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Journal of Bacteriology, April 2008, p. 2556-2564, Vol. 190, No. 7
0021-9193/08/$08.00+0     doi:10.1128/JB.01823-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Differential Substrate Specificity and Kinetic Behavior of Escherichia coli YfdW and Oxalobacter formigenes Formyl Coenzyme A Transferase{triangledown} ,{dagger}

Cory G. Toyota,1 Catrine L. Berthold,2 Arnaud Gruez,2 Stefán Jónsson,1,{ddagger} Ylva Lindqvist,3 Christian Cambillau,2 and Nigel G. J. Richards1*

Department of Chemistry, University of Florida, Gainesville, Florida 32611,1 AFMB-UMR 6098, CNRS-Universités Aix-Marseille I & II, Campus de Luminy, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 09,France,2 Department of Medical Biochemistry and Biophysics, Molecular Structural Biology, Karolinska Institutet, S-17177 Stockholm, Sweden3

Received 19 November 2007/ Accepted 25 January 2008

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.

* Corresponding author. Mailing address: Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, FL 32611-7200. Phone: (352) 392-3601. Fax: (352) 846-2095. E-mail: richards{at}qtp.ufl.edu

{triangledown} Published ahead of print on 1 February 2008.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

{ddagger} Deceased 30 July 2007.

Journal of Bacteriology, April 2008, p. 2556-2564, Vol. 190, No. 7
0021-9193/08/$08.00+0     doi:10.1128/JB.01823-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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