Recognition of Specific Uridines in tRNA Substrates by Dihydrouridine Synthases

The reduction of specific uridines to dihydrouridine is one of the most abundant modifications found in tRNA. Increased levels of the dihydrouridine modification are associated with cancer. Different subfamilies of dihydrouridine synthases (Dus) selectively reduce distinct uridines, located at spatially unique positions of folded tRNA. Because the catalytic center of all Dus enzymes is conserved, it was unclear how the same protein fold can be reprogrammed to ensure that nucleotides exposed at spatially distinct faces of tRNA can be accommodated in the same active site.Unexpectedly, crystal structures of U16-specific E.coli Dus in complex with tRNA_Phe and tRNA_Trp [1] show that the U16-specific subfamily binds their respective tRNA substrates in an almost reverse orientation to the U20-specific subfamily [2]. The tRNA docking orientation appears to be guided by subfamily-specific clusters of ‘binding signatures’ together with differences in the shape of the positively charged tRNA-binding surfaces. The exquisite substrate specificity of Dus enzymes is therefore controlled by a relatively simple mechanism involving major reorientation of the whole tRNA molecule.Interestingly, the X-ray structure of the type-2 human Dus reveals differences in the recognition domain and a unique beta-sheet insertion into the catalytic domain [3] which may influence tRNA recognition.