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PDBsum entry 1fmk
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Phosphotransferase
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PDB id
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1fmk
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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
385:595-602
(1997)
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PubMed id:
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Three-dimensional structure of the tyrosine kinase c-Src.
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W.Xu,
S.C.Harrison,
M.J.Eck.
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ABSTRACT
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The structure of a large fragment of the c-Src tyrosine kinase, comprising the
regulatory and kinase domains and the carboxy-terminal tall, has been determined
at 1.7 A resolution in a closed, inactive state. Interactions among domains,
stabilized by binding of the phosphorylated tail to the SH2 domain, lock the
molecule in a conformation that simultaneously disrupts the kinase active site
and sequesters the binding surfaces of the SH2 and SH3 domains. The structure
shows how appropriate cellular signals, or transforming mutations in v-Src,
could break these interactions to produce an open, active kinase.
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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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B.R.Groveman,
S.Xue,
V.Marin,
J.Xu,
M.K.Ali,
E.A.Bienkiewicz,
and
X.M.Yu
(2011).
Roles of the SH2 and SH3 domains in the regulation of neuronal Src kinase functions.
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FEBS J,
278,
643-653.
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D.F.Brennan,
A.C.Dar,
N.T.Hertz,
W.C.Chao,
A.L.Burlingame,
K.M.Shokat,
and
D.Barford
(2011).
A Raf-induced allosteric transition of KSR stimulates phosphorylation of MEK.
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Nature,
472,
366-369.
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PDB code:
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H.Liang,
T.Liu,
F.Chen,
Z.Liu,
and
S.Liu
(2011).
A full-length 3D structure for MAPK/ERK kinase 2 (MEK2).
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Sci China Life Sci,
54,
336-341.
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J.Yang,
N.Campobasso,
M.P.Biju,
K.Fisher,
X.Q.Pan,
J.Cottom,
S.Galbraith,
T.Ho,
H.Zhang,
X.Hong,
P.Ward,
G.Hofmann,
B.Siegfried,
F.Zappacosta,
Y.Washio,
P.Cao,
J.Qu,
S.Bertrand,
D.Y.Wang,
M.S.Head,
H.Li,
S.Moores,
Z.Lai,
K.Johanson,
G.Burton,
C.Erickson-Miller,
G.Simpson,
P.Tummino,
R.A.Copeland,
and
A.Oliff
(2011).
Discovery and characterization of a cell-permeable, small-molecule c-Abl kinase activator that binds to the myristoyl binding site.
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Chem Biol,
18,
177-186.
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PDB code:
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L.P.O'Reilly,
S.C.Watkins,
and
T.E.Smithgall
(2011).
An unexpected role for the clock protein timeless in developmental apoptosis.
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| |
PLoS One,
6,
e17157.
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N.Jura,
X.Zhang,
N.F.Endres,
M.A.Seeliger,
T.Schindler,
and
J.Kuriyan
(2011).
Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms.
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Mol Cell,
42,
9.
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R.Kristelly,
T.W.Qiu,
N.J.Gunn,
D.B.Scanlon,
and
T.D.Mulhern
(2011).
Bacterial expression and purification of active hematopoietic cell kinase.
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Protein Expr Purif,
78,
14-21.
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R.W.McLachlan,
and
A.S.Yap
(2011).
Protein tyrosine phosphatase activity is necessary for E-cadherin-activated Src signaling.
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Cytoskeleton (Hoboken),
68,
32-43.
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S.K.Yoo,
T.W.Starnes,
Q.Deng,
and
A.Huttenlocher
(2011).
Lyn is a redox sensor that mediates leukocyte wound attraction in vivo.
|
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Nature,
480,
109-112.
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T.Kondo,
K.Yokomine,
A.Nakagawa,
and
Y.Sakagami
(2011).
Analogs of the CLV3 Peptide: Synthesis and Structure-Activity Relationships Focused on Proline Residues.
|
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Plant Cell Physiol,
52,
30-36.
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A.Dusa,
C.Mouton,
C.Pecquet,
M.Herman,
and
S.N.Constantinescu
(2010).
JAK2 V617F constitutive activation requires JH2 residue F595: a pseudokinase domain target for specific inhibitors.
