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PDBsum entry 2w5b
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References listed in PDB file
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Key reference
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Title
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Insights into the conformational variability and regulation of human nek2 kinase.
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Authors
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I.Westwood,
D.M.Cheary,
J.E.Baxter,
M.W.Richards,
R.L.Van montfort,
A.M.Fry,
R.Bayliss.
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Ref.
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J Mol Biol, 2009,
386,
476-485.
[DOI no: ]
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PubMed id
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Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above have
been manually determined.
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Abstract
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The Nek family of serine/threonine kinases regulates centrosome and cilia
function; in addition, several of its members are potential targets for drug
discovery. Nek2 is dimeric, is cell cycle regulated and functions in the
separation of centrosomes at G2/M. Here, we report the crystal structures of
wild-type human Nek2 kinase domain bound to ADP at 1.55-A resolution and T175A
mutant in apo form as well as that bound to a non-hydrolyzable ATP analog. These
show that regions of the Nek2 structure around the nucleotide-binding site can
adopt several different but well-defined conformations. None of the
conformations was the same as that observed for the previously reported
inhibitor-bound structure, and the two nucleotides stabilized two conformations.
The structures suggest mechanisms for the auto-inhibition of Nek2 that we have
tested by mutagenesis. Comparison of the structures with Aurora-A and Cdk2 gives
insight into the structural mechanism of Nek2 activation. The production of
specific inhibitors that target individual kinases of the human genome is an
urgent challenge in drug discovery, and Nek2 is especially promising as a cancer
target. We not only identify potential challenges to the task of producing Nek2
inhibitors but also propose that the conformational variability provides an
opportunity for the design of Nek2 selective inhibitors because one of the
conformations may provide a unique target.
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Figure 1.
Fig. 1. Electron density maps at the DFG and HRD motifs of
Nek2. (a–c) 2mF[o] − DF[c] (gray) and mF[o] − DF[c]
(green, red) SigmaA-weighted electron density maps contoured at
1.0σ, 2.5σ and − 2.5σ around (a) Nek2-T175A^ATPγS, (b)
Nek2^ADP and (c) Nek2-T175A^Apo, respectively. Carbon atoms are
shown in yellow, orange and pale pink in (a), (b) and (c),
respectively. Oxygen atoms are shown in red, whereas nitrogen
atoms are shown in blue. The same color scheme for stick
representation is used in subsequent figures.
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Figure 2.
Fig. 2. The DFG motif and activation loop adopt different
conformations dependent on the bound ligand. (a) Superposition
of Nek2-T175A^ATPγS (yellow), Nek2^ADP (orange) and
Nek2-T175A^SU (green) protein structures shown as a ribbon in
two orientations related by a 90° rotation about the y-axis.
(b) Stereoview of Nek2-T175A^ATPγS (yellow carbon atoms) and
Nek2^ADP (orange carbon atoms) superposition at the DFG motif.
(c) Stereoview of Nek2-T175A^ATPγS (yellow carbon atoms) and
Nek2-T175A^SU (green carbon atoms) superposition at the DFG
motif. (d) Stereoview of Nek2-T175A^ATPγS (yellow carbon atoms)
and Nek2-T175A^Apo (light pink carbon atoms) superposition at
the DFG motif. (e) Schematic of the secondary structures adopted
by the four Nek2 structures and the amino acid sequence
surrounding the DFG motif in Nek2 and Aurora-A. (f)
Superposition of three Nek2 conformations of the DFG motif
together with the likely position adopted in the fully active
conformation based on the Aurora-A/TPX2 structure (magenta). The
orientation is that of panels (b) to (d) viewed from the bottom
left to the top right.
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The above figures are
reprinted
from an Open Access publication published by Elsevier:
J Mol Biol
(2009,
386,
476-485)
copyright 2009.
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