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Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases

DOI: 10.1073/pnas.1500161112 DOI Help
PMID: 25902496 PMID Help

Authors: Robert Byrne (University of York) , Huw Jenkins (University of York) , Daniel T. Peters (University of York) , Fiona Whelan (University of York) , James Stowell (University of York) , Naveed Aziz (University of York) , Pavel Kasatsky (Kurchatov Institute) , Marina V. Rodnina (Max Planck Institute for Biophysical Chemistry) , Eugene V. Koonin (National Library of Medicine, Bethesda) , Andrey L. Konevega (Kurchatov Institute) , Fred Antson (University of York)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Proceedings Of The National Academy Of Sciences , VOL 112 (19) , PAGES 6033 - 6037

State: Published (Approved)
Published: May 2015
Diamond Proposal Number(s): 1221 , 7864 , 9948

Abstract: The reduction of specific uridines to dihydrouridine is one of the most common modifications in tRNA. Increased levels of the dihydrouridine modification are associated with cancer. Dihydrouridine synthases (Dus) from different subfamilies selectively reduce distinct uridines, located at spatially unique positions of folded tRNA, into dihydrouridine. Because the catalytic center of all Dus enzymes is conserved, it is 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. We show that the Escherichia coli DusC is specific toward U16 of tRNA. Unexpectedly, crystal structures of DusC complexes with tRNAPhe and tRNATrp show that Dus subfamilies that selectively modify U16 or U20 in tRNA adopt identical folds but bind their respective tRNA substrates in an almost reverse orientation that differs by a 160° rotation. The tRNA docking orientation appears to be guided by subfamily-specific clusters of amino acids (“binding signatures”) together with differences in the shape of the positively charged tRNA-binding surfaces. tRNA orientations are further constrained by positional differences between the C-terminal “recognition” domains. The exquisite substrate specificity of Dus enzymes is therefore controlled by a relatively simple mechanism involving major reorientation of the whole tRNA molecule. Such reprogramming of the enzymatic specificity appears to be a unique evolutionary solution for altering tRNA recognition by the same protein fold.

Journal Keywords: Dihydrouridine Synthase; Trna Modification; ; Protein–Rna Interaction; Substrate Specificity; X-Ray Crystallography

Subject Areas: Biology and Bio-materials

Instruments: I02-Macromolecular Crystallography , I04-Macromolecular Crystallography , I24-Microfocus Macromolecular Crystallography

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