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PLoS One,
5,
e11157.
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A.Stein,
and
P.Aloy
(2010).
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures.
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PLoS Comput Biol,
6,
e1000789.
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C.B.McDonald,
K.L.Seldeen,
B.J.Deegan,
V.Bhat,
and
A.Farooq
(2010).
Assembly of the Sos1-Grb2-Gab1 ternary signaling complex is under allosteric control.
|
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Arch Biochem Biophys,
494,
216-225.
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H.Slanina,
A.König,
S.Hebling,
C.R.Hauck,
M.Frosch,
and
A.Schubert-Unkmeir
(2010).
Entry of Neisseria meningitidis into mammalian cells requires the Src family protein tyrosine kinases.
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Infect Immun,
78,
1905-1914.
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J.A.Worrall,
and
E.Vijgenboom
(2010).
Copper mining in Streptomyces: enzymes, natural products and development.
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Nat Prod Rep,
27,
742-756.
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K.Mahajan,
and
N.P.Mahajan
(2010).
Shepherding AKT and androgen receptor by Ack1 tyrosine kinase.
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J Cell Physiol,
224,
327-333.
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L.Min,
W.Wu,
R.E.Joseph,
D.B.Fulton,
L.Berg,
and
A.H.Andreotti
(2010).
Disrupting the intermolecular self-association of Itk enhances T cell signaling.
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J Immunol,
184,
4228-4235.
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M.A.Rahman,
T.Senga,
S.Ito,
T.Hyodo,
H.Hasegawa,
and
M.Hamaguchi
(2010).
S-nitrosylation at cysteine 498 of c-Src tyrosine kinase regulates nitric oxide-mediated cell invasion.
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J Biol Chem,
285,
3806-3814.
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O.Doppelt-Azeroual,
F.Delfaud,
F.Moriaud,
and
A.G.de Brevern
(2010).
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.
|
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Protein Sci,
19,
847-867.
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P.Gruszczyński,
M.Obuchowski,
and
R.Kaźmierkiewicz
(2010).
Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis.
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J Comput Aided Mol Des,
24,
733-747.
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P.Patwardhan,
and
M.D.Resh
(2010).
Myristoylation and membrane binding regulate c-Src stability and kinase activity.
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Mol Cell Biol,
30,
4094-4107.
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S.Gonfloni
(2010).
DNA damage stress response in germ cells: role of c-Abl and clinical implications.
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Oncogene,
29,
6193-6202.
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S.Herrero-González,
E.Gangoso,
C.Giaume,
C.C.Naus,
J.M.Medina,
and
A.Tabernero
(2010).
Connexin43 inhibits the oncogenic activity of c-Src in C6 glioma cells.
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Oncogene,
29,
5712-5723.
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S.I.O'Donoghue,
D.S.Goodsell,
A.S.Frangakis,
F.Jossinet,
R.A.Laskowski,
M.Nilges,
H.R.Saibil,
A.Schafferhans,
R.C.Wade,
E.Westhof,
and
A.J.Olson
(2010).
Visualization of macromolecular structures.
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Nat Methods,
7,
S42-S55.
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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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T.Zhou,
L.Commodore,
W.S.Huang,
Y.Wang,
T.K.Sawyer,
W.C.Shakespeare,
T.Clackson,
X.Zhu,
and
D.C.Dalgarno
(2010).
Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl purine template.
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Chem Biol Drug Des,
75,
18-28.
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PDB codes:
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X.Shi,
S.Opi,
A.Lugari,
A.Restouin,
T.Coursindel,
I.Parrot,
J.Perez,
E.Madore,
P.Zimmermann,
J.Corbeil,
M.Huang,
S.T.Arold,
Y.Collette,
and
X.Morelli
(2010).
Identification and biophysical assessment of the molecular recognition mechanisms between the human haemopoietic cell kinase Src homology domain 3 and ALG-2-interacting protein X.
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Biochem J,
431,
93.
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Y.H.Hsu,
and
J.A.Traugh
(2010).
Reciprocally coupled residues crucial for protein kinase Pak2 activity calculated by statistical coupling analysis.
|
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PLoS One,
5,
e9455.
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A.Quintás-Cardama,
and
J.Cortes
(2009).
