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PDBsum entry 1prl
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Complex (signal transduction/peptide)
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PDB id
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1prl
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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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DOI no:
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Science
266:1241-1247
(1994)
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PubMed id:
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Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions.
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S.Feng,
J.K.Chen,
H.Yu,
J.A.Simon,
S.L.Schreiber.
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ABSTRACT
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Solution structures of two Src homology 3 (SH3) domain-ligand complexes have
been determined by nuclear magnetic resonance. Each complex consists of the SH3
domain and a nine-residue proline-rich peptide selected from a large library of
ligands prepared by combinatorial synthesis. The bound ligands adopt a
left-handed polyproline type II (PPII) helix, although the amino to carboxyl
directionalities of their helices are opposite. The peptide orientation is
determined by a salt bridge formed by the terminal arginine residues of the
ligands and the conserved aspartate-99 of the SH3 domain. Residues at positions
3, 4, 6, and 7 of both peptides also intercalate into the ligand-binding site;
however, the respective proline and nonproline residues show exchanged binding
positions in the two complexes. These structural results led to a model for the
interactions of SH3 domains with proline-rich peptides that can be used to
predict critical residues in complexes of unknown structure. The model was used
to identify correctly both the binding orientation and the contact and
noncontact residues of a peptide derived from the nucleotide exchange factor Sos
in association with the amino-terminal SH3 domain of the adaptor protein Grb2.
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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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C.B.McDonald,
K.L.Seldeen,
B.J.Deegan,
V.Bhat,
and
A.Farooq
(2011).
Binding of the cSH3 domain of Grb2 adaptor to two distinct RXXK motifs within Gab1 docker employs differential mechanisms.
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J Mol Recognit,
24,
585-596.
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D.Gfeller,
F.Butty,
M.Wierzbicka,
E.Verschueren,
P.Vanhee,
H.Huang,
A.Ernst,
N.Dar,
I.Stagljar,
L.Serrano,
S.S.Sidhu,
G.D.Bader,
and
P.M.Kim
(2011).
The multiple-specificity landscape of modular peptide recognition domains.
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Mol Syst Biol,
7,
484.
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Y.Z.Weng,
D.T.Chang,
Y.F.Huang,
and
C.W.Lin
(2011).
A study on the flexibility of enzyme active sites.
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BMC Bioinformatics,
12,
S32.
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B.Xue,
A.K.Dunker,
and
V.N.Uversky
(2010).
Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction.
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Int J Mol Sci,
11,
3725-3747.
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C.Baumann,
C.K.Lindholm,
D.Rimoldi,
and
F.Lévy
(2010).
The E3 ubiquitin ligase Itch regulates sorting nexin 9 through an unconventional substrate recognition domain.
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FEBS J,
277,
2803-2814.
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J.Cai,
R.Ou,
Y.S.Xu,
L.Yang,
Z.Lin,
and
M.Shu
(2010).
Modeling and predicting interactions between the human amphiphysin SH3 domains and their peptide ligands based on amino acid information.
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J Pept Sci,
16,
627-632.
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M.Carducci,
L.Licata,
D.Peluso,
L.Castagnoli,
and
G.Cesareni
(2010).
Enriching the viral-host interactomes with interactions mediated by SH3 domains.
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Amino Acids,
38,
1541-1547.
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M.M.Miller,
S.Lapetina,
S.M.MacGrath,
M.K.Sfakianos,
T.D.Pollard,
and
A.J.Koleske
(2010).
Regulation of actin polymerization and adhesion-dependent cell edge protrusion by the Abl-related gene (Arg) tyrosine kinase and N-WASp.
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Biochemistry,
49,
2227-2234.
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O.Aitio,
M.Hellman,
A.Kazlauskas,
D.F.Vingadassalom,
J.M.Leong,
K.Saksela,
and
P.Permi
(2010).
Recognition of tandem PxxP motifs as a unique Src homology 3-binding mode triggers pathogen-driven actin assembly.
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Proc Natl Acad Sci U S A,
107,
21743-21748.
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PDB code:
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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.Hoffmann,
S.A.Funke,
K.Wiesehan,
S.Moedder,
J.M.Glück,
S.Feuerstein,
M.Gerdts,
J.Mötter,
and
D.Willbold
(2010).
