 |
PDBsum entry 1ctl
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Metal binding protein
|
PDB id
|
|
|
|
1ctl
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
Nat Struct Biol
1:388-398
(1994)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP.
|
|
G.C.Pérez-Alvarado,
C.Miles,
J.W.Michelsen,
H.A.Louis,
D.R.Winge,
M.C.Beckerle,
M.F.Summers.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The three dimensional solution structure of the carboxy terminal LIM domain of
the avian Cysteine Rich Protein (CRP) has been determined by nuclear magnetic
resonance spectroscopy. The domain contains two zinc atoms bound independently
in CCHC (C = Cys, H = His) and CCCC modules. Both modules contain two
orthogonally-arranged antiparallel beta-sheets, and the CCCC module contains an
alpha-helix at its C terminus. The modules pack due to hydrophobic interactions
forming a novel global fold. The structure of the C-terminal CCCC module is
essentially identical to that observed for the DNA-interactive CCCC modules of
the GATA-1 and steroid hormone receptor DNA binding domains, raising the
possibility that the LIM motif may have a DNA binding function.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
J.Krcmery,
T.Camarata,
A.Kulisz,
and
H.G.Simon
(2010).
Nucleocytoplasmic functions of the PDZ-LIM protein family: new insights into organ development.
|
| |
Bioessays,
32,
100-108.
|
|
|
|
|
|
|
L.Maurmann,
and
R.N.Bose
(2010).
Unwinding of zinc finger domain of DNA polymerase I by cis-diamminedichloroplatinum(II).
|
| |
Dalton Trans,
39,
7968-7979.
|
|
|
|
|
|
|
D.M.Alvarado,
R.Veile,
J.Speck,
M.Warchol,
and
M.Lovett
(2009).
Downstream targets of GATA3 in the vestibular sensory organs of the inner ear.
|
| |
Dev Dyn,
238,
3093-3102.
|
|
|
|
|
|
|
N.O.Deakin,
and
C.E.Turner
(2008).
Paxillin comes of age.
|
| |
J Cell Sci,
121,
2435-2444.
|
|
|
|
|
|
|
N.Wang,
J.S.Zhang,
Q.Zheng,
and
Y.Zhao
(2008).
The unique localization of ZFP185 at uropod of mouse T lymphocytes.
|
| |
Scand J Immunol,
67,
340-344.
|
|
|
|
|
|
|
D.Arnaud,
A.Déjardin,
J.C.Leplé,
M.C.Lesage-Descauses,
and
G.Pilate
(2007).
Genome-wide analysis of LIM gene family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa.
|
| |
DNA Res,
14,
103-116.
|
|
|
|
|
|
|
C.S.Hunter,
and
S.J.Rhodes
(2005).
LIM-homeodomain genes in mammalian development and human disease.
|
| |
Mol Biol Rep,
32,
67-77.
|
|
|
|
|
|
|
E.Tse,
A.J.Smith,
S.Hunt,
I.Lavenir,
A.Forster,
A.J.Warren,
G.Grutz,
L.Foroni,
M.B.Carlton,
W.H.Colledge,
T.Boehm,
and
T.H.Rabbitts
(2004).
Null mutation of the Lmo4 gene or a combined null mutation of the Lmo1/Lmo3 genes causes perinatal lethality, and Lmo4 controls neural tube development in mice.
|
| |
Mol Cell Biol,
24,
2063-2073.
|
|
|
|
|
|
|
H.El Mourabit,
S.Müller,
L.Tunggal,
M.Paulsson,
and
M.Aumailley
(2004).
Analysis of the adaptor function of the LIM domain-containing protein FHL2 using an affinity chromatography approach.
|
| |
J Cell Biochem,
92,
612-625.
|
|
|
|
|
|
|
J.E.Deane,
D.P.Ryan,
M.Sunde,
M.J.Maher,
J.M.Guss,
J.E.Visvader,
and
J.M.Matthews
(2004).
Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex.
|
| |
EMBO J,
23,
3589-3598.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.L.Kadrmas,
and
M.C.Beckerle
(2004).
The LIM domain: from the cytoskeleton to the nucleus.
|
| |
Nat Rev Mol Cell Biol,
5,
920-931.
|
|
|
|
|
|
|
A.Velyvis,
J.Vaynberg,
Y.Yang,
O.Vinogradova,
Y.Zhang,
C.Wu,
and
J.Qin
(2003).
