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PDBsum entry 2pna
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Signalling protein
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PDB id
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2pna
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* Residue conservation analysis
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Enzyme class:
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E.C.2.7.1.137
- phosphatidylinositol 3-kinase.
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Pathway:
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1-Phosphatidyl-myo-inositol Metabolism
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Reaction:
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a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + ATP = a 1,2-diacyl- sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + ADP + H+
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1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol)
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+
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ATP
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=
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1,2-diacyl- sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate)
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+
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ADP
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Nature
358:684-687
(1992)
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PubMed id:
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Structure of an SH2 domain of the p85 alpha subunit of phosphatidylinositol-3-OH kinase.
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G.W.Booker,
A.L.Breeze,
A.K.Downing,
G.Panayotou,
I.Gout,
M.D.Waterfield,
I.D.Campbell.
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ABSTRACT
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Receptor protein-tyrosine kinases, through phosphorylation of specific tyrosine
residues, generate high-affinity binding sites which direct assembly of
multienzyme signalling complexes. Many of these signalling proteins, including
phospholipase C gamma, GTPase-activating protein and phosphatidylinositol-3-OH
kinase, contain src-homology 2 (SH2) domains, which bind with high affinity and
specificity to tyrosine-phosphorylated sequences. The critical role played by
SH2 domains in signalling has been highlighted by recent studies showing that
mutation of specific phosphorylation sites on the platelet-derived growth factor
receptor impair its association with phosphatidylinositol-3-OH kinase,
preventing growth factor-induced mitogenesis. Here we report the solution
structure of an isolated SH2 domain from the 85K regulatory subunit of
phosphatidylinositol-3-OH kinase, determined using multidimensional nuclear
magnetic resonance spectroscopy. The structure is characterized by a central
region of beta-sheet flanked by two alpha-helices, with a highly flexible loop
close to functionally important residues previously identified by site-directed
mutagenesis.
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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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S.B.Gabelli,
D.Mandelker,
O.Schmidt-Kittler,
B.Vogelstein,
and
L.M.Amzel
(2010).
Somatic mutations in PI3Kalpha: structural basis for enzyme activation and drug design.
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Biochim Biophys Acta,
1804,
533-540.
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A.Arcaro,
and
A.S.Guerreiro
(2007).
The phosphoinositide 3-kinase pathway in human cancer: genetic alterations and therapeutic implications.
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Curr Genomics,
8,
271-306.
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B.A.Liu,
K.Jablonowski,
M.Raina,
M.Arcé,
T.Pawson,
and
P.D.Nash
(2006).
The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling.
|
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Mol Cell,
22,
851-868.
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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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S.C.Shekar,
H.Wu,
Z.Fu,
S.C.Yip,
Nagajyothi,
S.M.Cahill,
M.E.Girvin,
and
J.M.Backer
(2005).
Mechanism of constitutive phosphoinositide 3-kinase activation by oncogenic mutants of the p85 regulatory subunit.
|
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J Biol Chem,
280,
27850-27855.
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J.E.Kohn,
I.S.Millett,
J.Jacob,
B.Zagrovic,
T.M.Dillon,
N.Cingel,
R.S.Dothager,
S.Seifert,
P.Thiyagarajan,
T.R.Sosnick,
M.Z.Hasan,
V.S.Pande,
I.Ruczinski,
S.Doniach,
and
K.W.Plaxco
(2004).
Random-coil behavior and the dimensions of chemically unfolded proteins.
|
| |
Proc Natl Acad Sci U S A,
101,
12491-12496.
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P.Peschard,
N.Ishiyama,
T.Lin,
S.Lipkowitz,
and
M.Park
(2004).
A conserved DpYR motif in the juxtamembrane domain of the Met receptor family forms an atypical c-Cbl/Cbl-b tyrosine kinase binding domain binding site required for suppression of oncogenic activation.
|
| |
J Biol Chem,
279,
29565-29571.
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D.D.Ojennus,
S.E.Lehto,
and
D.S.Wuttke
(2003).
Electrostatic interactions in the reconstitution of an SH2 domain from constituent peptide fragments.
|
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Protein Sci,
12,
44-55.
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M.N.Holowaty,
Y.Sheng,
T.Nguyen,
C.Arrowsmith,
and
L.Frappier
(2003).
Protein interaction domains of the ubiquitin-specific protease, USP7/HAUSP.
|
| |
J Biol Chem,
278,
47753-47761.
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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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D.D.Ojennus,
M.R.Fleissner,
and
D.S.Wuttke
(2001).
Reconstitution of a native-like SH2 domain from disordered peptide fragments examined by multidimensional heteronuclear NMR.
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Protein Sci,
10,
2162-2175.