Competitively selected protein ligands pay their increase in specificity by a decrease in affinity.
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Mol Biosyst,
6,
116-123.
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Y.Zhang,
L.Xu,
J.Qiu,
Z.Li,
L.Li,
G.Ren,
A.Dong,
B.Li,
M.Ge,
S.Meng,
and
J.Wang
(2010).
Association between SNP rs10569304 on the second expressed region of hole gene and the congenital heart disease.
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J Huazhong Univ Sci Technolog Med Sci,
30,
430-436.
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A.Severin,
R.E.Joseph,
S.Boyken,
D.B.Fulton,
and
A.H.Andreotti
(2009).
Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain.
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J Mol Biol,
387,
726-743.
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C.B.McDonald,
K.L.Seldeen,
B.J.Deegan,
and
A.Farooq
(2009).
SH3 domains of Grb2 adaptor bind to PXpsiPXR motifs within the Sos1 nucleotide exchange factor in a discriminate manner.
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Biochemistry,
48,
4074-4085.
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C.Neufeld,
F.V.Filipp,
B.Simon,
A.Neuhaus,
N.Schüller,
C.David,
H.Kooshapur,
T.Madl,
R.Erdmann,
W.Schliebs,
M.Wilmanns,
and
M.Sattler
(2009).
Structural basis for competitive interactions of Pex14 with the import receptors Pex5 and Pex19.
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EMBO J,
28,
745-754.
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PDB codes:
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C.Schillinger,
P.Boisguerin,
and
G.Krause
(2009).
Domain Interaction Footprint: a multi-classification approach to predict domain-peptide interactions.
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Bioinformatics,
25,
1632-1639.
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E.J.Stollar,
B.Garcia,
P.A.Chong,
A.Rath,
H.Lin,
J.D.Forman-Kay,
and
A.R.Davidson
(2009).
Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p.
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J Biol Chem,
284,
26918-26927.
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PDB code:
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F.Kieken,
N.Mutsaers,
E.Dolmatova,
K.Virgil,
A.L.Wit,
A.Kellezi,
B.J.Hirst-Jensen,
H.S.Duffy,
and
P.L.Sorgen
(2009).
Structural and molecular mechanisms of gap junction remodeling in epicardial border zone myocytes following myocardial infarction.
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Circ Res,
104,
1103-1112.
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K.Neumann,
T.Oellerich,
H.Urlaub,
and
J.Wienands
(2009).
The B-lymphoid Grb2 interaction code.
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Immunol Rev,
232,
135-149.
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N.M.Levinson,
P.R.Visperas,
and
J.Kuriyan
(2009).
The tyrosine kinase Csk dimerizes through Its SH3 domain.
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PLoS One,
4,
e7683.
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R.E.Joseph,
and
A.H.Andreotti
(2009).
Conformational snapshots of Tec kinases during signaling.
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Immunol Rev,
228,
74-92.
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C.Ng,
R.A.Jackson,
J.P.Buschdorf,
Q.Sun,
G.R.Guy,
and
J.Sivaraman
(2008).
Structural basis for a novel intrapeptidyl H-bond and reverse binding of c-Cbl-TKB domain substrates.
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EMBO J,
27,
804-816.
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PDB codes:
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H.E.Lindfors,
P.E.de Koning,
J.W.Drijfhout,
B.Venezia,
and
M.Ubbink
(2008).
Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR.
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J Biomol NMR,
41,
157-167.
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K.Takeuchi,
H.Yang,
E.Ng,
S.Y.Park,
Z.Y.Sun,
E.L.Reinherz,
and
G.Wagner
(2008).
Structural and functional evidence that Nck interaction with CD3epsilon regulates T-cell receptor activity.
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J Mol Biol,
380,
704-716.
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PDB code:
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M.MacPartlin,
A.M.Smith,
B.J.Druker,
L.A.Honigberg,
and
M.W.Deininger
(2008).
Bruton's tyrosine kinase is not essential for Bcr-Abl-mediated transformation of lymphoid or myeloid cells.
|
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Leukemia,
22,
1354-1360.
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M.S.Cortese,
V.N.Uversky,
and
A.K.Dunker
(2008).
