Interaction of gp16 with pRNA and DNA for genome packaging by the motor of bacterial virus phi29

J Mol Biol. 2006 Feb 24;356(3):589-99. doi: 10.1016/j.jmb.2005.10.045. Epub 2005 Nov 9.


One striking feature in the assembly of linear double-stranded (ds) DNA viruses is that their genome is translocated into a preformed protein coat via a motor involving two non-structural components with certain characteristics of ATPase. In bacterial virus phi29, these two components include the protein gp16 and a packaging RNA (pRNA). The structure and function of other phi29 motor components have been well elucidated; however, studies on the role of gp16 have been seriously hampered by its hydrophobicity and self-aggregation. Such problems caused by insolubility also occur in the study of other viral DNA-packaging motors. Contradictory data have been published regarding the role and stoichiometry of gp16, which has been reported to bind every motor component, including pRNA, DNA, gp3, DNA-gp3, connector, pRNA-free procapsid, and procapsid/pRNA complex. Such conflicting data from a binding assay could be due to the self-aggregation of gp16. Our recent advance to produce soluble and highly active gp16 has enabled further studies on gp16. It was demonstrated in this report that gp16 bound to DNA non-specifically. gp16 bound to the pRNA-containing procapsid much more strongly than to the pRNA-free procapsid. The domain of pRNA for gp16 interaction was the 5'/3' paired helical region. The C18C19A20 bulge that is essential for DNA packaging was found to be dispensable for gp16 binding. This result confirms the published model that pRNA binds to the procapsid with its central domain and extends its 5'/3' DNA-packaging domain for gp16 binding. It suggests that gp16 serves as a linkage between pRNA and DNA, and as an essential DNA-contacting component during DNA translocation. The data also imply that, with the exception of the C18C19A20 bulge, the main role of the 5'/3' helical double-stranded region of pRNA is not for procapsid binding but for binding to gp16.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine Triphosphatases / metabolism*
  • Bacillus Phages / physiology*
  • Binding Sites
  • Biological Transport
  • Capsid / metabolism
  • DNA Packaging / physiology
  • DNA, Viral / metabolism*
  • DNA, Viral / physiology
  • DNA-Binding Proteins / metabolism*
  • Genome, Viral*
  • Molecular Motor Proteins / metabolism*
  • RNA, Viral / metabolism*
  • Signal Transduction / genetics
  • Viral Proteins / metabolism
  • Virus Assembly / physiology*


  • DNA, Viral
  • DNA-Binding Proteins
  • Molecular Motor Proteins
  • RNA, Viral
  • Viral Proteins
  • p3 protein, bacteriophage phi 29
  • Adenosine Triphosphatases
  • protein p16, bacteriophage phi29