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PDBsum entry 2pni
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Phosphotransferase
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PDB id
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2pni
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Contents |
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* Residue conservation analysis
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DOI no:
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Cell
73:813-822
(1993)
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PubMed id:
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Solution structure and ligand-binding site of the SH3 domain of the p85 alpha subunit of phosphatidylinositol 3-kinase.
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G.W.Booker,
I.Gout,
A.K.Downing,
P.C.Driscoll,
J.Boyd,
M.D.Waterfield,
I.D.Campbell.
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ABSTRACT
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SH3 domains are found in proteins associated with receptor tyrosine kinase
signal transduction complexes. The solution structure of the SH3 domain of the
85 kd regulatory subunit of phosphatidylinositol 3-kinase is shown to be a
compact beta barrel consisting of five beta strands arranged in two beta sheets
of three and two strands. The structure is similar to that of chicken brain
alpha spectrin but represents a distinct class of SH3 domain, with an insertion
between the second and third beta strands that may influence binding
specificity. 1H chemical shift changes induced by complex formation with a
synthetic peptide derived from the SH3-binding protein dynamin, together with
amino acid sequence comparisons, suggest that the ligand-binding site consists
of a hydrophobic surface flanked by two charged loops.
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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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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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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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R.Sulahian,
O.Cleaver,
and
L.J.Huang
(2009).
Ligand-induced EpoR internalization is mediated by JAK2 and p85 and is impaired by mutations responsible for primary familial and congenital polycythemia.
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Blood,
113,
5287-5297.
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A.Orte,
N.R.Birkett,
R.W.Clarke,
G.L.Devlin,
C.M.Dobson,
and
D.Klenerman
(2008).
Direct characterization of amyloidogenic oligomers by single-molecule fluorescence.
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Proc Natl Acad Sci U S A,
105,
14424-14429.
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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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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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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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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.Ventura,
J.Zurdo,
S.Narayanan,
M.Parreño,
R.Mangues,
B.Reif,
F.Chiti,
E.Giannoni,
C.M.Dobson,
F.X.Aviles,
and
L.Serrano
(2004).
Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case.
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Proc Natl Acad Sci U S A,
101,
7258-7263.
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J.C.Ferreon,
and
V.J.Hilser
(2003).
Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling.
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Protein Sci,
12,
982-996.
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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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M.Vidal,
V.Gigoux,
and
C.Garbay
(2001).
SH2 and SH3 domains as targets for anti-proliferative agents.
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Crit Rev Oncol Hematol,
40,
175-186.
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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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A.K.Chamberlain,
C.E.MacPhee,
J.Zurdo,
L.A.Morozova-Roche,
H.A.Hill,
C.M.Dobson,
and
J.J.Davis
(2000).
Ultrastructural organization of amyloid fibrils by atomic force microscopy.
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Biophys J,
79,
3282-3293.
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B.J.Irvin,
B.L.Williams,
A.E.Nilson,
H.O.Maynor,
and
R.T.Abraham
(2000).
Pleiotropic contributions of phospholipase C-gamma1 (PLC-gamma1) to T-cell antigen receptor-mediated signaling: reconstitution studies of a PLC-gamma1-deficient Jurkat T-cell line.
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Mol Cell Biol,
20,
9149-9161.
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N.Okishio,
M.Nagai,
R.Fukuda,
S.Nagatomo,
and
T.Kitagawa
(2000).
Interactions of phosphatidylinositol 3-kinase Src homology 3 domain with its ligand peptide studied by absorption, circular dichroism, and UV resonance raman spectroscopies.
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Biopolymers,
57,
208-217.
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T.Tominaga,
E.Sahai,
P.Chardin,
F.McCormick,
S.A.Courtneidge,
and
A.S.Alberts
(2000).
Diaphanous-related formins bridge Rho GTPase and Src tyrosine kinase signaling.
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Mol Cell,
5,
13-25.
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Z.S.Zhao,
E.Manser,
and
L.Lim
(2000).
Interaction between PAK and nck: a template for Nck targets and role of PAK autophosphorylation.
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Mol Cell Biol,
20,
3906-3917.
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A.G.Harpur,
M.J.Layton,
P.Das,
M.J.Bottomley,
G.Panayotou,
P.C.Driscoll,
and
M.D.Waterfield
(1999).
