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J. Biol. Chem., Vol. 280, Issue 52, 42919-42928, December 30, 2005

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Crystallographic Trapping of the Glutamyl-CoA Thioester Intermediate of Family I CoA Transferases^*

Erumbi S. Rangarajan, Yunge Li¶, Eunice Ajamian, Pietro Iannuzzi¶, Stephanie D. Kernaghan||, Marie E. Fraser||1, Miroslaw Cygler¶2, and Allan Matte¶3

From the Department of Biochemistry, McGill University, the Montreal Joint Center for Structural Biology, ^¶Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2 and the ^||Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada

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 Å resolution, respectively. YdiF is organized into tetramers, with each monomer having an open / 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 -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.

Received for publication, September 26, 2005 , and in revised form, October 21, 2005.

^* This work was supported in part by Canadian Institutes of Health Research Grant 200103GSP-90094-GMX-CFAA-19924. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. The atomic coordinates and structure factors (codes 2AHU (apo-YdiF), 2AHV and 2AHW (YdiF--glutamyl-CoA thioester), respectively) have been deposited in the Protein Data Bank,ResearchCollaboratoryforStructuralBioinformatics,RutgersUniversity,NewBrunswick, NJ (http://www.rcsb.org/).

¹ Supported in part by Canadian Institutes of Health Research Grant MOP-42446 and a Biomedical Scholar of the Alberta Heritage Foundation for Medical Research.

² To whom correspondence may be addressed. Tel.: 514-496-6321; Fax: 514-496-5143; E-mail: mirek.cygler{at}nrc-cnrc.gc.ca. ³ To whom correspondence may be addressed: Biotechnology Research Institute, 6100 Royalmount Ave., Montreal, Quebec H4P 2R2, Canada. Tel.: 514-496-2557; E-mail: allan.matte{at}nrc-cnrc.gc.ca.

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