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PDBsum entry 1pdr
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Signal transduction
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PDB id
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1pdr
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Contents |
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* Residue conservation analysis
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Nature
382:649-652
(1996)
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PubMed id:
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Crystal structure of a PDZ domain.
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J.H.Morais Cabral,
C.Petosa,
M.J.Sutcliffe,
S.Raza,
O.Byron,
F.Poy,
S.M.Marfatia,
A.H.Chishti,
R.C.Liddington.
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ABSTRACT
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PDZ domains (also known as DHR domains or GLGF repeats) are approximately
90-residue repeats found in a number of proteins implicated in ion-channel and
receptor clustering, and the linking of receptors to effector enzymes. PDZ
domains are protein-recognition modules; some recognize proteins containing the
consensus carboxy-terminal tripeptide motif S/TXV with high specificity. Other
PDZ domains form homotypic dimers: the PDZ domain of the neuronal enzyme nitric
oxide synthase binds to the PDZ domain of PSD-95, an interaction that has been
implicated in its synaptic association. Here we report the crystal structure of
the third PDZ domain of the human homologue of the Drosophila discs-large
tumour-suppressor gene product, DlgA. It consists of a five-stranded
antiparallel beta-barrel flanked by three alpha-helices. A groove runs over the
surface of the domain, ending in a conserved hydrophobic pocket and a buried
arginine; we suggest that this is the binding site for the C-terminal peptide.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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M.Sainlos,
C.Tigaret,
C.Poujol,
N.B.Olivier,
L.Bard,
C.Breillat,
K.Thiolon,
D.Choquet,
and
B.Imperiali
(2011).
Biomimetic divalent ligands for the acute disruption of synaptic AMPAR stabilization.
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Nat Chem Biol,
7,
81-91.
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PDB code:
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G.Kock,
M.Dicks,
R.Heumann,
K.S.Erdmann,
and
R.Stoll
(2010).
Sequence-specific 1H, 13C, and 15N assignment of the extended PDZ3 domain of the protein tyrosine phosphatase basophil-like PTP-BL.
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Biomol NMR Assign,
4,
199-202.
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H.J.Lee,
and
J.J.Zheng
(2010).
PDZ domains and their binding partners: structure, specificity, and modification.
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Cell Commun Signal,
8,
8.
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J.Li,
H.Kim,
D.G.Aceto,
J.Hung,
S.Aono,
and
K.J.Kemphues
(2010).
Binding to PKC-3, but not to PAR-3 or to a conventional PDZ domain ligand, is required for PAR-6 function in C. elegans.
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Dev Biol,
340,
88-98.
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Q.S.Du,
C.H.Wang,
S.M.Liao,
and
R.B.Huang
(2010).
Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain.
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PLoS One,
5,
e13207.
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S.Gianni,
Y.Ivarsson,
A.De Simone,
C.Travaglini-Allocatelli,
M.Brunori,
and
M.Vendruscolo
(2010).
Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain.
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Nat Struct Mol Biol,
17,
1431-1437.
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B.Sulka,
H.Lortat-Jacob,
R.Terreux,
F.Letourneur,
and
P.Rousselle
(2009).
Tyrosine dephosphorylation of the syndecan-1 PDZ binding domain regulates syntenin-1 recruitment.
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J Biol Chem,
284,
10659-10671.
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C.M.Petit,
J.Zhang,
P.J.Sapienza,
E.J.Fuentes,
and
A.L.Lee
(2009).
Hidden dynamic allostery in a PDZ domain.
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Proc Natl Acad Sci U S A,
106,
18249-18254.
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H.Chen,
S.Tong,
X.Li,
J.Wu,
Z.Zhu,
L.Niu,
and
M.Teng
(2009).
Structure of the second PDZ domain from human zonula occludens 2.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
327-330.
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PDB code:
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D.Bouvier,
F.Kieken,
A.Kellezi,
and
P.L.Sorgen
(2008).
Structural changes in the carboxyl terminus of the gap junction protein connexin 40 caused by the interaction with c-Src and zonula occludens-1.
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Cell Commun Adhes,
15,
107-118.
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L.Peng,
D.C.Popescu,
N.Wang,
and
B.H.Shieh
(2008).
Anchoring TRP to the INAD macromolecular complex requires the last 14 residues in its carboxyl terminus.
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J Neurochem,
104,
1526-1535.
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M.A.Estévez,
J.A.Henderson,
D.Ahn,
X.R.Zhu,
G.Poschmann,
H.Lübbert,
R.Marx,
and
J.M.Baraban
(2008).
The neuronal RhoA GEF, Tech, interacts with the synaptic multi-PDZ-domain-containing protein, MUPP1.
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J Neurochem,
106,
1287-1297.
