PDBsum entry 2vhq

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Hydrolase PDB id
Protein chains
302 a.a.
ATP ×3
_MG ×3
Waters ×590
PDB id:
Name: Hydrolase
Title: P4 protein from bacteriophage phi12 s252a mutant in complex with atp and mg
Structure: Ntpase p4. Chain: a, b, c. Synonym: p4. Engineered: yes. Mutation: yes
Source: Pseudomonas phage phi12. Bacteriophage phi12. Organism_taxid: 161736. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.15Å     R-factor:   0.198     R-free:   0.247
Authors: D.E.Kainov,E.J.Mancini,J.Telenius,J.Lisal,J.M.Grimes, D.H.Bamford,D.I.Stuart,R.Tuma
Key ref:
D.E.Kainov et al. (2007). Structural basis of mechano-chemical coupling in a hexameric molecular motor. J Biol Chem, 283, 3607. PubMed id: 18057007 DOI: 10.1074/jbc.M706366200
22-Nov-07     Release date:   04-Dec-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q94M05  (Q94M05_9VIRU) -  NTPase P4
331 a.a.
302 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     2 terms  


DOI no: 10.1074/jbc.M706366200 J Biol Chem 283:3607 (2007)
PubMed id: 18057007  
Structural basis of mechano-chemical coupling in a hexameric molecular motor.
D.E.Kainov, E.J.Mancini, J.Telenius, J.Lisal, J.M.Grimes, D.H.Bamford, D.I.Stuart, R.Tuma.
The P4 protein of bacteriophage phi12 is a hexameric molecular motor closely related to super family 4 (SF4) helicases. P4 converts chemical energy from ATP hydrolysis into mechanical work, to translocate single stranded RNA into a viral capsid. The molecular basis of mechano-chemical coupling, i.e. how small ~1A changes in the ATP binding site are amplified into nanometer scale motion along the nucleic acid, is not understood at atomic level. Here we study in atomic detail the mechano-chemical coupling using structural and biochemical analyses of P4 mutants. We show that a conserved region, comprising SF4 helicase motifs H3 and H4 and loop L2, constitutes the moving lever of the motor. The lever tip encompasses an RNA binding site which moves along the mechanical reaction coordinate. The lever is flanked by gamma-phosphate sensors (Asn234 and Ser252) which report the nucleotide state of neighboring subunits and control the lever position. Insertion of an arginine finger (Arg279) into the neighboring catalytic site is concomitant with lever movement and commences ATP hydrolysis. This assures cooperative sequential hydrolysis which 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.
  Selected figure(s)  
Figure 2.
Structure of the N234G mutant (stereo). A, structural superimposition and comparison of the nucleotide binding interface of the N234G mutant (green) and WT:AMPcPP (yellow) structures. Only structural features in the vicinity of the nucleotide-binding site, the P loop, and the L2 loop/α6 helix are highlighted. In addition, the mutated residue, Asn/Gly-234 is shown in a ball-and stick model representation. B, structures of the WT protein with AMPcPP (yellow) and ADP (blue) bound, respectively, are shown for reference in the same orientation as shown in A. Superposition of coordinates was conducted using SHP (53).
Figure 5.
Schematic description of the sequential coordination of hydrolysis. A, top panel shows a schematic representation of the conserved motifs in the context of one P4 subunit together with a bound ATP (yellow). B, initial state before hydrolysis. Only three consecutive subunits of the unraveled hexamer are shown for clarity (as perceived from the central channel, i.e. from the bound RNA “perspective”). C, hydrolysis and P[i] release from subunit i -1 allows the downward movement of helix α6 and insertion of the arginine finger Arg-279 into subunit i active site (ADP-P^* designates the transition state). The L2 loop drags down the bound RNA (cyan). D, next round of sequential hydrolysis. The stretched RNA (a stress loop, magenta) links L2 loops on i and i -1. RNA is brought to the vicinity and binds to L2 at subunit i + 1.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 283, 3607) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20379135 E.Crozat, A.Meglio, J.F.Allemand, C.E.Chivers, M.Howarth, C.Vénien-Bryan, I.Grainge, and D.J.Sherratt (2010).
Separating speed and ability to displace roadblocks during DNA translocation by FtsK.
  EMBO J, 29, 1423-1433.  
18329872 E.J.Enemark, and L.Joshua-Tor (2008).
On helicases and other motor proteins.
  Curr Opin Struct Biol, 18, 243-257.  
18940870 F.Xiao, H.Zhang, and P.Guo (2008).
Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging.
  Nucleic Acids Res, 36, 6620-6632.  
18423102 E.Nurmemmedov, M.Castelnovo, C.E.Catalano, and A.Evilevitch (2007).
Biophysics of viral infectivity: matching genome length with capsid size.
  Q Rev Biophys, 40, 327-356.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.