Crystallographic trapping of the glutamyl-CoA thioester intermediate of family I CoA transferases

J Biol Chem. 2005 Dec 30;280(52):42919-28. doi: 10.1074/jbc.M510522200. Epub 2005 Oct 27.


Coenzyme A transferases are involved in a broad range of biochemical processes in both prokaryotes and eukaryotes, and exhibit a diverse range of substrate specificities. The YdiF protein from Escherichia coli O157:H7 is an acyl-CoA transferase of unknown physiological function, and belongs to a large sequence family of CoA transferases, present in bacteria to humans, which utilize oxoacids as acceptors. In vitro measurements showed that YdiF displays enzymatic activity with short-chain acyl-CoAs. The crystal structures of YdiF and its complex with CoA, the first co-crystal structure for any Family I CoA transferase, have been determined and refined at 1.9 and 2.0 A resolution, respectively. YdiF is organized into tetramers, with each monomer having an open alpha/beta structure characteristic of Family I CoA transferases. Co-crystallization of YdiF with a variety of CoA thioesters in the absence of acceptor carboxylic acid resulted in trapping a covalent gamma-glutamyl-CoA thioester intermediate. The CoA binds within a well defined pocket at the N- and C-terminal domain interface, but makes contact only with the C-terminal domain. The structure of the YdiF complex provides a basis for understanding the different catalytic steps in the reaction of Family I CoA transferases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Carboxylic Acids / chemistry
  • Catalysis
  • Catalytic Domain
  • Chromatography, Gel
  • Cloning, Molecular
  • Coenzyme A / chemistry*
  • Coenzyme A-Transferases / chemistry*
  • Coenzyme A-Transferases / metabolism
  • Crystallization
  • Crystallography, X-Ray / methods*
  • Escherichia coli / enzymology*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Esters / chemistry*
  • Glutamic Acid / chemistry*
  • Histidine / chemistry
  • Mass Spectrometry
  • Models, Chemical
  • Models, Molecular
  • Molecular Conformation
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Quaternary
  • Protein Structure, Secondary
  • Protein Structure, Tertiary


  • Carboxylic Acids
  • Escherichia coli Proteins
  • Esters
  • Glutamic Acid
  • Histidine
  • Coenzyme A-Transferases
  • YdiF protein, E coli
  • Coenzyme A

Associated data

  • PDB/2AHU
  • PDB/2AHV
  • PDB/2AHW