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W.Zhou,
L.Zhang,
X.Guoxiang,
J.Mojsilovic-Petrovic,
K.Takamaya,
R.Sattler,
R.Huganir,
and
R.Kalb
(2008).
GluR1 controls dendrite growth through its binding partner, SAP97.
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J Neurosci,
28,
10220-10233.
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J.M.Elkins,
E.Papagrigoriou,
G.Berridge,
X.Yang,
C.Phillips,
C.Gileadi,
P.Savitsky,
and
D.A.Doyle
(2007).
Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions.
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Protein Sci,
16,
683-694.
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PDB codes:
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O.Gileadi,
S.Knapp,
W.H.Lee,
B.D.Marsden,
S.Müller,
F.H.Niesen,
K.L.Kavanagh,
L.J.Ball,
F.von Delft,
D.A.Doyle,
U.C.Oppermann,
and
M.Sundström
(2007).
The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.
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J Struct Funct Genomics,
8,
107-119.
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Q.Chen,
X.Niu,
Y.Xu,
J.Wu,
and
Y.Shi
(2007).
Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex.
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Protein Sci,
16,
1053-1062.
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PDB code:
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X.Chen,
J.C.Longgood,
C.Michnoff,
S.Wei,
D.E.Frantz,
and
L.Bezprozvanny
(2007).
High-throughput screen for small molecule inhibitors of Mint1-PDZ domains.
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Assay Drug Dev Technol,
5,
769-783.
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H.Kusunoki,
and
T.Kohno
(2006).
Solution structure of human erythroid p55 PDZ domain.
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Proteins,
64,
804-807.
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PDB code:
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I.von Ossowski,
E.Oksanen,
L.von Ossowski,
C.Cai,
M.Sundberg,
A.Goldman,
and
K.Keinänen
(2006).
Crystal structure of the second PDZ domain of SAP97 in complex with a GluR-A C-terminal peptide.
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FEBS J,
273,
5219-5229.
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PDB codes:
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K.Nagasaka,
S.Nakagawa,
T.Yano,
S.Takizawa,
Y.Matsumoto,
T.Tsuruga,
K.Nakagawa,
T.Minaguchi,
K.Oda,
O.Hiraike-Wada,
H.Ooishi,
T.Yasugi,
and
Y.Taketani
(2006).
Human homolog of Drosophila tumor suppressor Scribble negatively regulates cell-cycle progression from G1 to S phase by localizing at the basolateral membrane in epithelial cells.
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Cancer Sci,
97,
1217-1225.
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M.Joshi,
C.Vargas,
P.Boisguerin,
A.Diehl,
G.Krause,
P.Schmieder,
K.Moelling,
V.Hagen,
M.Schade,
and
H.Oschkinat
(2006).
Discovery of low-molecular-weight ligands for the AF6 PDZ domain.
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Angew Chem Int Ed Engl,
45,
3790-3795.
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PDB codes:
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S.Takizawa,
K.Nagasaka,
S.Nakagawa,
T.Yano,
K.Nakagawa,
T.Yasugi,
T.Takeuchi,
T.Kanda,
J.M.Huibregtse,
T.Akiyama,
and
Y.Taketani
(2006).
Human scribble, a novel tumor suppressor identified as a target of high-risk HPV E6 for ubiquitin-mediated degradation, interacts with adenomatous polyposis coli.
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Genes Cells,
11,
453-464.
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Y.Qian,
and
K.E.Prehoda
(2006).
Interdomain interactions in the tumor suppressor discs large regulate binding to the synaptic protein GukHolder.
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J Biol Chem,
281,
35757-35763.
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D.R.Glodowski,
T.Wright,
K.Martinowich,
H.C.Chang,
D.Beach,
and
C.Rongo
(2005).
Distinct LIN-10 domains are required for its neuronal function, its epithelial function, and its synaptic localization.
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Mol Biol Cell,
16,
1417-1426.
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H.Zhou,
Y.Xu,
Y.Yang,
A.Huang,
J.Wu,
and
Y.Shi
(2005).
Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from Neurexin and Bcr.
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J Biol Chem,
280,
13841-13847.
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PDB code:
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M.Groll,
M.Bochtler,
H.Brandstetter,
T.Clausen,
and
R.Huber
(2005).
Molecular machines for protein degradation.
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Chembiochem,
6,
222-256.
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S.Gianni,
A.Engström,
M.Larsson,
N.Calosci,
F.Malatesta,
L.Eklund,
C.C.Ngang,
C.Travaglini-Allocatelli,
and
P.Jemth
(2005).
The kinetics of PDZ domain-ligand interactions and implications for the binding mechanism.
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J Biol Chem,
280,
34805-34812.
