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PDBsum entry 1shf
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Phosphotransferase
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PDB id
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1shf
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.2.7.10.2
- non-specific protein-tyrosine kinase.
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Reaction:
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L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H+
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L-tyrosyl-[protein]
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+
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ATP
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=
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O-phospho-L-tyrosyl-[protein]
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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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Embo J
12:2617-2624
(1993)
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PubMed id:
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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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M.E.Noble,
A.Musacchio,
M.Saraste,
S.A.Courtneidge,
R.K.Wierenga.
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ABSTRACT
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The Src-homology 3 (SH3) region is a protein domain consisting of approximately
60 residues. It occurs in a large number of eukaryotic proteins involved in
signal transduction, cell polarization and membrane--cytoskeleton interactions.
The function is unknown, but it is probably involved in specific
protein--protein interactions. Here we report the crystal structure of the SH3
domain of Fyn (a Src family tyrosine kinase) at 1.9 A resolution. The crystals
have two SH3 molecules per asymmetric unit. These two Fyn SH3 domains are not
related by a local twofold axis. The crystal structures of spectrin and Fyn SH3
domains as well as the solution structure of the Src SH3 domain show that these
all have the same basic fold. A protein domain which has the same topology as
SH3 is present in the prokaryotic regulatory enzyme BirA. The comparison between
the crystal structures of Fyn and spectrin SH3 domains shows that a conserved
surface patch, consisting mainly of aromatic residues, is flanked by two
hairpin-like loops (residues 94-104 and 114-118 in Fyn). These loops are
different in tyrosine kinase and spectrin SH3 domains. They could modulate the
binding properties of the aromatic surface.
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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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M.I.Arbuckle,
N.H.Komiyama,
A.Delaney,
M.Coba,
E.M.Garry,
R.Rosie,
A.J.Allchorne,
L.H.Forsyth,
M.Bence,
H.J.Carlisle,
T.J.O'Dell,
R.Mitchell,
S.M.Fleetwood-Walker,
and
S.G.Grant
(2010).
The SH3 domain of postsynaptic density 95 mediates inflammatory pain through phosphatidylinositol-3-kinase recruitment.
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EMBO Rep,
11,
473-478.
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A.I.Bartlett,
and
S.E.Radford
(2009).
An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms.
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Nat Struct Mol Biol,
16,
582-588.
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G.R.Bowman,
and
V.S.Pande
(2009).
Simulated tempering yields insight into the low-resolution Rosetta scoring functions.
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Proteins,
74,
777-788.
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P.Neudecker,
P.Lundström,
and
L.E.Kay
(2009).
Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding.
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Biophys J,
96,
2045-2054.
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P.J.Farber,
and
A.Mittermaier
(2008).
Side chain burial and hydrophobic core packing in protein folding transition states.
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Protein Sci,
17,
644-651.
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R.Merkl,
and
M.Zwick
(2008).
H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.
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BMC Bioinformatics,
9,
151.
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N.Dimasi
(2007).
Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction.
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Int J Biochem Cell Biol,
39,
109-123.
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PDB code:
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P.Neudecker,
A.Zarrine-Afsar,
A.R.Davidson,
and
L.E.Kay
(2007).
Phi-value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy.
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Proc Natl Acad Sci U S A,
104,
15717-15722.
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Q.Wang,
M.A.Deloia,
Y.Kang,
C.Litchke,
N.Zhang,
M.A.Titus,
and
K.J.Walters
(2007).
The SH3 domain of a M7 interacts with its C-terminal proline-rich region.
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Protein Sci,
16,
189-196.
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PDB code:
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S.D.Stamenova,
M.E.French,
Y.He,
S.A.Francis,
Z.B.Kramer,
and
L.Hicke
(2007).
Ubiquitin binds to and regulates a subset of SH3 domains.
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Mol Cell,
25,
273-284.
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A.Zarrine-Afsar,
A.Mittermaier,
L.E.Kay,
and
A.R.Davidson
(2006).
Protein stabilization by specific binding of guanidinium to a functional arginine-binding surface on an SH3 domain.
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Protein Sci,
15,
162-170.
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K.Tatebayashi,
K.Yamamoto,
K.Tanaka,
T.Tomida,
T.Maruoka,
E.Kasukawa,
and
H.Saito
(2006).
Adaptor functions of Cdc42, Ste50, and Sho1 in the yeast osmoregulatory HOG MAPK pathway.
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EMBO J,
25,
3033-3044.
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D.Segal,
and
M.Eisenstein
(2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
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Proteins,
59,
580-591.
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M.Habeck,
M.Nilges,
and
W.Rieping
(2005).
Replica-exchange Monte Carlo scheme for bayesian data analysis.
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Phys Rev Lett,
94,
018105.
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W.Rieping,
M.Habeck,
and
M.Nilges
(2005).
Inferential structure determination.
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Science,
309,
303-306.