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R.A.Pauptit,
C.A.Dennis,
D.J.Derbyshire,
A.L.Breeze,
S.A.Weston,
S.Rowsell,
and
G.N.Murshudov
(2001).
NMR trial models: experiences with the colicin immunity protein Im7 and the p85alpha C-terminal SH2-peptide complex.
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Acta Crystallogr D Biol Crystallogr,
57,
1397-1404.
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PDB code:
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K.Palo,
U.Mets,
S.Jäger,
P.Kask,
and
K.Gall
(2000).
Fluorescence intensity multiple distributions analysis: concurrent determination of diffusion times and molecular brightness.
|
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Biophys J,
79,
2858-2866.
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R.O'Brien,
P.Rugman,
D.Renzoni,
M.Layton,
R.Handa,
K.Hilyard,
M.D.Waterfield,
P.C.Driscoll,
and
J.E.Ladbury
(2000).
Alternative modes of binding of proteins with tandem SH2 domains.
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Protein Sci,
9,
570-579.
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T.Weber,
B.Schaffhausen,
Y.Liu,
and
U.L.Günther
(2000).
NMR structure of the N-SH2 of the p85 subunit of phosphoinositide 3-kinase complexed to a doubly phosphorylated peptide reveals a second phosphotyrosine binding site.
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Biochemistry,
39,
15860-15869.
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PDB codes:
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P.L.Surdo,
M.J.Bottomley,
A.Arcaro,
G.Siegal,
G.Panayotou,
A.Sankar,
P.R.Gaffney,
A.M.Riley,
B.V.Potter,
M.D.Waterfield,
and
P.C.Driscoll
(1999).
Structural and biochemical evaluation of the interaction of the phosphatidylinositol 3-kinase p85alpha Src homology 2 domains with phosphoinositides and inositol polyphosphates.
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J Biol Chem,
274,
15678-15685.
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R.A.Grucza,
J.M.Bradshaw,
K.Fütterer,
and
G.Waksman
(1999).
SH2 domains: from structure to energetics, a dual approach to the study of structure-function relationships.
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Med Res Rev,
19,
273-293.
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D.A.Fruman,
R.E.Meyers,
and
L.C.Cantley
(1998).
Phosphoinositide kinases.
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Annu Rev Biochem,
67,
481-507.
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E.A.Ottinger,
M.C.Botfield,
and
S.E.Shoelson
(1998).
Tandem SH2 domains confer high specificity in tyrosine kinase signaling.
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J Biol Chem,
273,
729-735.
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J.Dorrestijn,
F.J.van Bussel,
J.A.Maassen,
and
D.S.Gomes de Mesquita
(1998).
Early steps in insulin action.
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Arch Physiol Biochem,
106,
269-289.
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K.L.Maxwell,
and
A.R.Davidson
(1998).
Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects.
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Biochemistry,
37,
16172-16182.
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J.Kuriyan,
and
D.Cowburn
(1997).
Modular peptide recognition domains in eukaryotic signaling.
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Annu Rev Biophys Biomol Struct,
26,
259-288.
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P.S.Charifson,
L.M.Shewchuk,
W.Rocque,
C.W.Hummel,
S.R.Jordan,
C.Mohr,
G.J.Pacofsky,
M.R.Peel,
M.Rodriguez,
D.D.Sternbach,
and
T.G.Consler
(1997).
Peptide ligands of pp60(c-src) SH2 domains: a thermodynamic and structural study.
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Biochemistry,
36,
6283-6293.
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PDB codes:
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T.D.Mulhern,
G.L.Shaw,
C.J.Morton,
A.J.Day,
and
I.D.Campbell
(1997).
The SH2 domain from the tyrosine kinase Fyn in complex with a phosphotyrosyl peptide reveals insights into domain stability and binding specificity.
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Structure,
5,
1313-1323.
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PDB codes:
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A.L.Breeze,
B.V.Kara,
D.G.Barratt,
M.Anderson,
J.C.Smith,
R.W.Luke,
J.R.Best,
and
S.A.Cartlidge
(1996).
Structure of a specific peptide complex of the carboxy-terminal SH2 domain from the p85 alpha subunit of phosphatidylinositol 3-kinase.
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EMBO J,
15,
3579-3589.
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PDB code:
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J.J.Barchi,
M.Nomizu,
A.Otaka,
P.P.Roller,
and
T.R.Burke
(1996).
Conformational analysis of cyclic hexapeptides designed as constrained ligands for the SH2 domain of the p85 subunit of phosphatidylinositol-3-OH kinase.
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Biopolymers,
38,
191-208.