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T.Jansén,
H.Kidron,
H.Taipaleenmäki,
T.Salminen,
and
P.Mäenpää
(2005).
Transcriptional profiles and structural models of the Synechocystis sp. PCC 6803 Deg proteases.
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Photosynth Res,
84,
57-63.
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W.R.Thelin,
C.A.Hodson,
and
S.L.Milgram
(2005).
Beyond the brush border: NHERF4 blazes new NHERF turf.
|
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J Physiol,
567,
13-19.
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C.Wilken,
K.Kitzing,
R.Kurzbauer,
M.Ehrmann,
and
T.Clausen
(2004).
Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease.
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Cell,
117,
483-494.
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PDB codes:
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J.L.Sanford,
T.A.Mays,
and
J.A.Rafael-Fortney
(2004).
CASK and Dlg form a PDZ protein complex at the mammalian neuromuscular junction.
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Muscle Nerve,
30,
164-171.
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M.L.Fitzgerald,
K.Okuhira,
G.F.Short,
J.J.Manning,
S.A.Bell,
and
M.W.Freeman
(2004).
ATP-binding cassette transporter A1 contains a novel C-terminal VFVNFA motif that is required for its cholesterol efflux and ApoA-I binding activities.
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J Biol Chem,
279,
48477-48485.
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C.C.Yun
(2003).
Concerted roles of SGK1 and the Na+/H+ exchanger regulatory factor 2 (NHERF2) in regulation of NHE3.
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Cell Physiol Biochem,
13,
29-40.
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C.Huang,
Q.Zhou,
P.Liang,
M.S.Hollander,
F.Sheikh,
X.Li,
M.Greaser,
G.D.Shelton,
S.Evans,
and
J.Chen
(2003).
Characterization and in vivo functional analysis of splice variants of cypher.
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J Biol Chem,
278,
7360-7365.
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K.S.Erdmann
(2003).
The protein tyrosine phosphatase PTP-Basophil/Basophil-like. Interacting proteins and molecular functions.
|
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Eur J Biochem,
270,
4789-4798.
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L.L.Parker,
J.R.Backstrom,
E.Sanders-Bush,
and
B.H.Shieh
(2003).
Agonist-induced phosphorylation of the serotonin 5-HT2C receptor regulates its interaction with multiple PDZ protein 1.
|
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J Biol Chem,
278,
21576-21583.
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M.van Ham,
H.Croes,
J.Schepens,
J.Fransen,
B.Wieringa,
and
W.Hendriks
(2003).
Cloning and characterization of mCRIP2, a mouse LIM-only protein that interacts with PDZ domain IV of PTP-BL.
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Genes Cells,
8,
631-644.
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N.J.Skelton,
M.F.Koehler,
K.Zobel,
W.L.Wong,
S.Yeh,
M.T.Pisabarro,
J.P.Yin,
L.A.Lasky,
and
S.S.Sidhu
(2003).
Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain.
|
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J Biol Chem,
278,
7645-7654.
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PDB code:
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Y.Mu,
T.Otsuka,
A.C.Horton,
D.B.Scott,
and
M.D.Ehlers
(2003).
Activity-dependent mRNA splicing controls ER export and synaptic delivery of NMDA receptors.
|
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Neuron,
40,
581-594.
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A.Piserchio,
M.Pellegrini,
S.Mehta,
S.M.Blackman,
E.P.Garcia,
J.Marshall,
and
D.F.Mierke
(2002).
The PDZ1 domain of SAP90. Characterization of structure and binding.
|
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J Biol Chem,
277,
6967-6973.
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PDB code:
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A.Y.Hung,
and
M.Sheng
(2002).
PDZ domains: structural modules for protein complex assembly.
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J Biol Chem,
277,
5699-5702.
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D.L.Silver
(2002).
A carboxyl-terminal PDZ-interacting domain of scavenger receptor B, type I is essential for cell surface expression in liver.
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J Biol Chem,
277,
34042-34047.
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F.Imamura,
S.Maeda,
T.Doi,
and
Y.Fujiyoshi
(2002).
Ligand binding of the second PDZ domain regulates clustering of PSD-95 with the Kv1.4 potassium channel.
|
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J Biol Chem,
277,
3640-3646.
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H.Brandstetter,
J.S.Kim,
M.Groll,
P.Göttig,
and
R.Huber
(2002).
Structural basis for the processive protein degradation by tricorn protease.
|
| |
Biol Chem,
383,
1157-1165.
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S.Karthikeyan,
T.Leung,
and
J.A.Ladias
(2002).
Structural determinants of the Na+/H+ exchanger regulatory factor interaction with the beta 2 adrenergic and platelet-derived growth factor receptors.
|
| |
J Biol Chem,
277,
18973-18978.
