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

Abstract

The yrdC family of genes codes for proteins that occur both independently and as a domain in proteins that have been implicated in regulation. An example 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 required 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; Sua5 could act either at the transcriptional or the posttranscriptional levels to compensate for an aberrant translation start codon in the cyc gene. To potentially learn more about the function of YrdC and proteins featuring this domain, the crystal structure of the YrdC protein from Escherichia coli was determined at a resolution of 2.0 Å. YrdC adopts a new fold with no obvious similarity to those of other proteins with known three-dimensional~3D! structure. The protein features a large concave surface on one side that exhibits a positive electrostatic potential. The dimensions of this depression, its curvature, and the fact that conserved basic amino acids are located at its floor suggest that YrdC may be a nucleic acid binding protein. An investigation of YrdC's binding affinities for single-and double-stranded RNA and DNA fragments as well as tRNAs demonstrates that YrdC binds preferentially to double-stranded RNA. Our work provides evidence that 3D structures of functionally uncharacterized gene products with unique sequences can yield novel folds and functional insights.

Functional analysis of 11 putative essential genes in Bacillus subtilis

“…Depletion of YjeE in E. coli results in a morphology that is consistent with defective cell wall synthesis (J. Handford, personal communication). However, we found that disruption of ydiB had only a mild effect on growth in B. subtilis, and cell morphology was unaffected Teplova et al (2000) in the ydiB deletion strain. Therefore, the functions of YdiB and its homologue in E. coli may differ.…”

“…Nucleic acid-binding studies have shown that YrdC binds preferentially to dsRNA (Teplova et al, 2000).…”

X‐ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7

“…7,8 The crystal structure of E. coli YrdC has been determined and a possible nucleic acid-binding site has been identified. 6 The Sua5 protein consists of an N-terminal YrdC domain and a C-terminal Sua5 domain. 6 The sua5 gene was first identified in Saccharomyces cerevisiae as a suppressor of a translation initiation defect in the leader region of the iso-1-cytochrome c (cyc1) gene, which is caused by the generation of an aberrant ATG start codon upstream of the gene as a consequence of a single basepair substitution.…”

Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus

“…A number of recent publications have demonstrated the validity of this approach (4)(5)(6), although in some cases it is more difficult to infer molecular function when the structure has a previously uncharacterized fold (7)(8)(9).…”