Molecular biology of bcr-abl1-positive chronic myeloid leukemia.
|
| |
Blood,
113,
1619-1630.
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A.Stein,
R.A.Pache,
P.Bernadó,
M.Pons,
and
P.Aloy
(2009).
Dynamic interactions of proteins in complex networks: a more structured view.
|
| |
FEBS J,
276,
5390-5405.
|
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B.B.Au-Yeung,
S.Deindl,
L.Y.Hsu,
E.H.Palacios,
S.E.Levin,
J.Kuriyan,
and
A.Weiss
(2009).
The structure, regulation, and function of ZAP-70.
|
| |
Immunol Rev,
228,
41-57.
|
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C.Brignatz,
M.P.Paronetto,
S.Opi,
M.Cappellari,
S.Audebert,
V.Feuillet,
G.Bismuth,
S.Roche,
S.T.Arold,
C.Sette,
and
Y.Collette
(2009).
Alternative splicing modulates autoinhibition and SH3 accessibility in the Src kinase Fyn.
|
| |
Mol Cell Biol,
29,
6438-6448.
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C.M.Agapakis,
and
P.A.Silver
(2009).
Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks.
|
| |
Mol Biosyst,
5,
704-713.
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D.J.Kemble,
and
G.Sun
(2009).
Direct and specific inactivation of protein tyrosine kinases in the Src and FGFR families by reversible cysteine oxidation.
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Proc Natl Acad Sci U S A,
106,
5070-5075.
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H.Lammert,
A.Schug,
and
J.N.Onuchic
(2009).
Robustness and generalization of structure-based models for protein folding and function.
|
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Proteins,
77,
881-891.
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I.Westwood,
D.M.Cheary,
J.E.Baxter,
M.W.Richards,
R.L.van Montfort,
A.M.Fry,
and
R.Bayliss
(2009).
Insights into the conformational variability and regulation of human Nek2 kinase.
|
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J Mol Biol,
386,
476-485.
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PDB codes:
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J.Zhao,
Y.Zhang,
S.S.Ithychanda,
Y.Tu,
K.Chen,
J.Qin,
and
C.Wu
(2009).
Migfilin interacts with Src and contributes to cell-matrix adhesion-mediated survival signaling.
|
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J Biol Chem,
284,
34308-34320.
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K.Huang,
Y.H.Wang,
A.Brown,
and
G.Sun
(2009).
Identification of N-terminal lobe motifs that determine the kinase activity of the catalytic domains and regulatory strategies of Src and Csk protein tyrosine kinases.
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J Mol Biol,
386,
1066-1077.
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L.C.Kim,
L.Song,
and
E.B.Haura
(2009).
Src kinases as therapeutic targets for cancer.
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Nat Rev Clin Oncol,
6,
587-595.
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L.Röglin,
F.Altenbrunn,
and
O.Seitz
(2009).
DNA and RNA-controlled switching of protein kinase activity.
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Chembiochem,
10,
758-765.
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M.A.Meyn,
and
T.E.Smithgall
(2009).
Chemical genetics identifies c-Src as an activator of primitive ectoderm formation in murine embryonic stem cells.
|
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Sci Signal,
2,
ra64.
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M.A.Seeliger,
P.Ranjitkar,
C.Kasap,
Y.Shan,
D.E.Shaw,
N.P.Shah,
J.Kuriyan,
and
D.J.Maly
(2009).
Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations.
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Cancer Res,
69,
2384-2392.
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PDB codes:
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M.E.Huot,
C.M.Brown,
N.Lamarche-Vane,
and
S.Richard
(2009).
An adaptor role for cytoplasmic Sam68 in modulating Src activity during cell polarization.
|
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Mol Cell Biol,
29,
1933-1943.
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M.H.Sheng,
and
K.H.Lau
(2009).
Role of protein-tyrosine phosphatases in regulation of osteoclastic activity.
|
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Cell Mol Life Sci,
66,
1946-1961.
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M.J.Wagner,
and
J.R.Smiley
(2009).
Herpes simplex virus requires VP11/12 to induce phosphorylation of the activation loop tyrosine (Y394) of the Src family kinase Lck in T lymphocytes.
|
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J Virol,
83,
12452-12461.