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PDB code:
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A.A.Di Nardo,
D.M.Korzhnev,
P.J.Stogios,
A.Zarrine-Afsar,
L.E.Kay,
and
A.R.Davidson
(2004).
Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation.
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Proc Natl Acad Sci U S A,
101,
7954-7959.
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A.Berchanski,
B.Shapira,
and
M.Eisenstein
(2004).
Hydrophobic complementarity in protein-protein docking.
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Proteins,
56,
130-142.
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A.Mittermaier,
and
L.E.Kay
(2004).
The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase.
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Protein Sci,
13,
1088-1099.
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D.M.Korzhnev,
X.Salvatella,
M.Vendruscolo,
A.A.Di Nardo,
A.R.Davidson,
C.M.Dobson,
and
L.E.Kay
(2004).
Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR.
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Nature,
430,
586-590.
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J.E.Ollerenshaw,
H.Kaya,
H.S.Chan,
and
L.E.Kay
(2004).
Sparsely populated folding intermediates of the Fyn SH3 domain: matching native-centric essential dynamics and experiment.
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Proc Natl Acad Sci U S A,
101,
14748-14753.
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N.Lu,
D.J.Guarnieri,
and
M.A.Simon
(2004).
Localization of Tec29 to ring canals is mediated by Src64 and PtdIns(3,4,5)P3-dependent mechanisms.
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EMBO J,
23,
1089-1100.
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B.Chan,
A.Lanyi,
H.K.Song,
J.Griesbach,
M.Simarro-Grande,
F.Poy,
D.Howie,
J.Sumegi,
C.Terhorst,
and
M.J.Eck
(2003).
SAP couples Fyn to SLAM immune receptors.
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Nat Cell Biol,
5,
155-160.
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PDB code:
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Q.Liu,
D.Berry,
P.Nash,
T.Pawson,
C.J.McGlade,
and
S.S.Li
(2003).
Structural basis for specific binding of the Gads SH3 domain to an RxxK motif-containing SLP-76 peptide: a novel mode of peptide recognition.
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Mol Cell,
11,
471-481.
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PDB code:
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H.Delbrück,
G.Ziegelin,
E.Lanka,
and
U.Heinemann
(2002).
An Src homology 3-like domain is responsible for dimerization of the repressor protein KorB encoded by the promiscuous IncP plasmid RP4.
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J Biol Chem,
277,
4191-4198.
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PDB codes:
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T.S.Ulmer,
J.M.Werner,
and
I.D.Campbell
(2002).
SH3-SH2 domain orientation in Src kinases: NMR studies of Fyn.
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Structure,
10,
901-911.
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A.Chapman-Smith,
T.D.Mulhern,
F.Whelan,
J.E.Cronan,
and
J.C.Wallace
(2001).
The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity.
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Protein Sci,
10,
2608-2617.
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L.H.Weaver,
K.Kwon,
D.Beckett,
and
B.W.Matthews
(2001).
Competing protein:protein interactions are proposed to control the biological switch of the E coli biotin repressor.
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Protein Sci,
10,
2618-2622.
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PDB codes:
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M.Nishida,
K.Nagata,
Y.Hachimori,
M.Horiuchi,
K.Ogura,
V.Mandiyan,
J.Schlessinger,
and
F.Inagaki
(2001).
Novel recognition mode between Vav and Grb2 SH3 domains.
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EMBO J,
20,
2995-3007.
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PDB codes:
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H.Kang,
C.Freund,
J.S.Duke-Cohan,
A.Musacchio,
G.Wagner,
and
C.E.Rudd
(2000).
SH3 domain recognition of a proline-independent tyrosine-based RKxxYxxY motif in immune cell adaptor SKAP55.
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EMBO J,
19,
2889-2899.
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K.Kwon,
and
D.Beckett
(2000).
Function of a conserved sequence motif in biotin holoenzyme synthetases.
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Protein Sci,
9,
1530-1539.
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A.Chapman-Smith,
and
J.E.Cronan
(1999).
In vivo enzymatic protein biotinylation.
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Biomol Eng,
16,
119-125.
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J.Myllyharju,
and
K.I.Kivirikko
(1999).
Identification of a novel proline-rich peptide-binding domain in prolyl 4-hydroxylase.
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EMBO J,
18,
306-312.
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A.J.Chien,
T.Gao,
E.Perez-Reyes,
and
M.M.Hosey
(1998).
Membrane targeting of L-type calcium channels. Role of palmitoylation in the subcellular localization of the beta2a subunit.
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J Biol Chem,
273,
23590-23597.
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A.Wechsler,
and
V.I.Teichberg
(1998).
Brain spectrin binding to the NMDA receptor is regulated by phosphorylation, calcium and calmodulin.
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EMBO J,
17,
3931-3939.
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D.J.Owen,
P.Wigge,
Y.Vallis,
J.D.Moore,
P.R.Evans,
and
H.T.McMahon
(1998).
