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PDBsum entry 2vhc
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References listed in PDB file
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Key reference
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Title
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Structural basis of mechano-Chemical coupling in a hexameric molecular motor.
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Authors
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D.E.Kainov,
E.J.Mancini,
J.Telenius,
J.Lisal,
J.M.Grimes,
D.H.Bamford,
D.I.Stuart,
R.Tuma.
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Ref.
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J Biol Chem, 2007,
283,
3607.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
283,
3607)
copyright 2007.
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