Crystal structure of the g2p (large terminase) nuclease domain from the bacteriophage SPP1 with bound Mn

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Structural Basis for the Nuclease Activity of a Bacteriophage Large Terminase.

Smits, C.Chechik, M.Kovalevskiy, O.V.Shevtsov, M.B.Foster, A.W.Alonso, J.C.Antson, A.A.

(2009) EMBO Rep 10: 592

  • DOI: https://doi.org/10.1038/embor.2009.53
  • Primary Citation of Related Structures:  
    2WBN, 2WC9

  • PubMed Abstract: 

    The DNA-packaging motor in tailed bacteriophages requires nuclease activity to ensure that the genome is packaged correctly. This nuclease activity is tightly regulated as the enzyme is inactive for the duration of DNA translocation. Here, we report the X-ray structure of the large terminase nuclease domain from bacteriophage SPP1. Similarity with the RNase H family endonucleases allowed interactions with the DNA to be predicted. A structure-based alignment with the distantly related T4 gp17 terminase shows the conservation of an extended beta-sheet and an auxiliary beta-hairpin that are not found in other RNase H family proteins. The model with DNA suggests that the beta-hairpin partly blocks the active site, and in vivo activity assays show that the nuclease domain is not functional in the absence of the ATPase domain. Here, we propose that the nuclease activity is regulated by movement of the beta-hairpin, altering active site access and the orientation of catalytically essential residues.

  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TERMINASE LARGE SUBUNIT212Bacillus phage SPP1Mutation(s): 0 
Gene Names: 2
EC: 3.1 (UniProt), 3.6.4 (UniProt)
Find proteins for P54308 (Bacillus phage SPP1)
Explore P54308 
Go to UniProtKB:  P54308
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54308
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.71α = 90
b = 69.71β = 90
c = 73.801γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-06-23
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Data collection