Alanine Scanning and Fe-BABE Probing of the Bacteriophage ø29 Prohead RNA-Connector Interaction

Rockney Atz, Shuhua Ma, Jiali Gao, Dwight L. Anderson, Shelley Grimes

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23 Scopus citations


The DNA packaging motor of the Bacillus subtilis bacteriophage ø29 prohead is comprised in part of an oligomeric ring of 174 base RNA molecules (pRNA) positioned near the N termini of subunits of the dodecameric head-tail connector. Deletion and alanine substitution mutants in the connector protein (gp10) N terminus were assembled into proheads in Escherichia coli and the particles tested for pRNA binding and DNA-gp3 packaging in vitro. The basic amino acid residues RKR at positions 3-5 of the gp10 N terminus were central to pRNA binding during assembly of an active DNA packaging motor. Conjugation of iron(S)-1-(p-bromoacetamidobenzyl) ethylenediaminetetraacetate (Fe-BABE) to residue S170C in the narrow end of the connector, near the N terminus, permitted hydroxyl radical probing of bound [32P]pRNA and identified two discrete sites proximal to this residue: the C-helix at the junction of the A, C and D helices, and the E helix and the CE loop/D loop of the intermolecular base pairing site.

Original languageEnglish (US)
Pages (from-to)239-248
Number of pages10
JournalJournal of Molecular Biology
Issue number1
StatePublished - May 25 2007

Bibliographical note

Funding Information:
We thank Jaya Koti and Laura Birkeland for preparing 120nt pRNA, Marc Morais for Figure 1 (c), Paul Jardine for helpful discussion, and Charlene Peterson for assistance in the preparation of the manuscript. This research was supported by NIH grants GM-059604, DE-03606 (to S.G.) and GM-46736 (to J.G.).


  • DNA packaging
  • RNA binding
  • bacteriophage ø29
  • directed hydroxyl radical probing
  • packaging motor assembly


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