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Contents |
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* Residue conservation analysis
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Enzyme class:
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Chain A:
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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Nature
362:87-91
(1993)
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PubMed id:
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Recognition of a high-affinity phosphotyrosyl peptide by the Src homology-2 domain of p56lck.
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M.J.Eck,
S.E.Shoelson,
S.C.Harrison.
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ABSTRACT
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The Src homology-2 (SH2) domains are modules of about 100 amino-acid residues
that are found in many intracellular signal-transduction proteins. They bind
phosphotyrosine-containing sequences with high affinity and specificity,
recognizing phosphotyrosine in the context of the immediately adjacent
polypeptide sequence. The protein p56lck (Lck) is a Src-like,
lymphocyte-specific tyrosine kinase. A phosphopeptide library screen has
recently been used to deduce an 'optimal' binding sequence for the Lck SH2
domain. There is selectivity for the residues Glu, Glu and Ile in the three
positions C-terminal to the phosphotyrosine. An 11-residue phosphopeptide
derived from the hamster polyoma middle-T antigen, EPQpYEEIPIYL, binds with an
approximately 1 nM dissociation constant to the Lck SH2 (ref. 17), an affinity
equivalent to that of the tightest known SH2-phosphopeptide complex. We report
here the high-resolution crystallographic analysis of the Lck SH2 domain in
complex with this phosphopeptide. Recent crystallographically derived structures
of the Src SH2 domain in complex with low-affinity peptides, which do not
contain the EEI consensus, and NMR-derived structures of unliganded Abl (ref.
19) and p85 (ref. 20) SH2 domains have revealed the conserved fold of the SH2
domain and the properties of a phosphotyrosine binding pocket. Our high-affinity
complex shows the presence of a second pocket for the residue (pY + 3) three
positions C-terminal to the phosphotyrosine (pY). The peptide is anchored by
insertion of the pY and pY + 3 side chains into their pockets and by a network
of hydrogen bonds to the peptide main chain. In the low-affinity
phosphopeptide/Src complexes, the pY + 3 residues do not insert into the
homologous binding pocket and the peptide main chain remains displaced from the
surface of the domain.
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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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T.Kaneko,
S.S.Sidhu,
and
S.S.Li
(2011).
Evolving specificity from variability for protein interaction domains.
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Trends Biochem Sci,
36,
183-190.
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X.Zhang,
O.Vadas,
O.Perisic,
K.E.Anderson,
J.Clark,
P.T.Hawkins,
L.R.Stephens,
and
R.L.Williams
(2011).
Structure of lipid kinase p110β/p85β elucidates an unusual SH2-domain-mediated inhibitory mechanism.
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Mol Cell,
41,
567-578.
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PDB code:
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J.Wojcik,
O.Hantschel,
F.Grebien,
I.Kaupe,
K.L.Bennett,
J.Barkinge,
R.B.Jones,
A.Koide,
G.Superti-Furga,
and
S.Koide
(2010).
A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain.
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Nat Struct Mol Biol,
17,
519-527.
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PDB code:
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M.W.Harr,
P.F.Caimi,
K.S.McColl,
F.Zhong,
S.N.Patel,
P.M.Barr,
and
C.W.Distelhorst
(2010).
Inhibition of Lck enhances glucocorticoid sensitivity and apoptosis in lymphoid cell lines and in chronic lymphocytic leukemia.
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Cell Death Differ,
17,
1381-1391.
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S.Virdee,
D.Macmillan,
and
G.Waksman
(2010).
Semisynthetic Src SH2 domains demonstrate altered phosphopeptide specificity induced by incorporation of unnatural lysine derivatives.
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Chem Biol,
17,
274-284.
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I.Lappalainen,
J.Thusberg,
B.Shen,
and
M.Vihinen
(2008).
Genome wide analysis of pathogenic SH2 domain mutations.
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Proteins,
72,
779-792.
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J.S.McMurray
(2008).
Structural basis for the binding of high affinity phosphopeptides to Stat3.
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Biopolymers,
90,
69-79.
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A.M.Spuches,
H.J.Argiros,
K.H.Lee,
L.L.Haas,
S.C.Pero,
D.N.Krag,
P.P.Roller,
D.E.Wilcox,
and
B.A.Lyons
(2007).
Calorimetric investigation of phosphorylated and non-phosphorylated peptide ligand binding to the human Grb7-SH2 domain.