Crystal structure of the amphiphysin-2 SH3 domain and its role in the prevention of dynamin ring formation.
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EMBO J,
17,
5273-5285.
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PDB code:
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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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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.Steven,
T.J.Kubiseski,
H.Zheng,
S.Kulkarni,
J.Mancillas,
A.Ruiz Morales,
C.W.Hogue,
T.Pawson,
and
J.Culotti
(1998).
UNC-73 activates the Rac GTPase and is required for cell and growth cone migrations in C. elegans.
|
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Cell,
92,
785-795.
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S.Arold,
R.O'Brien,
P.Franken,
M.P.Strub,
F.Hoh,
C.Dumas,
and
J.E.Ladbury
(1998).
RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef.
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Biochemistry,
37,
14683-14691.
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PDB code:
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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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J.E.Gready,
S.Ranganathan,
P.R.Schofield,
Y.Matsuo,
and
K.Nishikawa
(1997).
Predicted structure of the extracellular region of ligand-gated ion-channel receptors shows SH2-like and SH3-like domains forming the ligand-binding site.
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Protein Sci,
6,
983-998.
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K.S.Thorn,
H.E.Christensen,
R.Shigeta,
D.Huddler,
L.Shalaby,
U.Lindberg,
N.H.Chua,
and
C.E.Schutt
(1997).
The crystal structure of a major allergen from plants.
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Structure,
5,
19-32.
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PDB codes:
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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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M.I.Wahl,
A.C.Fluckiger,
R.M.Kato,
H.Park,
O.N.Witte,
and
D.J.Rawlings
(1997).
Phosphorylation of two regulatory tyrosine residues in the activation of Bruton's tyrosine kinase via alternative receptors.
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Proc Natl Acad Sci U S A,
94,
11526-11533.
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S.Arold,
P.Franken,
M.P.Strub,
F.Hoh,
S.Benichou,
R.Benarous,
and
C.Dumas
(1997).
The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling.
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Structure,
5,
1361-1372.
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PDB codes:
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T.Lila,
and
D.G.Drubin
(1997).
Evidence for physical and functional interactions among two Saccharomyces cerevisiae SH3 domain proteins, an adenylyl cyclase-associated protein and the actin cytoskeleton.
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Mol Biol Cell,
8,
367-385.
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A.Weijland,
G.Neubauer,
S.A.Courtneidge,
M.Mann,
R.K.Wierenga,
and
G.Superti-Furga
(1996).
The purification and characterization of the catalytic domain of Src expressed in Schizosaccharomyces pombe. Comparison of unphosphorylated and tyrosine phosphorylated species.
|
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Eur J Biochem,
240,
756-764.
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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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D.A.Renzoni,
D.J.Pugh,
G.Siligardi,
P.Das,
C.J.Morton,
C.Rossi,
M.D.Waterfield,
I.D.Campbell,
and
J.E.Ladbury
(1996).
Structural and thermodynamic characterization of the interaction of the SH3 domain from Fyn with the proline-rich binding site on the p85 subunit of PI3-kinase.
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Biochemistry,
35,
15646-15653.
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PDB codes:
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D.E.Afar,
H.Park,
B.W.Howell,
D.J.Rawlings,
J.Cooper,
and
O.N.Witte
(1996).
Regulation of Btk by Src family tyrosine kinases.
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| |
Mol Cell Biol,
16,
3465-3471.
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D.M.van Aalten,
A.Amadei,
R.Bywater,
J.B.Findlay,
H.J.Berendsen,
C.Sander,
and
P.F.Stouten
(1996).
A comparison of structural and dynamic properties of different simulation methods applied to SH3.
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Biophys J,
70,
684-692.
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H.Park,
M.I.Wahl,
D.E.Afar,
C.W.Turck,
D.J.Rawlings,
C.Tam,
A.M.Scharenberg,
J.P.Kinet,
and
O.N.Witte
(1996).
Regulation of Btk function by a major autophosphorylation site within the SH3 domain.
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| |
Immunity,
4,
515-525.
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M.T.Brown,
and
J.A.Cooper
(1996).
Regulation, substrates and functions of src.
|
| |
Biochim Biophys Acta,
1287,
121-149.
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M.T.Pisabarro,
and
L.Serrano
(1996).
Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain.
|
| |
Biochemistry,
35,
10634-10640.
|
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P.M.Finan,
C.J.Soames,
L.Wilson,
D.L.Nelson,
D.M.Stewart,
O.Truong,
J.J.Hsuan,
and
S.Kellie
(1996).
Identification of regions of the Wiskott-Aldrich syndrome protein responsible for association with selected Src homology 3 domains.
|
| |
J Biol Chem,
271,
26291-26295.
|
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S.C.Bunnell,
P.A.Henry,
R.Kolluri,
T.Kirchhausen,
R.J.Rickles,
and
L.J.Berg
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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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}
}
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