2VHQ

P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A mutant in complex with ATP AND MG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NTPASE P4A, B, C331Pseudomonas phage phi12Mutation(s): 1 
Gene Names: 4
UniProt
Find proteins for Q94M05 (Pseudomonas phage phi12)
Explore Q94M05 
Go to UniProtKB:  Q94M05
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ATP PDBBind:  2VHQ Kd: 1.40e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.244α = 90
b = 129.387β = 90
c = 158.978γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

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