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J Mol Recognit,
20,
245-252.
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A.P.Benfield,
B.B.Whiddon,
J.H.Clements,
and
S.F.Martin
(2007).
Structural and energetic aspects of Grb2-SH2 domain-swapping.
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Arch Biochem Biophys,
462,
47-53.
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PDB codes:
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C.J.Porter,
J.M.Matthews,
J.P.Mackay,
S.E.Pursglove,
J.W.Schmidberger,
P.J.Leedman,
S.C.Pero,
D.N.Krag,
M.C.Wilce,
and
J.A.Wilce
(2007).
Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation.
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BMC Struct Biol,
7,
58.
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PDB code:
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S.M.Grande,
G.Bannish,
E.M.Fuentes-Panana,
E.Katz,
and
J.G.Monroe
(2007).
Tonic B-cell and viral ITAM signaling: context is everything.
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Immunol Rev,
218,
214-234.
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E.Bergamin,
J.Wu,
and
S.R.Hubbard
(2006).
Structural basis for phosphotyrosine recognition by suppressor of cytokine signaling-3.
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Structure,
14,
1285-1292.
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PDB code:
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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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K.Hampel,
I.Kaufhold,
M.Zacharias,
F.D.Böhmer,
and
D.Imhof
(2006).
Phosphopeptide ligands of the SHP-1 N-SH2 domain: effects on binding and stimulation of phosphatase activity.
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ChemMedChem,
1,
869-877.
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S.Frese,
W.D.Schubert,
A.C.Findeis,
T.Marquardt,
Y.S.Roske,
T.E.Stradal,
and
D.W.Heinz
(2006).
The phosphotyrosine peptide binding specificity of Nck1 and Nck2 Src homology 2 domains.
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J Biol Chem,
281,
18236-18245.
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PDB codes:
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S.Geroult,
S.Virdee,
and
G.Waksman
(2006).
The role of water in computational and experimental derivation of binding thermodynamics in SH2 domains.
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Chem Biol Drug Des,
67,
38-45.
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T.R.Burke
(2006).
Development of Grb2 SH2 Domain Signaling Antagonists: A Potential New Class of Antiproliferative Agents.
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Int J Pept Res Ther,
12,
33-48.
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A.Scott,
D.Pantoja-Uceda,
S.Koshiba,
M.Inoue,
T.Kigawa,
T.Terada,
M.Shirouzu,
A.Tanaka,
S.Sugano,
S.Yokoyama,
and
P.Güntert
(2005).
Solution structure of the Src homology 2 domain from the human feline sarcoma oncogene Fes.
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J Biomol NMR,
31,
357-361.
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PDB code:
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B.A.Joughin,
B.Tidor,
and
M.B.Yaffe
(2005).
A computational method for the analysis and prediction of protein:phosphopeptide-binding sites.
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Protein Sci,
14,
131-139.
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C.J.Porter,
M.C.Wilce,
J.P.Mackay,
P.Leedman,
and
J.A.Wilce
(2005).
Grb7-SH2 domain dimerisation is affected by a single point mutation.
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Eur Biophys J,
34,
454-460.
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J.Hu,
and
S.R.Hubbard
(2005).
Structural characterization of a novel Cbl phosphotyrosine recognition motif in the APS family of adapter proteins.
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J Biol Chem,
280,
18943-18949.
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PDB code:
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M.Ivancic,
A.M.Spuches,
E.C.Guth,
M.A.Daugherty,
D.E.Wilcox,
and
B.A.Lyons
(2005).
Backbone nuclear relaxation characteristics and calorimetric investigation of the human Grb7-SH2/erbB2 peptide complex.
|
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Protein Sci,
14,
1556-1569.
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M.Nishi,
E.D.Werner,
B.C.Oh,
J.D.Frantz,
S.Dhe-Paganon,
L.Hansen,
J.Lee,
and
S.E.Shoelson
(2005).
Kinase activation through dimerization by human SH2-B.
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Mol Cell Biol,
25,
2607-2621.
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R.S.Depetris,
J.Hu,
I.Gimpelevich,
L.J.Holt,
R.J.Daly,
and
S.R.Hubbard
(2005).
Structural basis for inhibition of the insulin receptor by the adaptor protein Grb14.
|
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Mol Cell,
20,
325-333.
