Functional Diversity of the Rhodanese Homology Domain

Escherichia coli has eight genes predicted to encode sulfurtransferases having the active site consensus sequence Cys-Xaa-Xaa-Gly. One of these genes, ybbB, is frequently found within bacterial operons that contain selD, the selenophosphate synthetase gene, suggesting a role in selenium metabolism. We show that ybbB is required in vivo for the specific substitution of selenium for sulfur in 2-thiouridine residues in E. coli tRNA. This modified tRNA nucleoside, 5-methylaminomethyl-2-selenouridine (mnm⁵se²U), is located at the wobble position of the anticodons of tRNA^Lys, tRNA^Glu, and tRNA₁^Gln. Nucleoside analysis of tRNAs from wild-type and ybbB mutant strains revealed that production of mnm⁵se²U is lost in the ybbB mutant but that 5-methylaminomethyl-2-thiouridine, the mnm⁵se²U precursor, is unaffected by deletion of ybbB. Thus, ybbB is not required for the initial sulfurtransferase reaction but rather encodes a 2-selenouridine synthase that replaces a sulfur atom in 2-thiouridine in tRNA with selenium. Purified 2-selenouridine synthase containing a C-terminal His₆ tag exhibited spectral properties consistent with tRNA bound to the enzyme. In vitro mnm⁵se²U synthesis is shown to be dependent on 2-selenouridine synthase, SePO₃, and tRNA. Finally, we demonstrate that the conserved Cys⁹⁷ (but not Cys⁹⁶) in the rhodanese sequence motif Cys⁹⁶-Cys⁹⁷-Xaa-Xaa-Gly is required for 2-selenouridine synthase in vivo activity. These data are consistent with the ybbB gene encoding a tRNA 2-selenouridine synthase and identifies a new role for the rhodanese homology domain in enzymes.