Evolution of Enzymatic Activities in the Enolase Superfamily: Functional Assignment of Unknown Proteins in Bacillus Subtilis and Escherichia Coli as L-Ala-D/L-Glu Epimerases

Biochemistry. 2001 Dec 25;40(51):15707-15. doi: 10.1021/bi011640x.

Abstract

The members of the mechanistically diverse enolase superfamily catalyze different overall reactions by using a common catalytic strategy and structural scaffold. In the muconate lactonizing enzyme (MLE) subgroup of the superfamily, abstraction of a proton adjacent to a carboxylate group initiates reactions, including cycloisomerization (MLE), dehydration [o-succinylbenzoate synthase (OSBS)], and 1,1-proton transfer (catalyzed by an OSBS that also catalyzes a promiscuous N-acylamino acid racemase reaction). The realization that a member of the MLE subgroup could catalyze a 1,1-proton transfer reaction, albeit poorly, led to a search for other enzymes which might catalyze a 1,1-proton transfer as their physiological reaction. YcjG from Escherichia coli and YkfB from Bacillus subtilis, proteins of previously unknown function, were discovered to be L-Ala-D/L-Glu epimerases, although they also catalyze the epimerization of other dipeptides. The values of k(cat)/K(M) for L-Ala-D/L-Glu for both proteins are approximately 10(4) M(-1) s(-1). The genomic context and the substrate specificity of both YcjG and YkfB suggest roles in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Homologues possessing L-Ala-D/L-Glu epimerase activity have been identified in at least two other organisms.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alanine Racemase / chemistry
  • Alanine Racemase / genetics
  • Amino Acid Isomerases / chemistry*
  • Amino Acid Isomerases / genetics
  • Amino Acid Sequence
  • Aminopeptidases / chemistry
  • Bacillus subtilis / enzymology*
  • Bacillus subtilis / genetics
  • Dipeptides / chemistry
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Evolution, Molecular
  • Genes, Bacterial
  • Genome, Bacterial
  • Intramolecular Lyases / chemistry*
  • Intramolecular Lyases / genetics
  • Kinetics
  • Molecular Sequence Data
  • Phosphopyruvate Hydratase / chemistry*
  • Phosphopyruvate Hydratase / genetics
  • Racemases and Epimerases / chemistry*
  • Racemases and Epimerases / genetics
  • Sequence Homology, Amino Acid
  • Serine Endopeptidases / chemistry

Substances

  • Dipeptides
  • Aminopeptidases
  • Serine Endopeptidases
  • Phosphopyruvate Hydratase
  • Racemases and Epimerases
  • Amino Acid Isomerases
  • Alanine Racemase
  • glutamate racemase
  • mandelate racemase
  • Intramolecular Lyases
  • muconate cycloisomerase