Intrinsic disorder in scaffold proteins: getting more from less.
|
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Prog Biophys Mol Biol,
98,
85.
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P.Zhou,
F.Tian,
X.Chen,
and
Z.Shang
(2008).
Modeling and prediction of binding affinities between the human amphiphysin SH3 domain and its peptide ligands using genetic algorithm-Gaussian processes.
|
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Biopolymers,
90,
792-802.
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R.A.Robinson,
X.Lu,
E.Y.Jones,
and
C.Siebold
(2008).
Biochemical and structural studies of ASPP proteins reveal differential binding to p53, p63, and p73.
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Structure,
16,
259-268.
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PDB code:
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S.A.Solheim,
E.Petsalaki,
A.J.Stokka,
R.B.Russell,
K.Taskén,
and
T.Berge
(2008).
Interactions between the Fyn SH3-domain and adaptor protein Cbp/PAG derived ligands, effects on kinase activity and affinity.
|
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FEBS J,
275,
4863-4874.
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D.Adolph,
N.Flach,
K.Mueller,
D.H.Ostareck,
and
A.Ostareck-Lederer
(2007).
Deciphering the cross talk between hnRNP K and c-Src: the c-Src activation domain in hnRNP K is distinct from a second interaction site.
|
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Mol Cell Biol,
27,
1758-1770.
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F.Ferron,
G.Rebowski,
S.H.Lee,
and
R.Dominguez
(2007).
Structural basis for the recruitment of profilin-actin complexes during filament elongation by Ena/VASP.
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EMBO J,
26,
4597-4606.
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PDB codes:
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M.Meiyappan,
G.Birrane,
and
J.A.Ladias
(2007).
Structural basis for polyproline recognition by the FE65 WW domain.
|
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J Mol Biol,
372,
970-980.
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PDB codes:
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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.J.Wrenn,
R.M.Weisinger,
D.R.Halpin,
and
P.B.Harbury
(2007).
Synthetic ligands discovered by in vitro selection.
|
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J Am Chem Soc,
129,
13137-13143.
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S.K.Panda,
D.Thakral,
and
S.Rehman
(2007).
Hepatitis E virus.
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Rev Med Virol,
17,
151-180.
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V.Anggono,
and
P.J.Robinson
(2007).
Syndapin I and endophilin I bind overlapping proline-rich regions of dynamin I: role in synaptic vesicle endocytosis.
|
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J Neurochem,
102,
931-943.
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A.Sanjay,
T.Miyazaki,
C.Itzstein,
E.Purev,
W.C.Horne,
and
R.Baron
(2006).
Identification and functional characterization of an Src homology domain 3 domain-binding site on Cbl.
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FEBS J,
273,
5442-5456.
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B.E.Slack,
M.S.Siniaia,
and
J.K.Blusztajn
(2006).
Collagen type I selectively activates ectodomain shedding of the discoidin domain receptor 1: involvement of Src tyrosine kinase.
|
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J Cell Biochem,
98,
672-684.
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C.Gu,
S.G.Tangye,
X.Sun,
Y.Luo,
Z.Lin,
and
J.Wu
(2006).
The X-linked lymphoproliferative disease gene product SAP associates with PAK-interacting exchange factor and participates in T cell activation.
|
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Proc Natl Acad Sci U S A,
103,
14447-14452.
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D.Monos,
J.Heliopoulos,
E.Argyris,
P.Cordopatis,
A.Zompra,
and
M.Kamoun
(2006).
Analysis of the CD2 and spliceosomal Sm B/B' polyproline-arginine motifs defined by a monoclonal antibody using a phage-displayed random peptide library.
|
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J Mol Recognit,
19,
535-541.
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D.Shimazu,
N.Yamamoto,
A.Umino,
S.Ishii,
S.Sakurai,
and
T.Nishikawa
(2006).
Inhibition of D-serine accumulation in the Xenopus oocyte by expression of the rat ortholog of human 3'-phosphoadenosine 5'-phosphosulfate transporter gene isolated from the neocortex as D-serine modulator-1.
|
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J Neurochem,
96,
30-42.
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E.Ferraro,
A.Via,
G.Ausiello,
and
M.Helmer-Citterich
(2006).
A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity.
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Bioinformatics,
22,
2333-2339.
