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

14 Scopus citations


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
Issue number19
StatePublished - Oct 2012

ASJC Scopus subject areas

  • Genetics


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