Structural and functional insights into PINCH LIM4 domain-mediated integrin signaling.
|
| |
Nat Struct Biol,
10,
558-564.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.N.Gill
(2003).
Decoding the LIM development code.
|
| |
Trans Am Clin Climatol Assoc,
114,
179-189.
|
|
|
|
|
|
|
L.M.Hoffman,
D.A.Nix,
B.Benson,
R.Boot-Hanford,
E.Gustafsson,
C.Jamora,
A.S.Menzies,
K.L.Goh,
C.C.Jensen,
F.B.Gertler,
E.Fuchs,
R.Fässler,
and
M.C.Beckerle
(2003).
Targeted disruption of the murine zyxin gene.
|
| |
Mol Cell Biol,
23,
70-79.
|
|
|
|
|
|
|
M.Shimojo,
and
L.B.Hersh
(2003).
REST/NRSF-interacting LIM domain protein, a putative nuclear translocation receptor.
|
| |
Mol Cell Biol,
23,
9025-9031.
|
|
|
|
|
|
|
M.Wang,
Y.Hu,
and
M.E.Stearns
(2003).
A novel IL-10 signalling mechanism regulates TIMP-1 expression in human prostate tumour cells.
|
| |
Br J Cancer,
88,
1605-1614.
|
|
|
|
|
|
|
B.Khurana,
T.Khurana,
N.Khaire,
and
A.A.Noegel
(2002).
Functions of LIM proteins in cell polarity and chemotactic motility.
|
| |
EMBO J,
21,
5331-5342.
|
|
|
|
|
|
|
P.Kosarev,
K.F.Mayer,
and
C.S.Hardtke
(2002).
Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.
|
| |
Genome Biol,
3,
RESEARCH0016.
|
|
|
|
|
|
|
S.Cho,
and
D.W.Hoffman
(2002).
Structure of the beta subunit of translation initiation factor 2 from the archaeon Methanococcus jannaschii: a representative of the eIF2beta/eIF5 family of proteins.
|
| |
Biochemistry,
41,
5730-5742.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
Y.Liu,
G.A.Hair,
S.D.Boden,
M.Viggeswarapu,
and
L.Titus
(2002).
Overexpressed LIM mineralization proteins do not require LIM domains to induce bone.
|
| |
J Bone Miner Res,
17,
406-414.
|
|
|
|
|
|
|
J.F.Loring,
X.Wen,
J.M.Lee,
J.Seilhamer,
and
R.Somogyi
(2001).
A gene expression profile of Alzheimer's disease.
|
| |
DNA Cell Biol,
20,
683-695.
|
|
|
|
|
|
|
H.T.Chen,
P.Legault,
J.Glushka,
J.G.Omichinski,
and
R.A.Scott
(2000).
Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription.
|
| |
Protein Sci,
9,
1743-1752.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Kanungo,
S.J.Pratt,
H.Marie,
and
G.D.Longmore
(2000).
Ajuba, a cytosolic LIM protein, shuttles into the nucleus and affects embryonal cell proliferation and fate decisions.
|
| |
Mol Biol Cell,
11,
3299-3313.
|
|
|
|
|
|
|
D.C.Edwards,
and
G.N.Gill
(1999).
Structural features of LIM kinase that control effects on the actin cytoskeleton.
|
| |
J Biol Chem,
274,
11352-11361.
|
|
|
|
|
|
|
J.R.Henderson,
T.Macalma,
D.Brown,
J.A.Richardson,
E.N.Olson,
and
M.C.Beckerle
(1999).
The LIM protein, CRP1, is a smooth muscle marker.
|
| |
Dev Dyn,
214,
229-238.
|
|
|
|
|
|
|
L.Aravind,
and
G.Subramanian
(1999).
Origin of multicellular eukaryotes - insights from proteome comparisons.
|
| |
Curr Opin Genet Dev,
9,
688-694.
|
|
|
|
|
|
|
P.M.Guy,
D.A.Kenny,
and
G.N.Gill
(1999).
The PDZ domain of the LIM protein enigma binds to beta-tropomyosin.
|
| |
Mol Biol Cell,
10,
1973-1984.
|
|
|
|
|
|
|
R.K.Goyal,
P.Lin,
J.Kanungo,
A.S.Payne,
A.J.Muslin,
and
G.D.Longmore
(1999).
Ajuba, a novel LIM protein, interacts with Grb2, augments mitogen-activated protein kinase activity in fibroblasts, and promotes meiotic maturation of Xenopus oocytes in a Grb2- and Ras-dependent manner.
|
| |
Mol Cell Biol,
19,
4379-4389.
|
|
|
|
|
|
|
S.Brown,
M.J.McGrath,
L.M.Ooms,
R.Gurung,
M.M.Maimone,
and
C.A.Mitchell
(1999).
Characterization of two isoforms of the skeletal muscle LIM protein 1, SLIM1. Localization of SLIM1 at focal adhesions and the isoform slimmer in the nucleus of myoblasts and cytoplasm of myotubes suggests distinct roles in the cytoskeleton and in nuclear-cytoplasmic communication.
|
| |
J Biol Chem,
274,
27083-27091.
|
|
|
|
|
|
|
B.P.Lipsky,
C.R.Beals,
and
D.E.Staunton
(1998).
Leupaxin is a novel LIM domain protein that forms a complex with PYK2.
|
| |
J Biol Chem,
273,
11709-11713.
|
|
|
|
|
|
|
C.Alli,
and
G.G.Consalez
(1998).
Linkage mapping of Csrp to proximal mouse chromosome 3.
|
| |
Mamm Genome,
9,
172-173.
|
|
|
|
|
|
|
J.Curtiss,
and
J.S.Heilig
(1998).
DeLIMiting development.
|
| |
Bioessays,
20,
58-69.
|
|
|
|
|
|
|
N.D.Clarke,
and
J.M.Berg
(1998).
Zinc fingers in Caenorhabditis elegans: finding families and probing pathways.
|
| |
Science,
282,
2018-2022.
|
|
|
|
|
|
|
R.Konrat,
B.Kräutler,
R.Weiskirchen,
and
K.Bister
(1998).
Structure of cysteine- and glycine-rich protein CRP2. Backbone dynamics reveal motional freedom and independent spatial orientation of the lim domains.
|
| |
J Biol Chem,
273,
23233-23240.
|
|
|
|
|
|
|
A.P.Eijkelenboom,
F.M.van den Ent,
A.Vos,
J.F.Doreleijers,
K.Hård,
T.D.Tullius,
R.H.Plasterk,
R.Kaptein,
and
R.Boelens
(1997).
The solution structure of the amino-terminal HHCC domain of HIV-2 integrase: a three-helix bundle stabilized by zinc.
|
| |
Curr Biol,
7,
739-746.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.A.Nix,
and
M.C.Beckerle
(1997).
Nuclear-cytoplasmic shuttling of the focal contact protein, zyxin: a potential mechanism for communication between sites of cell adhesion and the nucleus.
|
| |
J Cell Biol,
138,
1139-1147.
|
|
|
|
|
|
|
D.Curtis,
D.K.Treiber,
F.Tao,
P.D.Zamore,
J.R.Williamson,
and
R.Lehmann
(1997).
A CCHC metal-binding domain in Nanos is essential for translational regulation.
|
| |
EMBO J,
16,
834-843.
|
|
|
|
|
|
|
H.A.Louis,
J.D.Pino,
K.L.Schmeichel,
P.Pomiès,
and
M.C.Beckerle
(1997).
Comparison of three members of the cysteine-rich protein family reveals functional conservation and divergent patterns of gene expression.
|
| |
J Biol Chem,
272,
27484-27491.
|
|
|
|
|
|
|
I.A.Wadman,
H.Osada,
G.G.Grütz,
A.D.Agulnick,
H.Westphal,
A.Forster,
and
T.H.Rabbitts
(1997).
The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins.
|
| |
EMBO J,
16,
3145-3157.
|
|
|
|
|
|
|
J.D.Johnson,
W.Zhang,
A.Rudnick,
W.J.Rutter,
and
M.S.German
(1997).
Transcriptional synergy between LIM-homeodomain proteins and basic helix-loop-helix proteins: the LIM2 domain determines specificity.
|
| |
Mol Cell Biol,
17,
3488-3496.
|
|
|
|
|
|
|
K.L.Schmeichel,
and
M.C.Beckerle
(1997).
Molecular dissection of a LIM domain.
|
| |
Mol Biol Cell,
8,
219-230.
|
|
|
|
|
|
|
P.Pomiès,
H.A.Louis,
and
M.C.Beckerle
(1997).
