title: Structure of the RNA claw of the DNA packaging motor of bacteriophage Φ29.
abstract: Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage 29 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.
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
authors.forename: Elena
authors.initials: E
authors.lastname: Harjes
authors.forename: Aya
authors.initials: A
authors.lastname: Kitamura
authors.forename: Wei
authors.initials: W
authors.lastname: Zhao
authors.forename: Marc C
authors.initials: MC
authors.lastname: Morais
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Jardine
authors.forename: Shelley
authors.initials: S
authors.lastname: Grimes
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Matsuo
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D017103:Bacillus Phages / Q000201:enzymology / Q000235:genetics*; D001483:Base Sequence; D042003:DNA Packaging; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D014764:Viral Proteins / Q000378:metabolism
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases