The structure of the yrdC gene product from Escherichia coli reveals a newfold and suggests a role in RNA binding

The yrdC family of genes codes for proteins that occur both independently a nd as a domain in proteins that have been implicated in regulation. An exam ple for the latter case is the sua5 gene from yeast. Sua5 was identified as a suppressor of a translation initiation defect in cytochrome c and is req uired for normal growth in yeast (Na JG, Pinto I, Hampsey M, 1992, Genetics 11:791-801). However, the function of the Sua5 protein remains unknown: Su a5 could act either at the transcriptional or the posttranscriptional level s to compensate for an aberrant translation start codon in the cyc gene. To potentially learn more about the function of YrdC and proteins featuring t his domain, the crystal structure of the YrdC protein from Escherichia coli was determined at a resolution of 2.0 Angstrom. YrdC adopts a new fold wit h no obvious similarity to those of other proteins with known three-dimensi onal (3D) structure. The protein features a large concave surface on one si de that exhibits a positive electrostatic potential. The dimensions of this depression, its curvature, and the fact that conserved basic amino acids a re located at its floor suggest that YrdC may be a nucleic acid binding pro tein. An investigation of YrdC's binding affinities for single- and double- stranded RNA and DNA fragments as well as tRNAs demonstrates that YrdC bind s preferentially to double-stranded RNA. Our work provides evidence that 3D structures of functionally uncharacterized gene products with unique seque nces can yield novel folds and functional insights.