Structure of PaP3 small terminase

Experimental Data Snapshot

  • Resolution: 3.01 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

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This is version 1.2 of the entry. See complete history


Biophysical analysis of Pseudomonas-phage PaP3 small terminase suggests a mechanism for sequence-specific DNA-binding by lateral interdigitation.

Niazi, M.Florio, T.J.Yang, R.Lokareddy, R.K.Swanson, N.A.Gillilan, R.E.Cingolani, G.

(2020) Nucleic Acids Res 48: 11721-11736

  • DOI: https://doi.org/10.1093/nar/gkaa866
  • Primary Citation of Related Structures:  
    6W7T, 7JOQ

  • PubMed Abstract: 

    The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
small terminase subunit152Bruynoghevirus PaP3Mutation(s): 0 
Gene Names: orf1
Find proteins for Q8H9R5 (Bruynoghevirus PaP3)
Explore Q8H9R5 
Go to UniProtKB:  Q8H9R5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8H9R5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.01 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.302α = 90
b = 121.152β = 90
c = 129.664γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100888
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesOD017987
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA56036

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description