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PDBsum entry 1w2d
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References listed in PDB file
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Key reference
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Title
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Structure of a human inositol 1,4,5-Trisphosphate 3-Kinase: substrate binding reveals why it is not a phosphoinositide 3-Kinase.
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Authors
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B.González,
M.J.Schell,
A.J.Letcher,
D.B.Veprintsev,
R.F.Irvine,
R.L.Williams.
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Ref.
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Mol Cell, 2004,
15,
689-701.
[DOI no: ]
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PubMed id
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Abstract
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Mammalian cells produce a variety of inositol phosphates (InsPs), including
Ins(1,4,5)P3 that serves both as a second messenger and as a substrate for
inositol polyphosphate kinases (IPKs), which further phosphorylate it. We report
the structure of an IPK, the human Ins(1,4,5)P3 3-kinase-A, both free and in
complexes with substrates and products. This enzyme catalyzes transfer of a
phosphate from ATP to the 3-OH of Ins(1,4,5)P3, and its X-ray crystal structure
provides a template for understanding a broad family of InsP kinases. The
catalytic domain consists of three lobes. The N and C lobes bind ATP and
resemble protein and lipid kinases, despite insignificant sequence similarity.
The third lobe binds inositol phosphate and is a unique four-helix insertion in
the C lobe. This lobe embraces all of the phosphates of Ins(1,4,5)P3 in a
positively charged pocket, explaining the enzyme's substrate specificity and its
inability to phosphorylate PtdIns(4,5)P2, the membrane-resident analog of
Ins(1,4,5)P3.
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Figure 1.
Figure 1. The Overall Fold of IP[3]-3K Catalytic Domain(A)
A ribbon diagram of IP[3]-3K in a complex with
Mn^2+/AMPPNP/Ins(1,4,5)P[3]. The N lobe is colored orange, the C
lobe yellow, the IP lobe purple, and the hinge green. The
conserved IDFG, GSSLL, and DxK motifs are colored pink, cyan,
and brown, respectively. This and all other molecular
illustrations were prepared with PYMOL.(B) A topology diagram of
the catalytic domain. Helix α0[N] is ordered only in the
absence of substrates or products. The dashed arrow indicates an
additional strand that would be characteristic of the N lobes of
PKs.(C) Ribbon diagrams of the catalytic domains of PI3Kγ and
PIPKIIβ with N and C lobes colored as in (A).
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Figure 3.
Figure 3. Substrate Binding by IP[3]-3K(A) A view of the
active site showing the ATP analog and Ins(1,4,5)P[3] bound to
the enzyme. The subdomains and motifs are colored as in Figure
1. Side chains interacting with the ligands are shown as sticks
and ligand-bound water molecules as white spheres.(B) A
schematic of the interactions with the ligands made with
LIGPLOT.(C) A surface illustration of the IP[3]-3K catalytic
domain colored by electrostatic potential with negatively
charged regions red and positive blue. The bound AMPPNP is shown
as green sticks and the Ins(1,4,5)P[3] as yellow sticks.(D) A
close-up of the ATP binding pocket in the presence of AMPPNP
(left) and in its absence (right), showing Trp188 and His194
from the putative auto-inhibitory region mimicking the
interactions formed by ATP.
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The above figures are
reprinted
by permission from Cell Press:
Mol Cell
(2004,
15,
689-701)
copyright 2004.
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