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M.Malakhova,
I.Kurinov,
K.Liu,
D.Zheng,
I.D'Angelo,
J.H.Shim,
V.Steinman,
A.M.Bode,
and
Z.Dong
(2009).
Structural diversity of the active N-terminal kinase domain of p90 ribosomal S6 kinase 2.
|
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PLoS One,
4,
e8044.
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PDB code:
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M.P.Kim,
S.I.Park,
S.Kopetz,
and
G.E.Gallick
(2009).
Src family kinases as mediators of endothelial permeability: effects on inflammation and metastasis.
|
| |
Cell Tissue Res,
335,
249-259.
|
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N.Jura,
N.F.Endres,
K.Engel,
S.Deindl,
R.Das,
M.H.Lamers,
D.E.Wemmer,
X.Zhang,
and
J.Kuriyan
(2009).
Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment.
|
| |
Cell,
137,
1293-1307.
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PDB code:
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N.K.Banavali,
and
B.Roux
(2009).
Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases.
|
| |
Proteins,
74,
378-389.
|
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N.M.Levinson,
P.R.Visperas,
and
J.Kuriyan
(2009).
The tyrosine kinase Csk dimerizes through Its SH3 domain.
|
| |
PLoS One,
4,
e7683.
|
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N.Yokoyama,
and
C.C.Malbon
(2009).
Dishevelled-2 docks and activates Src in a Wnt-dependent manner.
|
| |
J Cell Sci,
122,
4439-4451.
|
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P.C.Whitford,
J.K.Noel,
S.Gosavi,
A.Schug,
K.Y.Sanbonmatsu,
and
J.N.Onuchic
(2009).
An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.
|
| |
Proteins,
75,
430-441.
|
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P.Filippakopoulos,
S.Müller,
and
S.Knapp
(2009).
SH2 domains: modulators of nonreceptor tyrosine kinase activity.
|
| |
Curr Opin Struct Biol,
19,
643-649.
|
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P.J.Mintz,
M.Cardó-Vila,
M.G.Ozawa,
A.Hajitou,
R.Rangel,
L.Guzman-Rojas,
D.R.Christianson,
M.A.Arap,
R.J.Giordano,
G.R.Souza,
J.Easley,
A.Salameh,
S.Oliviero,
R.R.Brentani,
E.Koivunen,
W.Arap,
and
R.Pasqualini
(2009).
An unrecognized extracellular function for an intracellular adapter protein released from the cytoplasm into the tumor microenvironment.
|
| |
Proc Natl Acad Sci U S A,
106,
2182-2187.
|
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|
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R.Barouch-Bentov,
J.Che,
C.C.Lee,
Y.Yang,
A.Herman,
Y.Jia,
A.Velentza,
J.Watson,
L.Sternberg,
S.Kim,
N.Ziaee,
A.Miller,
C.Jackson,
M.Fujimoto,
M.Young,
S.Batalov,
Y.Liu,
M.Warmuth,
T.Wiltshire,
M.P.Cooke,
and
K.Sauer
(2009).
A conserved salt bridge in the G loop of multiple protein kinases is important for catalysis and for in vivo Lyn function.
|
| |
Mol Cell,
33,
43-52.
|
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R.E.Iacob,
T.Pene-Dumitrescu,
J.Zhang,
N.S.Gray,
T.E.Smithgall,
and
J.R.Engen
(2009).
Conformational disturbance in Abl kinase upon mutation and deregulation.
|
| |
Proc Natl Acad Sci U S A,
106,
1386-1391.
|
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|
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|
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R.J.Salmond,
A.Filby,
I.Qureshi,
S.Caserta,
and
R.Zamoyska
(2009).
T-cell receptor proximal signaling via the Src-family kinases, Lck and Fyn, influences T-cell activation, differentiation, and tolerance.
|
| |
Immunol Rev,
228,
9.
|
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S.Deindl,
T.A.Kadlecek,
X.Cao,
J.Kuriyan,
and
A.Weiss
(2009).
Stability of an autoinhibitory interface in the structure of the tyrosine kinase ZAP-70 impacts T cell receptor response.
|
| |
Proc Natl Acad Sci U S A,
106,
20699-20704.
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PDB codes:
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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|
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