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PDBsum entry 1pht
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Phosphotransferase
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PDB id
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1pht
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Contents |
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* Residue conservation analysis
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DOI no:
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J Mol Biol
257:632-643
(1996)
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PubMed id:
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Crystal structure of P13K SH3 domain at 20 angstroms resolution.
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J.Liang,
J.K.Chen,
S.T.Schreiber,
J.Clardy.
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ABSTRACT
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The P13K SH3 domain, residues 1 to 85 of the P1-3 kinase p85 subunit, has been
characterized by X-ray diffraction. Crystals belonging to space group P4(3)2(1)2
diffract to 2.0 angstroms resolution and the structure was phased by single
isomorphous replacement and anomalous scattering (SIRAS). As expected, the
domain is a compact beta barrel with an over-all confirmation very similar to
the independently determined NMR structures. The X-ray structure illuminates a
discrepancy between the two NMR structures on the conformation of the loop
region unique to P13K SH3. Furthermore, the ligand binding pockets of P13K SH3
domain are occupied by amino acid residues from symmetry-related P13K SH3
molecules: the C-terminal residues I(82) SPP of one and R18 of another. The
interaction modes clearly resemble those observed for the P13K SH3 domain
complexed with the synthetic peptide RLP1, a class 1 ligand, although there are
significant differences. The solid-state interactions suggest a model of
protein-protein aggregation that could be mediated by SH3 domains.
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Selected figure(s)
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Figure 5.
Figure 5. Stereo view of the PI3K
SH3 domain in C
a
tracing. Non-
charged residues in the ligand
binding area are drawn in black,
negatively charged residues are red
and positively charged residues are
blue.
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Figure 7.
Figure 7. Comparison of interaction modes for PI3K
SH3 domain complexes with: (a) class I peptides; (b)
C-terminal residues of SH3(A and R18 of SH3(B; (c)
class II peptides.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
257,
632-643)
copyright 1996.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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R.Batra-Safferling,
J.Granzin,
S.Mödder,
S.Hoffmann,
and
D.Willbold
(2010).
Structural studies of the phosphatidylinositol 3-kinase (PI3K) SH3 domain in complex with a peptide ligand: role of the anchor residue in ligand binding.
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Biol Chem,
391,
33-42.
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PDB codes:
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H.Wu,
S.C.Shekar,
R.J.Flinn,
M.El-Sibai,
B.S.Jaiswal,
K.I.Sen,
V.Janakiraman,
S.Seshagiri,
G.J.Gerfen,
M.E.Girvin,
and
J.M.Backer
(2009).
Regulation of Class IA PI 3-kinases: C2 domain-iSH2 domain contacts inhibit p85/p110alpha and are disrupted in oncogenic p85 mutants.
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Proc Natl Acad Sci U S A,
106,
20258-20263.
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V.N.Uversky
(2008).
Amyloidogenesis of natively unfolded proteins.
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Curr Alzheimer Res,
5,
260-287.
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F.Nasertorabi,
K.Tars,
K.Becherer,
R.Kodandapani,
L.Liljas,
K.Vuori,
and
K.R.Ely
(2006).
Molecular basis for regulation of Src by the docking protein p130Cas.
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J Mol Recognit,
19,
30-38.
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PDB code:
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H.C.Ahn,
Y.T.Le,
P.S.Nagchowdhuri,
E.F.Derose,
C.Putnam-Evans,
R.E.London,
J.L.Markley,
and
K.H.Lim
(2006).
NMR characterizations of an amyloidogenic conformational ensemble of the PI3K SH3 domain.
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Protein Sci,
15,
2552-2557.
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S.Reich,
L.H.Puckey,
C.L.Cheetham,
R.Harris,
A.A.Ali,
U.Bhattacharyya,
K.Maclagan,
K.A.Powell,
C.Prodromou,
L.H.Pearl,
P.C.Driscoll,
and
R.Savva
(2006).
Combinatorial Domain Hunting: An effective approach for the identification of soluble protein domains adaptable to high-throughput applications.
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Protein Sci,
15,
2356-2365.
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C.Massenet,
S.Chenavas,
C.Cohen-Addad,
M.C.Dagher,
G.Brandolin,
E.Pebay-Peyroula,
and
F.Fieschi
(2005).
Effects of p47phox C terminus phosphorylations on binding interactions with p40phox and p67phox. Structural and functional comparison of p40phox and p67phox SH3 domains.
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J Biol Chem,
280,
13752-13761.
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PDB codes:
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S.Y.Ren,
E.Bolton,
M.G.Mohi,
A.Morrione,
B.G.Neel,
and
T.Skorski
(2005).
Phosphatidylinositol 3-kinase p85{alpha} subunit-dependent interaction with BCR/ABL-related fusion tyrosine kinases: molecular mechanisms and biological consequences.
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Mol Cell Biol,
25,
8001-8008.
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S.Cao,
J.Yao,
and
V.Shah
(2003).
The proline-rich domain of dynamin-2 is responsible for dynamin-dependent in vitro potentiation of endothelial nitric-oxide synthase activity via selective effects on reductase domain function.
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J Biol Chem,
278,
5894-5901.
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S.Djordjevic,
and
P.C.Driscoll
(2002).
Structural insight into substrate specificity and regulatory mechanisms of phosphoinositide 3-kinases.
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Trends Biochem Sci,
27,
426-432.
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N.Okishio,
T.Tanaka,
R.Fukuda,
and
M.Nagai
(2001).
Role of the conserved acidic residue Asp21 in the structure of phosphatidylinositol 3-kinase Src homology 3 domain: circular dichroism and nuclear magnetic resonance studies.
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Biochemistry,
40,
119-129.
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J.I.Guijarro,
M.Sunde,
J.A.Jones,
I.D.Campbell,
and
C.M.Dobson
(1998).
Amyloid fibril formation by an SH3 domain.
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Proc Natl Acad Sci U S A,
95,
4224-4228.
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K.W.Plaxco,
J.I.Guijarro,
C.J.Morton,
M.Pitkeathly,
I.D.Campbell,
and
C.M.Dobson
(1998).
The folding kinetics and thermodynamics of the Fyn-SH3 domain.
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Biochemistry,
37,
2529-2537.
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S.Knapp,
P.T.Mattson,
P.Christova,
K.D.Berndt,
A.Karshikoff,
M.Vihinen,
C.I.Smith,
and
R.Ladenstein
(1998).
Thermal unfolding of small proteins with SH3 domain folding pattern.
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Proteins,
31,
309-319.
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D.C.Dalgarno,
M.C.Botfield,
and
R.J.Rickles
(1997).
SH3 domains and drug design: ligands, structure, and biological function.
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Biopolymers,
43,
383-400.
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H.V.Patel,
S.R.Tzeng,
C.Y.Liao,
S.H.Chen,
and
J.W.Cheng
(1997).
SH3 domain of Bruton's tyrosine kinase can bind to proline-rich peptides of TH domain of the kinase and p120cbl.
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Proteins,
29,
545-552.
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A.J.Wilkinson
(1996).
Accommodating structurally diverse peptides in proteins.
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Chem Biol,
3,
519-524.
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M.T.Pisabarro,
and
L.Serrano
(1996).
Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain.
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Biochemistry,
35,
10634-10640.
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S.J.McClure,
and
P.J.Robinson
(1996).
Dynamin, endocytosis and intracellular signalling (review).
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Mol Membr Biol,
13,
189-215.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