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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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P.Ruzza,
G.Siligardi,
A.Donella-Deana,
A.Calderan,
R.Hussain,
C.Rubini,
L.Cesaro,
A.Osler,
A.Guiotto,
L.A.Pinna,
and
G.Borin
(2006).
4-Fluoroproline derivative peptides: effect on PPII conformation and SH3 affinity.
|
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J Pept Sci,
12,
462-471.
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Q.Zhang,
S.M.Thomas,
V.W.Lui,
S.Xi,
J.M.Siegfried,
H.Fan,
T.E.Smithgall,
G.B.Mills,
and
J.R.Grandis
(2006).
Phosphorylation of TNF-alpha converting enzyme by gastrin-releasing peptide induces amphiregulin release and EGF receptor activation.
|
| |
Proc Natl Acad Sci U S A,
103,
6901-6906.
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T.Hou,
K.Chen,
W.A.McLaughlin,
B.Lu,
and
W.Wang
(2006).
Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain.
|
| |
PLoS Comput Biol,
2,
e1.
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V.Musi,
B.Birdsall,
G.Fernandez-Ballester,
R.Guerrini,
S.Salvatori,
L.Serrano,
and
A.Pastore
(2006).
New approaches to high-throughput structure characterization of SH3 complexes: the example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae.
|
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Protein Sci,
15,
795-807.
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PDB code:
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X.Li,
Y.Chen,
Y.Liu,
J.Gao,
F.Gao,
M.Bartlam,
J.Y.Wu,
and
Z.Rao
(2006).
Structural basis of Robo proline-rich motif recognition by the srGAP1 Src homology 3 domain in the Slit-Robo signaling pathway.
|
| |
J Biol Chem,
281,
28430-28437.
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PDB code:
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A.Rath,
A.R.Davidson,
and
C.M.Deber
(2005).
The structure of "unstructured" regions in peptides and proteins: role of the polyproline II helix in protein folding and recognition.
|
| |
Biopolymers,
80,
179-185.
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D.Jozic,
N.Cárdenes,
Y.L.Deribe,
G.Moncalián,
D.Hoeller,
Y.Groemping,
I.Dikic,
K.Rittinger,
and
J.Bravo
(2005).
Cbl promotes clustering of endocytic adaptor proteins.
|
| |
Nat Struct Mol Biol,
12,
972-979.
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PDB codes:
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D.Wildes,
and
S.Marqusee
(2005).
Hydrogen exchange and ligand binding: ligand-dependent and ligand-independent protection in the Src SH3 domain.
|
| |
Protein Sci,
14,
81-88.
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E.Ferraro,
A.Via,
G.Ausiello,
and
M.Helmer-Citterich
(2005).
A neural strategy for the inference of SH3 domain-peptide interaction specificity.
|
| |
BMC Bioinformatics,
6,
S13.
|
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F.Bauer,
K.Schweimer,
H.Meiselbach,
S.Hoffmann,
P.Rösch,
and
H.Sticht
(2005).
Structural characterization of Lyn-SH3 domain in complex with a herpesviral protein reveals an extended recognition motif that enhances binding affinity.
|
| |
Protein Sci,
14,
2487-2498.
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PDB code:
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I.Levchenko,
R.A.Grant,
J.M.Flynn,
R.T.Sauer,
and
T.A.Baker
(2005).
Versatile modes of peptide recognition by the AAA+ adaptor protein SspB.
|
| |
Nat Struct Mol Biol,
12,
520-525.
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PDB code:
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Regulation of Btk function by a major autophosphorylation site within the SH3 domain.
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Immunity,
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Multiple SH3 domain interactions regulate NADPH oxidase assembly in whole cells.
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The solution structure of human thioredoxin complexed with its target from Ref-1 reveals peptide chain reversal.
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Structure,
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PDB codes:
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J.Shi,
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CR16, a novel proline-rich protein expressed in rat brain neurons, binds to SH3 domains and is a MAP kinase substrate.
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J Mol Neurosci,
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Structure of rat procathepsin B: model for inhibition of cysteine protease activity by the proregion.
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Structure,
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PDB codes:
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Biochemistry,
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Mol Divers,
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WW domains of Nedd4 bind to the proline-rich PY motifs in the epithelial Na+ channel deleted in Liddle's syndrome.
