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PDBsum entry 1shb
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Phosphotransferase
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PDB id
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1shb
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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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Nature
358:646-653
(1992)
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PubMed id:
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Crystal structure of the phosphotyrosine recognition domain SH2 of v-src complexed with tyrosine-phosphorylated peptides.
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G.Waksman,
D.Kominos,
S.C.Robertson,
N.Pant,
D.Baltimore,
R.B.Birge,
D.Cowburn,
H.Hanafusa,
B.J.Mayer,
M.Overduin,
M.D.Resh,
C.B.Rios,
L.Silverman,
J.Kuriyan.
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ABSTRACT
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Three-dimensional structures of complexes of the SH2 domain of the v-src
oncogene product with two phosphotyrosyl peptides have been determined by X-ray
crystallography at resolutions of 1.5 and 2.0 A, respectively. A central
antiparallel beta-sheet in the structure is flanked by two alpha-helices, with
peptide binding mediated by the sheet, intervening loops and one of the helices.
The specific recognition of phosphotyrosine involves amino-aromatic interactions
between lysine and arginine side chains and the ring system in addition to
hydrogen-bonding interactions with the phosphate.
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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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J.Li,
S.Nayak,
and
M.Mrksich
(2010).
Rate enhancement of an interfacial biochemical reaction through localization of substrate and enzyme by an adaptor domain.
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J Phys Chem B,
114,
15113-15118.
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J.Nachman,
G.Gish,
C.Virag,
T.Pawson,
R.Pomès,
and
E.Pai
(2010).
Conformational determinants of phosphotyrosine peptides complexed with the Src SH2 domain.
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PLoS One,
5,
e11215.
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J.D.Taylor,
A.Ababou,
R.R.Fawaz,
C.J.Hobbs,
M.A.Williams,
and
J.E.Ladbury
(2008).
Structure, dynamics, and binding thermodynamics of the v-Src SH2 domain: implications for drug design.
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Proteins,
73,
929-940.
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PDB code:
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S.J.Mills,
F.Vandeput,
M.N.Trusselle,
S.T.Safrany,
C.Erneux,
and
B.V.Potter
(2008).
Benzene polyphosphates as tools for cell signalling: inhibition of inositol 1,4,5-trisphosphate 5-phosphatase and interaction with the PH domain of protein kinase Balpha.
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Chembiochem,
9,
1757-1766.
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S.Ren,
V.N.Uversky,
Z.Chen,
A.K.Dunker,
and
Z.Obradovic
(2008).
Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions.
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BMC Genomics,
9,
S26.
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A.S.Wavreille,
M.Garaud,
Y.Zhang,
and
D.Pei
(2007).
Defining SH2 domain and PTP specificity by screening combinatorial peptide libraries.
|
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Methods,
42,
207-219.
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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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G.Ye,
N.H.Nam,
A.Kumar,
A.Saleh,
D.B.Shenoy,
M.M.Amiji,
X.Lin,
G.Sun,
and
K.Parang
(2007).
Synthesis and evaluation of tripodal peptide analogues for cellular delivery of phosphopeptides.
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J Med Chem,
50,
3604-3617.
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H.Sahoo,
and
W.M.Nau
(2007).
Phosphorylation-induced conformational changes in short peptides probed by fluorescence resonance energy transfer in the 10A domain.
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Chembiochem,
8,
567-573.
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J.E.Ladbury
(2007).
Measurement of the formation of complexes in tyrosine kinase-mediated signal transduction.
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Acta Crystallogr D Biol Crystallogr,
63,
26-31.
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J.E.Mills,
P.C.Whitford,
J.Shaffer,
J.N.Onuchic,
J.A.Adams,
and
P.A.Jennings
(2007).
A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.
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J Mol Biol,
365,
1460-1468.
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Y.Ahmadibeni,
M.Hanley,
M.White,
M.Ayrapetov,
X.Lin,
G.Sun,
and
K.Parang
(2007).
Metal-binding properties of a dicysteine-containing motif in protein tyrosine kinases.
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Chembiochem,
8,
1592-1605.
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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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D.Imhof,
A.S.Wavreille,
A.May,
M.Zacharias,
S.Tridandapani,
and
D.Pei
(2006).
Sequence specificity of SHP-1 and SHP-2 Src homology 2 domains. Critical roles of residues beyond the pY+3 position.
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J Biol Chem,
281,
20271-20282.
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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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J.L.Wilsbacher,
S.L.Moores,
and
J.S.Brugge
(2006).
An active form of Vav1 induces migration of mammary epithelial cells by stimulating secretion of an epidermal growth factor receptor ligand.
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Cell Commun Signal,
4,
5.