Intermolecular interactions of the p85alpha regulatory subunit of phosphatidylinositol 3-kinase.
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J Biol Chem,
274,
12323-12332.
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D.K.Wilkins,
S.B.Grimshaw,
V.Receveur,
C.M.Dobson,
J.A.Jones,
and
L.J.Smith
(1999).
Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques.
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Biochemistry,
38,
16424-16431.
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H.Mano
(1999).
Tec family of protein-tyrosine kinases: an overview of their structure and function.
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Cytokine Growth Factor Rev,
10,
267-280.
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J.L.Jiménez,
J.I.Guijarro,
E.Orlova,
J.Zurdo,
C.M.Dobson,
M.Sunde,
and
H.R.Saibil
(1999).
Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing.
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EMBO J,
18,
815-821.
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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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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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J.Yu,
Y.Zhang,
J.McIlroy,
T.Rordorf-Nikolic,
G.A.Orr,
and
J.M.Backer
(1998).
Regulation of the p85/p110 phosphatidylinositol 3'-kinase: stabilization and inhibition of the p110alpha catalytic subunit by the p85 regulatory subunit.
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Mol Cell Biol,
18,
1379-1387.
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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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R.K.Rasmussen,
H.Ji,
J.S.Eddes,
R.L.Moritz,
G.E.Reid,
R.J.Simpson,
and
D.S.Dorow
(1998).
Two-dimensional electrophoretic analysis of mixed lineage kinase 2 N-terminal domain binding proteins.
|
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Electrophoresis,
19,
809-817.
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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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I.de Mendez,
N.Homayounpour,
and
T.L.Leto
(1997).
Specificity of p47phox SH3 domain interactions in NADPH oxidase assembly and activation.
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Mol Cell Biol,
17,
2177-2185.
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J.R.Engen,
T.E.Smithgall,
W.H.Gmeiner,
and
D.L.Smith
(1997).
Identification and localization of slow, natural, cooperative unfolding in the hematopoietic cell kinase SH3 domain by amide hydrogen exchange and mass spectrometry.
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Biochemistry,
36,
14384-14391.
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K.V.Kishan,
G.Scita,
W.T.Wong,
P.P.Di Fiore,
and
M.E.Newcomer
(1997).
The SH3 domain of Eps8 exists as a novel intertwined dimer.
|
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Nat Struct Biol,
4,
739-743.
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PDB code:
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B.Guan,
B.Hartmann,
Y.H.Kho,
M.Gorczyca,
and
V.Budnik
(1996).
The Drosophila tumor suppressor gene, dlg, is involved in structural plasticity at a glutamatergic synapse.
|
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Curr Biol,
6,
695-706.
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C.J.Morton,
D.J.Pugh,
E.L.Brown,
J.D.Kahmann,
D.A.Renzoni,
and
I.D.Campbell
(1996).
Solution structure and peptide binding of the SH3 domain from human Fyn.
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Structure,
4,
705-714.
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PDB codes:
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F.Parker,
F.Maurier,
I.Delumeau,
M.Duchesne,
D.Faucher,
L.Debussche,
A.Dugue,
F.Schweighoffer,
and
B.Tocque
(1996).
A Ras-GTPase-activating protein SH3-domain-binding protein.
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Mol Cell Biol,
16,
2561-2569.
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M.S.McAlister,
H.R.Mott,
P.A.van der Merwe,
I.D.Campbell,
S.J.Davis,
and
P.C.Driscoll
(1996).
NMR analysis of interacting soluble forms of the cell-cell recognition molecules CD2 and CD48.
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Biochemistry,
35,
5982-5991.
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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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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.
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Protein Sci,
5,
405-413.
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A.E.Gammie,
L.J.Kurihara,
R.B.Vallee,
and
M.D.Rose
(1995).
DNM1, a dynamin-related gene, participates in endosomal trafficking in yeast.
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J Cell Biol,
130,
553-566.
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B.S.Knudsen,
J.Zheng,
S.M.Feller,
J.P.Mayer,
S.K.Burrell,
D.Cowburn,
and
H.Hanafusa
(1995).
Affinity and specificity requirements for the first Src homology 3 domain of the Crk proteins.
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EMBO J,
14,
2191-2198.