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PDB codes:
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S.Radtke,
S.Haan,
A.Jörissen,
H.M.Hermanns,
S.Diefenbach,
T.Smyczek,
H.Schmitz-Vandeleur,
P.C.Heinrich,
I.Behrmann,
and
C.Haan
(2005).
The Jak1 SH2 domain does not fulfill a classical SH2 function in Jak/STAT signaling but plays a structural role for receptor interaction and up-regulation of receptor surface expression.
|
| |
J Biol Chem,
280,
25760-25768.
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A.L.Watters,
and
D.Baker
(2004).
Searching for folded proteins in vitro and in silico.
|
| |
Eur J Biochem,
271,
1615-1622.
|
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E.Hong,
J.Shin,
H.I.Kim,
S.T.Lee,
and
W.Lee
(2004).
Solution structure and backbone dynamics of the non-receptor protein-tyrosine kinase-6 Src homology 2 domain.
|
| |
J Biol Chem,
279,
29700-29708.
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PDB code:
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M.On,
J.M.Billingsley,
M.H.Jouvin,
and
J.P.Kinet
(2004).
Molecular dissection of the FcRbeta signaling amplifier.
|
| |
J Biol Chem,
279,
45782-45790.
|
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|
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M.Soler-Lopez,
C.Petosa,
M.Fukuzawa,
R.Ravelli,
J.G.Williams,
and
C.W.Müller
(2004).
Structure of an activated Dictyostelium STAT in its DNA-unbound form.
|
| |
Mol Cell,
13,
791-804.
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PDB codes:
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P.J.Scharf,
J.Witney,
R.Daly,
and
B.A.Lyons
(2004).
Solution structure of the human Grb14-SH2 domain and comparison with the structures of the human Grb7-SH2/erbB2 peptide complex and human Grb10-SH2 domain.
|
| |
Protein Sci,
13,
2541-2546.
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S.Cho,
C.A.Velikovsky,
C.P.Swaminathan,
J.C.Houtman,
L.E.Samelson,
and
R.A.Mariuzza
(2004).
Structural basis for differential recognition of tyrosine-phosphorylated sites in the linker for activation of T cells (LAT) by the adaptor Gads.
|
| |
EMBO J,
23,
1441-1451.
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PDB codes:
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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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E.G.Stein,
R.Ghirlando,
and
S.R.Hubbard
(2003).
Structural basis for dimerization of the Grb10 Src homology 2 domain. Implications for ligand specificity.
|
| |
J Biol Chem,
278,
13257-13264.
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PDB code:
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J.Hu,
J.Liu,
R.Ghirlando,
A.R.Saltiel,
and
S.R.Hubbard
(2003).
Structural basis for recruitment of the adaptor protein APS to the activated insulin receptor.
|
| |
Mol Cell,
12,
1379-1389.
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PDB codes:
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J.Tong,
S.Elowe,
P.Nash,
and
T.Pawson
(2003).
Manipulation of EphB2 regulatory motifs and SH2 binding sites switches MAPK signaling and biological activity.
|
| |
J Biol Chem,
278,
6111-6119.
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M.Scalley-Kim,
P.Minard,
and
D.Baker
(2003).
Low free energy cost of very long loop insertions in proteins.
|
| |
Protein Sci,
12,
197-206.
|
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N.Schiering,
S.Knapp,
M.Marconi,
M.M.Flocco,
J.Cui,
R.Perego,
L.Rusconi,
and
C.Cristiani
(2003).
Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met and its complex with the microbial alkaloid K-252a.
|
| |
Proc Natl Acad Sci U S A,
100,
12654-12659.
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PDB codes:
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D.De Souza,
L.J.Fabri,
A.Nash,
D.J.Hilton,
N.A.Nicola,
and
M.Baca
(2002).
SH2 domains from suppressor of cytokine signaling-3 and protein tyrosine phosphatase SHP-2 have similar binding specificities.
|
| |
Biochemistry,
41,
9229-9236.
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M.B.Yaffe
(2002).
Phosphotyrosine-binding domains in signal transduction.
|
| |
Nat Rev Mol Cell Biol,
3,
177-186.
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M.Hörtner,
U.Nielsch,
L.M.Mayr,
P.C.Heinrich,
and
S.Haan
(2002).
A new high affinity binding site for suppressor of cytokine signaling-3 on the erythropoietin receptor.
|
| |
Eur J Biochem,
269,
2516-2526.
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R.J.Mallis,
K.N.Brazin,
D.B.Fulton,
and
A.H.Andreotti
(2002).
