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PDBsum entry 3dc4
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Motor protein
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PDB id
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3dc4
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References listed in PDB file
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Key reference
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Title
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Atpase cycle of the nonmotile kinesin nod allows microtubule end tracking and drives chromosome movement.
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Authors
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J.C.Cochran,
C.V.Sindelar,
N.K.Mulko,
K.A.Collins,
S.E.Kong,
R.S.Hawley,
F.J.Kull.
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Ref.
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Cell, 2009,
136,
110-122.
[DOI no: ]
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PubMed id
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Abstract
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Segregation of nonexchange chromosomes during Drosophila melanogaster meiosis
requires the proper function of NOD, a nonmotile kinesin-10. We have determined
the X-ray crystal structure of the NOD catalytic domain in the ADP- and
AMPPNP-bound states. These structures reveal an alternate conformation of the
microtubule binding region as well as a nucleotide-sensitive relay of hydrogen
bonds at the active site. Additionally, a cryo-electron microscopy
reconstruction of the nucleotide-free microtubule-NOD complex shows an atypical
binding orientation. Thermodynamic studies show that NOD binds tightly to
microtubules in the nucleotide-free state, yet other nucleotide states,
including AMPPNP, are weakened. Our pre-steady-state kinetic analysis
demonstrates that NOD interaction with microtubules occurs slowly with weak
activation of ADP product release. Upon rapid substrate binding, NOD detaches
from the microtubule prior to the rate-limiting step of ATP hydrolysis, which is
also atypical for a kinesin. We propose a model for NOD's microtubule plus-end
tracking that drives chromosome movement.
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Figure 1.
Figure 1. X-Ray Crystal Structure of NOD•ADP and
NOD•AMPPNP
(A) Structure of NOD•ADP is shown. ADP is
displayed as a ball-and-stick model.
(B) NOD•AMPPNP is
shown as in (A).
(C and D) Superposition of NOD•ADP
(blue) and NOD•AMPPNP (orange) through alignment of the P loop
(G87-S94) as viewed from the top (C) and from the side (D).
Arrows highlight the differences between the two states in Sw1,
Sw2, α3, and L11.
(E) Configuration of hydrogen bonds
between Sw1/Sw2 residues in NOD•ADP. Hydrogen bonds with
measured distances are highlighted with magenta dashed lines.
The water molecules that coordinate Mg^2+ are shown as red
spheres.
(F) Active site configuration of hydrogen bonds
for NOD•AMPPNP in a similar orientation as (E).
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Figure 2.
Figure 2. L5 and MT Binding Region in NOD Show Unique
Conformation Compared to Other Kinesins
(A) Comparison of
L5 in different kinesin families (gray) after P loop
superposition. The N-terminal half of L5 in NOD (blue) packs
against α3.
(B) Detailed view of L5 in NOD (blue) compared
to L5 in kinesin-5 (orange) bound to monastrol (Mon). The pocket
formed by P101 and P102 on L5 and L180, H181, and L184 on α3 is
shown.
(C) NOD•ADP (blue) was superposed with KHC•ADP
(gold) and oriented to show the β5-L8 lobe.
(D–F) NOD's
“Sw2 cluster” (blue) is compared to the “ADP-like”
conformation in kinesin-1 ([D], 1bg2, magenta), the
“ATP-like” conformation in kinesin-1 ([E], 1mkj, gold), and
KIF2C ([F], 1v8j, red). View is from the MT binding surface.
Clockwise rotation of NOD's α4 relative to kinesin-1's α4 is
highlighted in (D) and (E).
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The above figures are
reprinted
from an Open Access publication published by Cell Press:
Cell
(2009,
136,
110-122)
copyright 2009.
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