Differential substrate specificity and kinetic behavior of Escherichia coli YfdW and Oxalobacter formigenes formyl coenzyme A transferase

J Bacteriol. 2008 Apr;190(7):2556-64. doi: 10.1128/JB.01823-07. Epub 2008 Feb 1.


The yfdXWUVE operon appears to encode proteins that enhance the ability of Escherichia coli MG1655 to survive under acidic conditions. Although the molecular mechanisms underlying this phenotypic behavior remain to be elucidated, findings from structural genomic studies have shown that the structure of YfdW, the protein encoded by the yfdW gene, is homologous to that of the enzyme that mediates oxalate catabolism in the obligate anaerobe Oxalobacter formigenes, O. formigenes formyl coenzyme A transferase (FRC). We now report the first detailed examination of the steady-state kinetic behavior and substrate specificity of recombinant, wild-type YfdW. Our studies confirm that YfdW is a formyl coenzyme A (formyl-CoA) transferase, and YfdW appears to be more stringent than the corresponding enzyme (FRC) in Oxalobacter in employing formyl-CoA and oxalate as substrates. We also report the effects of replacing Trp-48 in the FRC active site with the glutamine residue that occupies an equivalent position in the E. coli protein. The results of these experiments show that Trp-48 precludes oxalate binding to a site that mediates substrate inhibition for YfdW. In addition, the replacement of Trp-48 by Gln-48 yields an FRC variant for which oxalate-dependent substrate inhibition is modified to resemble that seen for YfdW. Our findings illustrate the utility of structural homology in assigning enzyme function and raise the question of whether oxalate catabolism takes place in E. coli upon the up-regulation of the yfdXWUVE operon under acidic conditions.

Publication types

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

MeSH terms

  • Acyl Coenzyme A / metabolism
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Binding Sites / genetics
  • Coenzyme A-Transferases / chemistry
  • Coenzyme A-Transferases / genetics
  • Coenzyme A-Transferases / metabolism*
  • Crystallography, X-Ray
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Glutamine / genetics
  • Glutamine / metabolism
  • Kinetics
  • Molecular Sequence Data
  • Molecular Structure
  • Oxalates / metabolism
  • Oxalobacter formigenes / enzymology*
  • Oxalobacter formigenes / genetics
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Structural Homology, Protein
  • Structure-Activity Relationship
  • Substrate Specificity
  • Tryptophan / genetics
  • Tryptophan / metabolism


  • Acyl Coenzyme A
  • Bacterial Proteins
  • Escherichia coli Proteins
  • Oxalates
  • Glutamine
  • formyl-coenzyme A
  • Tryptophan
  • Coenzyme A-Transferases
  • YfdW protein, E coli
  • formyl-coenzyme A transferase