Structural characterization of a proline-driven conformational switch within the Itk SH2 domain.
|
| |
Nat Struct Biol,
9,
900-905.
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PDB codes:
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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.
|
| |
Protein Sci,
10,
2162-2175.
|
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|
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G.M.Verkhivker,
D.Bouzida,
D.K.Gehlhaar,
P.A.Rejto,
L.Schaffer,
S.Arthurs,
A.B.Colson,
S.T.Freer,
V.Larson,
B.A.Luty,
T.Marrone,
and
P.W.Rose
(2001).
Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains.
|
| |
Proteins,
45,
456-470.
|
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|
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M.Morra,
J.Lu,
F.Poy,
M.Martin,
J.Sayos,
S.Calpe,
C.Gullo,
D.Howie,
S.Rietdijk,
A.Thompson,
A.J.Coyle,
C.Denny,
M.B.Yaffe,
P.Engel,
M.J.Eck,
and
C.Terhorst
(2001).
Structural basis for the interaction of the free SH2 domain EAT-2 with SLAM receptors in hematopoietic cells.
|
| |
EMBO J,
20,
5840-5852.
|
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PDB code:
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R.Ruijtenbeek,
J.A.Kruijtzer,
W.van de Wiel,
M.J.Fischer,
M.Flück,
F.A.Redegeld,
R.M.Liskamp,
and
F.P.Nijkamp
(2001).
Peptoid - peptide hybrids that bind Syk SH2 domains involved in signal transduction.
|
| |
Chembiochem,
2,
171-179.
|
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|
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T.R.Burke,
Z.J.Yao,
D.G.Liu,
J.Voigt,
and
Y.Gao
(2001).
Phosphoryltyrosyl mimetics in the design of peptide-based signal transduction inhibitors.
|
| |
Biopolymers,
60,
32-44.
|
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A.Kodama,
T.Matozaki,
A.Fukuhara,
M.Kikyo,
M.Ichihashi,
and
Y.Takai
(2000).
Involvement of an SHP-2-Rho small G protein pathway in hepatocyte growth factor/scatter factor-induced cell scattering.
|
| |
Mol Biol Cell,
11,
2565-2575.
|
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C.C.Smith,
J.Nelson,
L.Aurelian,
M.Gober,
and
B.B.Goswami
(2000).
Ras-GAP binding and phosphorylation by herpes simplex virus type 2 RR1 PK (ICP10) and activation of the Ras/MEK/MAPK mitogenic pathway are required for timely onset of virus growth.
|
| |
J Virol,
74,
10417-10429.
|
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D.Durocher,
I.A.Taylor,
D.Sarbassova,
L.F.Haire,
S.L.Westcott,
S.P.Jackson,
S.J.Smerdon,
and
M.B.Yaffe
(2000).
The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms.
|
| |
Mol Cell,
6,
1169-1182.
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PDB code:
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D.Durocher,
S.J.Smerdon,
M.B.Yaffe,
and
S.P.Jackson
(2000).
The FHA domain in DNA repair and checkpoint signaling.
|
| |
Cold Spring Harb Symp Quant Biol,
65,
423-431.
|
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|
|
D.J.Owen,
P.Ornaghi,
J.C.Yang,
N.Lowe,
P.R.Evans,
P.Ballario,
D.Neuhaus,
P.Filetici,
and
A.A.Travers
(2000).
The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p.
|
| |
EMBO J,
19,
6141-6149.
|
|
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PDB code:
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G.G.Chiang,
and
B.M.Sefton
(2000).
Phosphorylation of a Src kinase at the autophosphorylation site in the absence of Src kinase activity.
|
| |
J Biol Chem,
275,
6055-6058.
|
|
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|
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K.D.Beebe,
P.Wang,
G.Arabaci,
and
D.Pei
(2000).
Determination of the binding specificity of the SH2 domains of protein tyrosine phosphatase SHP-1 through the screening of a combinatorial phosphotyrosyl peptide library.
|
| |
Biochemistry,
39,
13251-13260.
|
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|
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M.S.Kimber,
J.Nachman,
A.M.Cunningham,
G.D.Gish,
T.Pawson,
and
E.F.Pai
(2000).
Structural basis for specificity switching of the Src SH2 domain.
|
| |
Mol Cell,
5,
1043-1049.
|
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PDB codes:
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|
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PDB code:
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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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