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Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism

DOI: 10.1093/nar/gkw1354 DOI Help

Authors: Rui-gang Xu (University of York) , Huw T. Jenkins (University of York) , Maria Chechik (University of York) , Elena Blagova (University of York) , Anna Lopatina (Institute of Molecular Genetics, Russian Academy of Sciences) , Evgeny Klimuk (Skolkovo Institute of Science and Technology) , Leonid Minakhin (Institute for Microbiology, Rutgers, The State University of New Jersey) , Konstantin Severinov (Institute of Molecular Genetics, Russian Academy of Sciences; Skolkovo Institute of Science and Technology; Institute for Microbiology, Rutgers, The State University of New Jersey) , Sandra J. Greive (University of York) , Alfred A. Antson (University of York)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Nucleic Acids Research

State: Published (Approved)
Published: January 2017
Diamond Proposal Number(s): 7864 , 9948 , 13587

Open Access Open Access

Abstract: Bacteriophages and large dsDNA viruses encode sophisticated machinery to translocate their DNA into a preformed empty capsid. An essential part of this machine, the large terminase protein, processes viral DNA into constituent units utilizing its nuclease activity. Crystal structures of the large terminase nuclease from the thermophilic bacteriophage G20c show that it is most similar to the RuvC family of the RNase H-like endonucleases. Like RuvC proteins, the nuclease requires either Mn2+, Mg2+ or Co2+ ions for activity, but is inactive with Zn2+ and Ca2+. High resolution crystal structures of complexes with different metals reveal that in the absence of DNA, only one catalytic metal ion is accommodated in the active site. Binding of the second metal ion may be facilitated by conformational variability, which enables the two catalytic aspartic acids to be brought closer to each other. Structural comparison indicates that in common with the RuvC family, the location of the two catalytic metals differs from other members of the RNase H family. In contrast to a recently proposed mechanism, the available data do not support binding of the two metals at an ultra-short interatomic distance. Thus we postulate that viral terminases cleave DNA by the canonical RuvC-like mechanism.

Journal Keywords: bacteriophages; catalysis; dna; ions; metals; nuclease; crystal structure

Subject Areas: Chemistry, Biology and Bio-materials

Instruments: I02-Macromolecular Crystallography , I03-Macromolecular Crystallography , I04-Macromolecular Crystallography