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J.S.Woo,
J.H.Imm,
C.K.Min,
K.J.Kim,
S.S.Cha,
and
B.H.Oh
(2006).
Structural and functional insights into the B30.2/SPRY domain.
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EMBO J,
25,
1353-1363.
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PDB code:
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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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H.Sondermann,
and
J.Kuriyan
(2005).
C2 can do it, too.
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Cell,
121,
158-160.
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PDB code:
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L.J.Ball,
R.Kühne,
J.Schneider-Mergener,
and
H.Oschkinat
(2005).
Recognition of Proline-Rich Motifs by Protein-Protein-Interaction Domains.
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Angew Chem Int Ed Engl,
44,
2852-2869.
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P.W.Fowler,
S.Jha,
and
P.V.Coveney
(2005).
Grid-based steered thermodynamic integration accelerates the calculation of binding free energies.
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Philos Transact A Math Phys Eng Sci,
363,
1999-2015.
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S.W.Cowan-Jacob,
G.Fendrich,
P.W.Manley,
W.Jahnke,
D.Fabbro,
J.Liebetanz,
and
T.Meyer
(2005).
The crystal structure of a c-Src complex in an active conformation suggests possible steps in c-Src activation.
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Structure,
13,
861-871.
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PDB code:
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Y.Sakurai,
T.Mizuno,
H.Hiroaki,
K.Gohda,
J.Oku,
and
T.Tanaka
(2005).
High thermal stability imparted by a designed tandem Arg-Trp stretch in an alpha-helical coiled coil.
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Angew Chem Int Ed Engl,
44,
6180-6183.
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Y.Wang,
E.L.Botvinick,
Y.Zhao,
M.W.Berns,
S.Usami,
R.Y.Tsien,
and
S.Chien
(2005).
Visualizing the mechanical activation of Src.
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Nature,
434,
1040-1045.
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A.Dreuw,
S.Radtke,
S.Pflanz,
B.E.Lippok,
P.C.Heinrich,
and
H.M.Hermanns
(2004).
Characterization of the signaling capacities of the novel gp130-like cytokine receptor.
|
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J Biol Chem,
279,
36112-36120.
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M.On,
J.M.Billingsley,
M.H.Jouvin,
and
J.P.Kinet
(2004).
Molecular dissection of the FcRbeta signaling amplifier.
|
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J Biol Chem,
279,
45782-45790.
|
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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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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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M.Wiederkehr-Adam,
P.Ernst,
K.Müller,
E.Bieck,
F.O.Gombert,
J.Ottl,
P.Graff,
F.Grossmüller,
and
M.H.Heim
(2003).
Characterization of phosphopeptide motifs specific for the Src homology 2 domains of signal transducer and activator of transcription 1 (STAT1) and STAT3.
|
| |
J Biol Chem,
278,
16117-16128.
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N.P.Mahajan,
and
H.S.Earp
(2003).
An SH2 domain-dependent, phosphotyrosine-independent interaction between Vav1 and the Mer receptor tyrosine kinase: a mechanism for localizing guanine nucleotide-exchange factor action.
|
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J Biol Chem,
278,
42596-42603.
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A.Pandey,
N.Ibarrola,
I.Kratchmarova,
M.M.Fernandez,
S.N.Constantinescu,
O.Ohara,
S.Sawasdikosol,
H.F.Lodish,
and
M.Mann
(2002).
A novel Src homology 2 domain-containing molecule, Src-like adapter protein-2 (SLAP-2), which negatively regulates T cell receptor signaling.
|
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J Biol Chem,
277,
19131-19138.
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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.
|
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Biochemistry,
41,
9229-9236.
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M.B.Yaffe
(2002).
Phosphotyrosine-binding domains in signal transduction.
|
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Nat Rev Mol Cell Biol,
3,
177-186.
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M.J.Cross,
L.Lu,
P.Magnusson,
D.Nyqvist,
K.Holmqvist,
M.Welsh,
and
L.Claesson-Welsh
(2002).
The Shb adaptor protein binds to tyrosine 766 in the FGFR-1 and regulates the Ras/MEK/MAPK pathway via FRS2 phosphorylation in endothelial cells.
|
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Mol Biol Cell,
13,
2881-2893.
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S.Kim,
R.Zagozdzon,
A.Meisler,
J.D.Baleja,
Y.Fu,
S.Avraham,
and
H.Avraham
(2002).
Csk homologous kinase (CHK) and ErbB-2 interactions are directly coupled with CHK negative growth regulatory function in breast cancer.
|
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J Biol Chem,
277,
36465-36470.
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B.Al-Lazikani,
F.B.Sheinerman,
and
B.Honig
(2001).
Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases.
|
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Proc Natl Acad Sci U S A,
98,
14796-14801.
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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.
|
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Proteins,
45,
456-470.
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K.L.Constantine
(2001).
Evaluation of site-directed spin labeling for characterizing protein-ligand complexes using simulated restraints.
|
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Biophys J,
81,
1275-1284.
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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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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.A.Henriques,
J.E.Ladbury,
and
R.M.Jackson
(2000).
Comparison of binding energies of SrcSH2-phosphotyrosyl peptides with structure-based prediction using surface area based empirical parameterization.
|
| |
Protein Sci,
9,
1975-1985.
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D.D.Billadeau,
S.M.Mackie,
R.A.Schoon,
and
P.J.Leibson
(2000).
The Rho family guanine nucleotide exchange factor Vav-2 regulates the development of cell-mediated cytotoxicity.
|
| |
J Exp Med,
192,
381-392.
|
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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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J.E.Ladbury,
and
S.Arold
(2000).
Searching for specificity in SH domains.
|
| |
Chem Biol,
7,
R3-R8.
|
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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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M.H.Rhee,
I.Nevo,
M.L.Bayewitch,
O.Zagoory,
and
Z.Vogel
(2000).
Functional role of tryptophan residues in the fourth transmembrane domain of the CB(2) cannabinoid receptor.
|
| |
J Neurochem,
75,
2485-2491.
|
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N.G.Oikonomakos,
V.T.Skamnaki,
K.E.Tsitsanou,
N.G.Gavalas,
and
L.N.Johnson
(2000).
A new allosteric site in glycogen phosphorylase b as a target for drug interactions.
|
| |
Structure,
8,
575-584.
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PDB code:
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S.C.Robertson,
J.A.Tynan,
and
D.J.Donoghue
(2000).
RTK mutations and human syndromeswhen good receptors turn bad.
|
| |
Trends Genet,
16,
265-271.
|
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|
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S.M.Violette,
W.C.Shakespeare,
C.Bartlett,
W.Guan,
J.A.Smith,
R.J.Rickles,
R.S.Bohacek,
D.A.Holt,
R.Baron,
and
T.K.Sawyer
(2000).
A Src SH2 selective binding compound inhibits osteoclast-mediated resorption.
|
| |
Chem Biol,
7,
225-235.
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S.P.Edgcomb,
B.M.Baker,
and
K.P.Murphy
(2000).
The energetics of phosphate binding to a protein complex.
|
| |
Protein Sci,
9,
927-933.
|
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S.R.Tzeng,
M.T.Pai,
F.D.Lung,
C.W.Wu,
P.P.Roller,
B.Lei,
C.J.Wei,
S.C.Tu,
S.H.Chen,
W.J.Soong,
and
J.W.Cheng
(2000).
Stability and peptide binding specificity of Btk SH2 domain: molecular basis for X-linked agammaglobulinemia.
|
| |
Protein Sci,
9,
2377-2385.
|
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|
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W.Shakespeare,
M.Yang,
R.Bohacek,
F.Cerasoli,
K.Stebbins,
R.Sundaramoorthi,
M.Azimioara,
C.Vu,
S.Pradeepan,
C.Metcalf,
C.Haraldson,
T.Merry,
D.Dalgarno,
S.Narula,
M.Hatada,
X.Lu,
M.R.van Schravendijk,
S.Adams,
S.Violette,
J.Smith,
W.Guan,
C.Bartlett,
J.Herson,
J.Iuliucci,
M.Weigele,
and
T.Sawyer
(2000).
Structure-based design of an osteoclast-selective, nonpeptide src homology 2 inhibitor with in vivo antiresorptive activity.
|
| |
Proc Natl Acad Sci U S A,
97,
9373-9378.
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Mol Cell Biol,
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Mol Cell Biol,
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Nat Genet,
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The SH2/SH3 domain-containing protein GRB2 interacts with tyrosine-phosphorylated IRS1 and Shc: implications for insulin control of ras signalling.
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EMBO J,
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EMBO J,
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Cell,
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PDB codes:
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The sites of phosphorylation by protein kinase C and an intact SH2 domain are required for the enhanced response to beta-adrenergic agonists in cells overexpressing c-src.
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Mol Cell Biol,
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Mol Cell Biol,
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Ash/Grb-2, a SH2/SH3-containing protein, couples to signaling for mitogenesis and cytoskeletal reorganization by EGF and PDGF.
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EMBO J,
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Proc Natl Acad Sci U S A,
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Phosphatidylinositol (PI) 3-kinase and PI 4-kinase binding to the CD4-p56lck complex: the p56lck SH3 domain binds to PI 3-kinase but not PI 4-kinase.
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Mol Cell Biol,
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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
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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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