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EMBO J,
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Drosophila photoreceptor axon guidance and targeting requires the dreadlocks SH2/SH3 adapter protein.
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Cell,
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Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.
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Molecular basis for the binding of SH3 ligands with non-peptide elements identified by combinatorial synthesis.
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Chem Biol,
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PDB codes:
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S.Grzesiek,
A.Bax,
G.M.Clore,
A.M.Gronenborn,
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The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase.
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Nat Struct Biol,
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PDB code:
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S.Grzesiek,
S.J.Stahl,
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The CD4 determinant for downregulation by HIV-1 Nef directly binds to Nef. Mapping of the Nef binding surface by NMR.
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Biochemistry,
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S.Yamasaki,
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The kinase, SH3, and SH2 domains of Lck play critical roles in T-cell activation after ZAP-70 membrane localization.
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Mol Cell Biol,
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The quaking gene product necessary in embryogenesis and myelination combines features of RNA binding and signal transduction proteins.
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Nat Genet,
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Crystallographic analysis of endogenous peptides associated with HLA-DR1 suggests a common, polyproline II-like conformation for bound peptides.
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Proc Natl Acad Sci U S A,
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Probing the chemical basis of binding activity in an SH3 domain by protein signature analysis.
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Chem Biol,
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W.A.Lim
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Reading between the lines: SH3 recognition of an intact protein.
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Structure,
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Curr Biol,
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Affinity and specificity requirements for the first Src homology 3 domain of the Crk proteins.
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EMBO J,
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D.Cowburn,
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A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein.
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EMBO J,
14,
5006-5015.
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D.N.Sgouras,
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R.J.Fisher,
D.G.Blair,
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ERF: an ETS domain protein with strong transcriptional repressor activity, can suppress ets-associated tumorigenesis and is regulated by phosphorylation during cell cycle and mitogenic stimulation.
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EMBO J,
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Complete nucleotide sequence, expression, and chromosomal localisation of human mixed-lineage kinase 2.
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Eur J Biochem,
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Cell,
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The protein product of the c-cbl protooncogene is phosphorylated after B cell receptor stimulation and binds the SH3 domain of Bruton's tyrosine kinase.
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J Exp Med,
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Grb2 SH3 binding to peptides from Sos: evaluation of a general model for SH3-ligand interactions.
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Chem Biol,
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J.M.Robinson,
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Histochem Cell Biol,
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J.W.Becker,
A.I.Marcy,
L.L.Rokosz,
M.G.Axel,
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C.K.Esser,
W.K.Hagmann,
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Stromelysin-1: three-dimensional structure of the inhibited catalytic domain and of the C-truncated proenzyme.
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Protein Sci,
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PDB codes:
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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.
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Proc Natl Acad Sci U S A,
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A family of phosphoinositide 3-kinases in Drosophila identifies a new mediator of signal transduction.
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Phage display selection of ligand residues important for Src homology 3 domain binding specificity.
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Proc Natl Acad Sci U S A,
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The murine form of TXK, a novel TEC kinase expressed in thymus maps to chromosome 5.
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Mamm Genome,
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S.Feng,
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R.J.Rickles,
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Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands.
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Proc Natl Acad Sci U S A,
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PDB codes:
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T.Raabe,
J.P.Olivier,
B.Dickson,
X.Liu,
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Biochemical and genetic analysis of the Drk SH2/SH3 adaptor protein of Drosophila.
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EMBO J,
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Mutations altering the mitochondrial-cytoplasmic distribution of Mod5p implicate the actin cytoskeleton and mRNA 3' ends and/or protein synthesis in mitochondrial delivery.
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W.H.Robinson,
H.E.Neuman de Vegvar,
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J.W.Rhee,
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Human CD6 possesses a large, alternatively spliced cytoplasmic domain.
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Eur J Immunol,
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A.Sali,
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Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk.
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Structure,
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PDB codes:
|
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|
Z.Weng,
R.J.Rickles,
S.Feng,
S.Richard,
A.S.Shaw,
S.L.Schreiber,
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J.S.Brugge
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Structure-function analysis of SH3 domains: SH3 binding specificity altered by single amino acid substitutions.
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Mol Cell Biol,
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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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