PDBsum entry 2vhc

Hydrolase

PDB id: 2vhc

Contents

Protein chains

289 a.a.

Ligands

APC ×3

Metals

_MN ×3

Waters ×725

PDB id:

2vhc

Name:

Hydrolase

Title:

P4 protein from bacteriophage phi12 n234g mutant in complex with ampcpp and mn

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.

Resolution:

2.35Å R-factor: 0.177 R-free: 0.237

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

Date:

20-Nov-07 Release date: 04-Dec-07

Protein chains

Q94M05  (Q94M05_9VIRU) -  NTPase P4 from Pseudomonas phage phi12

Seq: 331 a.a.

Struc: 289 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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.

ABSTRACT

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.