2LQZ

Structure of the RNA claw of the DNA packaging motor of bacteriophage 29

Summary for 2LQZ

• Entry DOI: 10.2210/pdb2lqz/pdb
• NMR Information: BMRB: 18336
• Descriptor: RNA (27-MER) (1 entity in total)
• Functional Keywords: rna, bulge
• Total number of polymer chains: 1
• Total formula weight: 8586.13

Authors

Harjes, E.J.,Matsuo, H.J.,Kitamura, A.J. (deposition date: 2012-03-19, release date: 2012-08-01, Last modification date: 2024-05-15)

Primary citation

Harjes, E.,Kitamura, A.,Zhao, W.,Morais, M.C.,Jardine, P.J.,Grimes, S.,Matsuo, H.
Structure of the RNA claw of the DNA packaging motor of bacteriophage 29.
Nucleic Acids Res., 40:9953-9963, 2012

PubMed 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.

PubMed: 22879380
DOI: 10.1093/nar/gks724

Experimental method

SOLUTION NMR