Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 106.68 kDa 
• Atom Count: 7508 
• Residue Count: 867 
• Unique protein chains: 1

2VHJ

P4 PROTEIN FROM BACTERIOPHAGE PHI12 S252A mutant in complex with ADP

• DOI: 10.2210/pdb2VHJ/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas phage phi12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-21 Released: 2007-12-04 
• Deposition Author(s): Kainov, D.E., Mancini, E.J., Telenius, J., Lisal, J., Grimes, J.M., Bamford, D.H., Stuart, D.I., Tuma, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

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

• PubMed: 18057007 
• DOI: 10.1074/jbc.M706366200
• Primary Citation of Related Structures:  
  2VHC, 2VHT, 2VHU, 2VHQ, 2VHJ


• 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NTPASE P4	A, B, C	331	Pseudomonas phage phi12	Mutation(s): 1  Gene Names: 4
Find proteins for Q94M05 (Pseudomonas phage phi12) Explore Q94M05  Go to UniProtKB:  Q94M05

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A, B, C	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ADP	Kd :  125000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 104.94	α = 90
b = 128.852	β = 90
c = 158.266	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-21 
• Released Date: 2007-12-04 
Deposition Author(s): Kainov, D.E., Mancini, E.J., Telenius, J., Lisal, J., Grimes, J.M., Bamford, D.H., Stuart, D.I., Tuma, R.

Revision History 

• 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