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C.S.Abrams,
and
W.Zhao
(1995).
SH3 domains specifically regulate kinase activity of expressed Src family proteins.
|
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J Biol Chem,
270,
333-339.
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D.Fushman,
S.Cahill,
M.A.Lemmon,
J.Schlessinger,
and
D.Cowburn
(1995).
Solution structure of pleckstrin homology domain of dynamin by heteronuclear NMR spectroscopy.
|
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Proc Natl Acad Sci U S A,
92,
816-820.
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D.S.Dorow,
L.Devereux,
G.F.Tu,
G.Price,
J.K.Nicholl,
G.R.Sutherland,
and
R.J.Simpson
(1995).
Complete nucleotide sequence, expression, and chromosomal localisation of human mixed-lineage kinase 2.
|
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Eur J Biochem,
234,
492-500.
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J.A.Simon,
and
S.L.Schreiber
(1995).
Grb2 SH3 binding to peptides from Sos: evaluation of a general model for SH3-ligand interactions.
|
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Chem Biol,
2,
53-60.
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J.Petersen,
D.Weilguny,
R.Egel,
and
O.Nielsen
(1995).
Characterization of fus1 of Schizosaccharomyces pombe: a developmentally controlled function needed for conjugation.
|
| |
Mol Cell Biol,
15,
3697-3707.
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K.Alexandropoulos,
G.Cheng,
and
D.Baltimore
(1995).
Proline-rich sequences that bind to Src homology 3 domains with individual specificities.
|
| |
Proc Natl Acad Sci U S A,
92,
3110-3114.
|
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L.H.Wang,
T.C.Südhof,
and
R.G.Anderson
(1995).
The appendage domain of alpha-adaptin is a high affinity binding site for dynamin.
|
| |
J Biol Chem,
270,
10079-10083.
|
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M.Puliti,
D.Radzioch,
R.Mazzolla,
R.Barluzzi,
F.Bistoni,
and
E.Blasi
(1995).
Influence of the Bcg locus on macrophage response to the dimorphic fungus Candida albicans.
|
| |
Infect Immun,
63,
4170-4173.
|
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M.Sudol,
P.Bork,
A.Einbond,
K.Kastury,
T.Druck,
M.Negrini,
K.Huebner,
and
D.Lehman
(1995).
Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain.
|
| |
J Biol Chem,
270,
14733-14741.
|
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S.Feng,
C.Kasahara,
R.J.Rickles,
and
S.L.Schreiber
(1995).
Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands.
|
| |
Proc Natl Acad Sci U S A,
92,
12408-12415.
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PDB codes:
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T.Erpel,
G.Superti-Furga,
and
S.A.Courtneidge
(1995).
Mutational analysis of the Src SH3 domain: the same residues of the ligand binding surface are important for intra- and intermolecular interactions.
|
| |
EMBO J,
14,
963-975.
|
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A.Musacchio,
M.Saraste,
and
M.Wilmanns
(1994).
High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides.
|
| |
Nat Struct Biol,
1,
546-551.
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PDB codes:
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C.H.Barton,
J.K.White,
T.I.Roach,
and
J.M.Blackwell
(1994).
NH2-terminal sequence of macrophage-expressed natural resistance-associated macrophage protein (Nramp) encodes a proline/serine-rich putative Src homology 3-binding domain.
|
| |
J Exp Med,
179,
1683-1687.
|
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C.J.Morton,
and
I.D.Campbell
(1994).
SH3 domains. Molecular 'Velcro'.
|
| |
Curr Biol,
4,
615-617.
|
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D.Cussac,
M.Frech,
and
P.Chardin
(1994).
Binding of the Grb2 SH2 domain to phosphotyrosine motifs does not change the affinity of its SH3 domains for Sos proline-rich motifs.
|
| |
EMBO J,
13,
4011-4021.
|
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D.Kohda,
H.Terasawa,
S.Ichikawa,
K.Ogura,
H.Hatanaka,
V.Mandiyan,
A.Ullrich,
J.Schlessinger,
and
F.Inagaki
(1994).
Solution structure and ligand-binding site of the carboxy-terminal SH3 domain of GRB2.
|
| |
Structure,
2,
1029-1040.
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PDB codes:
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Where a reference describes a PDB structure, the PDB
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