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J.Rahuel,
B.Gay,
D.Erdmann,
A.Strauss,
C.Garcia-Echeverría,
P.Furet,
G.Caravatti,
H.Fretz,
J.Schoepfer,
and
M.G.Grütter
(1996).
Structural basis for specificity of Grb2-SH2 revealed by a novel ligand binding mode.
|
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Nat Struct Biol,
3,
586-589.
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PDB code:
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K.H.Thornton,
W.T.Mueller,
P.McConnell,
G.Zhu,
A.R.Saltiel,
and
V.Thanabal
(1996).
Nuclear magnetic resonance solution structure of the growth factor receptor-bound protein 2 Src homology 2 domain.
|
| |
Biochemistry,
35,
11852-11864.
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PDB code:
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K.Müller,
F.O.Gombert,
U.Manning,
F.Grossmüller,
P.Graff,
H.Zaegel,
J.F.Zuber,
F.Freuler,
C.Tschopp,
and
G.Baumann
(1996).
Rapid identification of phosphopeptide ligands for SH2 domains. Screening of peptide libraries by fluorescence-activated bead sorting.
|
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J Biol Chem,
271,
16500-16505.
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R.T.Nolte,
M.J.Eck,
J.Schlessinger,
S.E.Shoelson,
and
S.C.Harrison
(1996).
Crystal structure of the PI 3-kinase p85 amino-terminal SH2 domain and its phosphopeptide complexes.
|
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Nat Struct Biol,
3,
364-374.
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PDB codes:
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S.Réty,
K.Fütterer,
R.A.Grucza,
C.M.Munoz,
W.A.Frazier,
and
G.Waksman
(1996).
pH-Dependent self-association of the Src homology 2 (SH2) domain of the Src homologous and collagen-like (SHC) protein.
|
| |
Protein Sci,
5,
405-413.
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U.Hemmann,
C.Gerhartz,
B.Heesel,
J.Sasse,
G.Kurapkat,
J.Grötzinger,
A.Wollmer,
Z.Zhong,
J.E.Darnell,
L.Graeve,
P.C.Heinrich,
and
F.Horn
(1996).
Differential activation of acute phase response factor/Stat3 and Stat1 via the cytoplasmic domain of the interleukin 6 signal transducer gp130. II. Src homology SH2 domains define the specificity of stat factor activation.
|
| |
J Biol Chem,
271,
12999-13007.
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U.L.Günther,
Y.Liu,
D.Sanford,
W.W.Bachovchin,
and
B.Schaffhausen
(1996).
NMR analysis of interactions of a phosphatidylinositol 3'-kinase SH2 domain with phosphotyrosine peptides reveals interdependence of major binding sites.
|
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Biochemistry,
35,
15570-15581.
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W.J.Metzler,
B.Leiting,
K.Pryor,
L.Mueller,
and
B.T.Farmer
(1996).
The three-dimensional solution structure of the SH2 domain from p55blk kinase.
|
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Biochemistry,
35,
6201-6211.
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PDB codes:
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B.Schaffhausen
(1995).
SH2 domain structure and function.
|
| |
Biochim Biophys Acta,
1242,
61-75.
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E.M.Phizicky,
and
S.Fields
(1995).
Protein-protein interactions: methods for detection and analysis.
|
| |
Microbiol Rev,
59,
94.
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H.Flaswinkel,
M.Barner,
and
M.Reth
(1995).
The tyrosine activation motif as a target of protein tyrosine kinases and SH2 domains.
|
| |
Semin Immunol,
7,
21-27.
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K.M.Shokat
(1995).
Tyrosine kinases: modular signaling enzymes with tunable specificities.
|
| |
Chem Biol,
2,
509-514.
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S.S.Narula,
R.W.Yuan,
S.E.Adams,
O.M.Green,
J.Green,
T.B.Philips,
L.D.Zydowsky,
M.C.Botfield,
M.Hatada,
and
E.R.Laird
(1995).
Solution structure of the C-terminal SH2 domain of the human tyrosine kinase Syk complexed with a phosphotyrosine pentapeptide.
|
| |
Structure,
3,
1061-1073.
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PDB codes:
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C.H.Lee,
D.Kominos,
S.Jacques,
B.Margolis,
J.Schlessinger,
S.E.Shoelson,
and
J.Kuriyan
(1994).
Crystal structures of peptide complexes of the amino-terminal SH2 domain of the Syp tyrosine phosphatase.
|
| |
Structure,
2,
423-438.
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PDB codes:
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C.M.Pleiman,
C.Abrams,
L.T.Gauen,
W.Bedzyk,
J.Jongstra,
A.S.Shaw,
and
J.C.Cambier
(1994).
Distinct p53/56lyn and p59fyn domains associate with nonphosphorylated and phosphorylated Ig-alpha.
|
| |
Proc Natl Acad Sci U S A,
91,
4268-4272.
|
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|
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D.Liu,
and
L.H.Wang
(1994).
