Structure of the RNA claw of the DNA packaging motor of bacteriophage φ29

Elena Harjes, Aya Kitamura, Wei Zhao, Marc C. Morais, Paul J. Jardine, Shelley Grimes, Hiroshi Matsuo

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage r29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base bulge (18-CCA-20) in the pRNA A-helix was shown to abolish packaging activity. Here, we solved the structure of this crucial bulge by nuclear magnetic resonance (NMR) using a 27mer RNA fragment containing the bulge (27b). The bulge actually involves five nucleotides (17-UCCA-20 and A100), as U17 and A100 are not base paired as predicted. Mutational analysis showed these newly identified bulge residues are important for DNA packaging. The bulge introduces a 33-35° bend in the helical axis, and inter-helical motion around this bend appears to be restricted. A model of the functional 120b pRNA was generated using a 27b NMR structure and the crystal structure of the 66b prohead-binding domain. Fitting this model into a cryo-EM map generated a pentameric pRNA structure; five helices projecting from the pRNA ring resemble an RNA claw. Biochemical analysis suggested that this shape is important for coordinated motor action required for DNA translocation.

Original languageEnglish (US)
Pages (from-to)9953-9963
Number of pages11
JournalNucleic acids research
Volume40
Issue number19
DOIs
StatePublished - Oct 2012

Bibliographical note

Funding Information:
National Institutes of Health (NIH) [GM-059604 and GM-095516]. Funding for NMR instrumentation was provided by the Office of the Vice President for Research, the Medical School, the College of Biological Science, NIH, NSF and the Minnesota Medical Foundation; NIH [P41RR02301, P41GM66326, RR02781 and RR08438 to the National Magnetic Resonance Facility at Madison]; National Science Foundation [DMB-8415048, OIA-9977486 and BIR-9214394 to the National Magnetic Resonance Facility at Madison]. Funding for open access charge: NIH [GM-059604].

Copyright:
Copyright 2013 Elsevier B.V., All rights reserved.

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