CRP1, a LIM domain protein implicated in muscle differentiation, interacts with alpha-actinin.
|
| |
J Cell Biol,
139,
157-168.
|
|
|
|
|
|
|
R.Toyama,
and
I.B.Dawid
(1997).
lim6, a novel LIM homeobox gene in the zebrafish: comparison of its expression pattern with lim1.
|
| |
Dev Dyn,
209,
406-417.
|
|
|
|
|
|
|
A.G.Elefanty,
M.Antoniou,
N.Custodio,
M.Carmo-Fonseca,
and
F.G.Grosveld
(1996).
GATA transcription factors associate with a novel class of nuclear bodies in erythroblasts and megakaryocytes.
|
| |
EMBO J,
15,
319-333.
|
|
|
|
|
|
|
A.Szabo,
R.Korszun,
F.U.Hartl,
and
J.Flanagan
(1996).
A zinc finger-like domain of the molecular chaperone DnaJ is involved in binding to denatured protein substrates.
|
| |
EMBO J,
15,
408-417.
|
|
|
|
|
|
|
B.E.Stronach,
S.E.Siegrist,
and
M.C.Beckerle
(1996).
Two muscle-specific LIM proteins in Drosophila.
|
| |
J Cell Biol,
134,
1179-1195.
|
|
|
|
|
|
|
D.Yablonski,
I.Marbach,
and
A.Levitzki
(1996).
Dimerization of Ste5, a mitogen-activated protein kinase cascade scaffold protein, is required for signal transduction.
|
| |
Proc Natl Acad Sci U S A,
93,
13864-13869.
|
|
|
|
|
|
|
R.C.Larson,
I.Lavenir,
T.A.Larson,
R.Baer,
A.J.Warren,
I.Wadman,
K.Nottage,
and
T.H.Rabbitts
(1996).
Protein dimerization between Lmo2 (Rbtn2) and Tal1 alters thymocyte development and potentiates T cell tumorigenesis in transgenic mice.
|
| |
EMBO J,
15,
1021-1027.
|
|
|
|
|
|
|
R.Wu,
K.Durick,
Z.Songyang,
L.C.Cantley,
S.S.Taylor,
and
G.N.Gill
(1996).
Specificity of LIM domain interactions with receptor tyrosine kinases.
|
| |
J Biol Chem,
271,
15934-15941.
|
|
|
|
|
|
|
T.Macalma,
J.Otte,
M.E.Hensler,
S.M.Bockholt,
H.A.Louis,
M.Kalff-Suske,
K.H.Grzeschik,
D.von der Ahe,
and
M.C.Beckerle
(1996).
Molecular characterization of human zyxin.
|
| |
J Biol Chem,
271,
31470-31478.
|
|
|
|
|
|
|
Z.Dauter,
K.S.Wilson,
L.C.Sieker,
J.M.Moulis,
and
J.Meyer
(1996).
Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.
|
| |
Proc Natl Acad Sci U S A,
93,
8836-8840.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
G.N.Gill
(1995).
The enigma of LIM domains.
|
| |
Structure,
3,
1285-1289.
|
|
|
|
|
|
|
H.Osada,
G.Grutz,
H.Axelson,
A.Forster,
and
T.H.Rabbitts
(1995).
Association of erythroid transcription factors: complexes involving the LIM protein RBTN2 and the zinc-finger protein GATA1.
|
| |
Proc Natl Acad Sci U S A,
92,
9585-9589.
|
|
|
|
|
|
|
M.Taira,
J.L.Evrard,
A.Steinmetz,
and
I.B.Dawid
(1995).
Classification of LIM proteins.
|
| |
Trends Genet,
11,
431-432.
|
|
|
|
|
|
|
R.Weiskirchen,
J.D.Pino,
T.Macalma,
K.Bister,
and
M.C.Beckerle
(1995).
The cysteine-rich protein family of highly related LIM domain proteins.
|
| |
J Biol Chem,
270,
28946-28954.
|
|
|
|
|
|
|
C.R.McLaughlin,
Q.Tao,
and
M.E.Abood
(1994).
Isolation and developmental expression of a rat cDNA encoding a cysteine-rich zinc finger protein.
|
| |
Nucleic Acids Res,
22,
5477-5483.
|
|
|
|
|
|
|
R.Feuerstein,
X.Wang,
D.Song,
N.E.Cooke,
and
S.A.Liebhaber
(1994).
The LIM/double zinc-finger motif functions as a protein dimerization domain.
|
| |
Proc Natl Acad Sci U S A,
91,
10655-10659.
|
|
|
|
|
|
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.
|
|
Links