Oncogenes, Protein Tyrosine Kinases, and Signal Transduction.
|
| |
J Biomed Sci,
1,
65-82.
|
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G.L.Johnson,
and
R.R.Vaillancourt
(1994).
Sequential protein kinase reactions controlling cell growth and differentiation.
|
| |
Curr Opin Cell Biol,
6,
230-238.
|
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|
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G.Panchamoorthy,
T.Fukazawa,
L.Stolz,
G.Payne,
K.Reedquist,
S.Shoelson,
Z.Songyang,
L.Cantley,
C.Walsh,
and
H.Band
(1994).
Physical and functional interactions between SH2 and SH3 domains of the Src family protein tyrosine kinase p59fyn.
|
| |
Mol Cell Biol,
14,
6372-6385.
|
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K.V.Prasad,
Y.C.Cai,
M.Raab,
B.Duckworth,
L.Cantley,
S.E.Shoelson,
and
C.E.Rudd
(1994).
T-cell antigen CD28 interacts with the lipid kinase phosphatidylinositol 3-kinase by a cytoplasmic Tyr(P)-Met-Xaa-Met motif.
|
| |
Proc Natl Acad Sci U S A,
91,
2834-2838.
|
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|
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M.D.Carr,
C.J.Bauer,
M.J.Gradwell,
and
J.Feeney
(1994).
Solution structure of a trefoil-motif-containing cell growth factor, porcine spasmolytic protein.
|
| |
Proc Natl Acad Sci U S A,
91,
2206-2210.
|
|
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PDB code:
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|
|
M.Hensmann,
G.W.Booker,
G.Panayotou,
J.Boyd,
J.Linacre,
M.Waterfield,
and
I.D.Campbell
(1994).
Phosphopeptide binding to the N-terminal SH2 domain of the p85 alpha subunit of PI 3'-kinase: a heteronuclear NMR study.
|
| |
Protein Sci,
3,
1020-1030.
|
|
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|
|
M.Thelen,
M.P.Wymann,
and
H.Langen
(1994).
Wortmannin binds specifically to 1-phosphatidylinositol 3-kinase while inhibiting guanine nucleotide-binding protein-coupled receptor signaling in neutrophil leukocytes.
|
| |
Proc Natl Acad Sci U S A,
91,
4960-4964.
|
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|
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M.Yoakim,
W.Hou,
Z.Songyang,
Y.Liu,
L.Cantley,
and
B.Schaffhausen
(1994).
Genetic analysis of a phosphatidylinositol 3-kinase SH2 domain reveals determinants of specificity.
|
| |
Mol Cell Biol,
14,
5929-5938.
|
|
|
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|
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R.Dhand,
K.Hara,
I.Hiles,
B.Bax,
I.Gout,
G.Panayotou,
M.J.Fry,
K.Yonezawa,
M.Kasuga,
and
M.D.Waterfield
(1994).
PI 3-kinase: structural and functional analysis of intersubunit interactions.
|
| |
EMBO J,
13,
511-521.
|
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|
|
B.J.Mayer,
and
D.Baltimore
(1993).
Signalling through SH2 and SH3 domains.
|
| |
Trends Cell Biol,
3,
8.
|
|
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|
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C.M.Pleiman,
M.R.Clark,
L.K.Gauen,
S.Winitz,
K.M.Coggeshall,
G.L.Johnson,
A.S.Shaw,
and
J.C.Cambier
(1993).
Mapping of sites on the Src family protein tyrosine kinases p55blk, p59fyn, and p56lyn which interact with the effector molecules phospholipase C-gamma 2, microtubule-associated protein kinase, GTPase-activating protein, and phosphatidylinositol 3-kinase.
|
| |
Mol Cell Biol,
13,
5877-5887.
|
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|
|
E.Friedman,
P.V.Gejman,
G.A.Martin,
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(1993).
Nonsense mutations in the C-terminal SH2 region of the GTPase activating protein (GAP) gene in human tumours.
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Nat Genet,
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G.Panayotou,
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and
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(1993).
Solution structure and ligand-binding site of the SH3 domain of the p85 alpha subunit of phosphatidylinositol 3-kinase.
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| |
Cell,
73,
813-822.
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|
PDB codes:
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|
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|
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|
|
L.Stephens,
A.Eguinoa,
S.Corey,
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Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin.
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PDB code:
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M.J.Fry,
G.Panayotou,
G.W.Booker,
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Specific phosphopeptide binding regulates a conformational change in the PI 3-kinase SH2 domain associated with enzyme activation.
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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
code is
shown on the right.
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|
Links
