P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A mutant in complex with ADP

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report

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Structural Basis of Mechanochemical Coupling in a Hexameric Molecular Motor.

Kainov, D.E.Mancini, E.J.Telenius, J.Lisal, J.Grimes, J.M.Bamford, D.H.Stuart, D.I.Tuma, R.

(2008) J Biol Chem 283: 3607

  • DOI: https://doi.org/10.1074/jbc.M706366200
  • Primary Citation of Related Structures:  
    2VHC, 2VHJ, 2VHQ, 2VHT, 2VHU

  • PubMed Abstract: 

    The P4 protein of bacteriophage phi12 is a hexameric molecular motor closely related to superfamily 4 helicases. P4 converts chemical energy from ATP hydrolysis into mechanical work, to translocate single-stranded RNA into a viral capsid. The molecular basis of mechanochemical coupling, i.e. how small approximately 1 A changes in the ATP-binding site are amplified into nanometer scale motion along the nucleic acid, is not understood at the atomic level. Here we study in atomic detail the mechanochemical coupling using structural and biochemical analyses of P4 mutants. We show that a conserved region, consisting of superfamily 4 helicase motifs H3 and H4 and loop L2, constitutes the moving lever of the motor. The lever tip encompasses an RNA-binding site that moves along the mechanical reaction coordinate. The lever is flanked by gamma-phosphate sensors (Asn-234 and Ser-252) that report the nucleotide state of neighboring subunits and control the lever position. Insertion of an arginine finger (Arg-279) into the neighboring catalytic site is concomitant with lever movement and commences ATP hydrolysis. This ensures cooperative sequential hydrolysis that is tightly coupled to mechanical motion. Given the structural conservation, the mutated residues may play similar roles in other hexameric helicases and related molecular motors.

  • Organizational Affiliation

    Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter P. O. Box 65, Helsinki FIN-00014, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
331Pseudomonas phage phi12Mutation(s): 1 
Find proteins for Q94M05 (Pseudomonas phage phi12)
Explore Q94M05 
Go to UniProtKB:  Q94M05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94M05
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
C10 H15 N5 O10 P2
Binding Affinity Annotations 
IDSourceBinding Affinity
ADP PDBBind:  2VHJ Kd: 1.25e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.94α = 90
b = 128.852β = 90
c = 158.266γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance