tartronate semialdehyde
  • Pyruvic Acid
  • Selenomethionine
  • Aldehyde-Lyases
  • 2-dehydro-3-deoxygalactarate aldolase

Associated data

  • PDB/1DXE
  • PDB/1DXF