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PDB codes:
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T.Krojer,
M.Garrido-Franco,
R.Huber,
M.Ehrmann,
and
T.Clausen
(2002).
Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine.
|
| |
Nature,
416,
455-459.
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PDB code:
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W.Feng,
J.S.Fan,
M.Jiang,
Y.W.Shi,
and
M.Zhang
(2002).
PDZ7 of glutamate receptor interacting protein binds to its target via a novel hydrophobic surface area.
|
| |
J Biol Chem,
277,
41140-41146.
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PDB code:
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A.G.Lau,
and
R.A.Hall
(2001).
Oligomerization of NHERF-1 and NHERF-2 PDZ domains: differential regulation by association with receptor carboxyl-termini and by phosphorylation.
|
| |
Biochemistry,
40,
8572-8580.
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A.O.Stemmer-Rachamimov,
T.Wiederhold,
G.P.Nielsen,
M.James,
D.Pinney-Michalowski,
J.E.Roy,
W.A.Cohen,
V.Ramesh,
and
D.N.Louis
(2001).
NHE-RF, a merlin-interacting protein, is primarily expressed in luminal epithelia, proliferative endometrium, and estrogen receptor-positive breast carcinomas.
|
| |
Am J Pathol,
158,
57-62.
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B.Z.Harris,
B.J.Hillier,
and
W.A.Lim
(2001).
Energetic determinants of internal motif recognition by PDZ domains.
|
| |
Biochemistry,
40,
5921-5930.
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G.Webster,
T.Leung,
S.Karthikeyan,
G.Birrane,
and
J.A.Ladias
(2001).
Crystallographic characterization of the PDZ1 domain of the human Na+/H+ exchanger regulatory factor.
|
| |
Acta Crystallogr D Biol Crystallogr,
57,
714-716.
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M.E.Kimple,
D.P.Siderovski,
and
J.Sondek
(2001).
Functional relevance of the disulfide-linked complex of the N-terminal PDZ domain of InaD with NorpA.
|
| |
EMBO J,
20,
4414-4422.
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PDB code:
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M.Sheng,
and
C.Sala
(2001).
PDZ domains and the organization of supramolecular complexes.
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| |
Annu Rev Neurosci,
24,
1.
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Q.Zhang,
J.S.Fan,
and
M.Zhang
(2001).
Interdomain chaperoning between PSD-95, Dlg, and Zo-1 (PDZ) domains of glutamate receptor-interacting proteins.
|
| |
J Biol Chem,
276,
43216-43220.
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S.Galande,
L.A.Dickinson,
I.S.Mian,
M.Sikorska,
and
T.Kohwi-Shigematsu
(2001).
SATB1 cleavage by caspase 6 disrupts PDZ domain-mediated dimerization, causing detachment from chromatin early in T-cell apoptosis.
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| |
Mol Cell Biol,
21,
5591-5604.
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V.Raghuram,
D.O.Mak,
and
J.K.Foskett
(2001).
Regulation of cystic fibrosis transmembrane conductance regulator single-channel gating by bivalent PDZ-domain-mediated interaction.
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| |
Proc Natl Acad Sci U S A,
98,
1300-1305.
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C.C.Garner,
J.Nash,
and
R.L.Huganir
(2000).
PDZ domains in synapse assembly and signalling.
|
| |
Trends Cell Biol,
10,
274-280.
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G.Fuh,
M.T.Pisabarro,
Y.Li,
C.Quan,
L.A.Lasky,
and
S.S.Sidhu
(2000).
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PDB code:
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PDB code:
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E.Cuppen,
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PDZ motifs in PTP-BL and RIL bind to internal protein segments in the LIM domain protein RIL.
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ZO-3, a novel member of the MAGUK protein family found at the tight junction, interacts with ZO-1 and occludin.
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PDB code:
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J.Schultz,
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Specific interactions between the syntrophin PDZ domain and voltage-gated sodium channels.
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Nat Struct Biol,
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PDB code:
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Signal transduction molecules at the glutamatergic postsynaptic membrane.
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Structure of interleukin 16 resembles a PDZ domain with an occluded peptide binding site.
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PDB code:
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The LIN-2/LIN-7/LIN-10 complex mediates basolateral membrane localization of the C. elegans EGF receptor LET-23 in vulval epithelial cells.
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Coordination of an array of signaling proteins through homo- and heteromeric interactions between PDZ domains and target proteins.
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An atypical PKC directly associates and colocalizes at the epithelial tight junction with ASIP, a mammalian homologue of Caenorhabditis elegans polarity protein PAR-3.
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The human testis determining factor SRY binds a nuclear factor containing PDZ protein interaction domains.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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|
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