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* Residue conservation analysis
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Enzyme class:
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Chains A, B:
E.C.?
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Nature
375:203-211
(1995)
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PubMed id:
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Structural determinants of nuclear receptor assembly on DNA direct repeats.
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F.Rastinejad,
T.Perlmann,
R.M.Evans,
P.B.Sigler.
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ABSTRACT
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Nuclear receptor heterodimers recognize response elements composed of two direct
repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base
pairs. The 1.9 A crystal structure of the complex formed by the DNA-binding
domains of the 9-cis retinoic acid receptor and thyroid hormone receptor bound
to a thyroid-response element shows that the subunits interact through a
DNA-supported interface involving the carboxy-terminal extension of the
DNA-binding domain of the thyroid hormone receptor. The stereochemistry suggests
a mechanism by which heterodimers recognize the inter-half-site spacing between
direct repeats.
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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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J.Zhang,
M.J.Chalmers,
K.R.Stayrook,
L.L.Burris,
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D.J.Kojetin,
J.A.Dodge,
T.P.Burris,
and
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(2011).
DNA binding alters coactivator interaction surfaces of the intact VDR-RXR complex.
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Nat Struct Mol Biol,
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556-563.
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and
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Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings.
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Nat Struct Mol Biol,
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Molecular evidence for a functional ecdysone signaling system in Brugia malayi.
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PLoS Negl Trop Dis,
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I.H.Chan,
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A conserved lysine in the thyroid hormone receptor-alpha1 DNA-binding domain, mutated in hepatocellular carcinoma, serves as a sensor for transcriptional regulation.
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Mol Cancer Res,
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M.van Dijk,
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Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.
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R.R.Attia,
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B.D.Putcha,
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Direct interdomain interactions can mediate allosterism in the thyroid receptor.
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J Biol Chem,
284,
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B.Xu,
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(2009).
Dax-1 and steroid receptor RNA activator (SRA) function as transcriptional coactivators for steroidogenic factor 1 in steroidogenesis.
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Mol Cell Biol,
29,
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I.H.Chan,
and
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(2009).
Thyroid hormone receptor mutants implicated in human hepatocellular carcinoma display an altered target gene repertoire.
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Oncogene,
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L.S.Chan,
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Cross-Talk between PPARs and the Partners of RXR: A Molecular Perspective.
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PPAR Res,
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925309.
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B.J.Mengeling,
S.Lee,
and
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(2008).
Coactivator recruitment is enhanced by thyroid hormone receptor trimers.
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| |
Mol Cell Endocrinol,
280,
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M.D.Krasowski,
E.J.Reschly,
and
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(2008).
Intrinsic disorder in nuclear hormone receptors.
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| |
J Proteome Res,
7,
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P.Lu,
G.B.Rha,
M.Melikishvili,
G.Wu,
B.C.Adkins,
M.G.Fried,
and
Y.I.Chi
(2008).
Structural Basis of Natural Promoter Recognition by a Unique Nuclear Receptor, HNF4{alpha}: DIABETES GENE PRODUCT.
|
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J Biol Chem,
283,
33685-33697.
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PDB code:
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S.C.Roemer,
J.Adelman,
M.E.Churchill,
and
D.P.Edwards
(2008).
Mechanism of high-mobility group protein B enhancement of progesterone receptor sequence-specific DNA binding.
|
| |
Nucleic Acids Res,
36,
3655-3666.
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T.Krusiński,
M.Wietrzych,
I.Grad,
A.Ozyhar,
and
P.Dobryszycki
(2008).
Equilibrium Analysis of the DNA Binding Domain of the Ultraspiracle Protein Interaction with the Response Element from the hsp27 Gene Promoter-the Application of Molecular Beacon Technology.
|
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J Fluoresc,
18,
1.
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V.Chandra,
P.Huang,
Y.Hamuro,
S.Raghuram,
Y.Wang,
T.P.Burris,
and
F.Rastinejad
(2008).
Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA.
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Nature,
456,
350-356.
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PDB codes:
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D.L.Bain,
A.F.Heneghan,
K.D.Connaghan-Jones,
and
M.T.Miura
(2007).
Nuclear receptor structure: implications for function.
|
| |
Annu Rev Physiol,
69,
201-220.
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D.Nguyen,
M.Bail,
G.Pesant,
V.N.Dupont,
E.Rouault,
J.Deschênes,
W.Rocha,
G.Melançon,
S.V.Steinberg,
and
S.Mader
(2007).
Rational design of an estrogen receptor mutant with altered DNA-binding specificity.
|
| |
Nucleic Acids Res,
35,
3465-3477.
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L.F.Velasco,
M.Togashi,
P.G.Walfish,
R.P.Pessanha,
F.N.Moura,
G.B.Barra,
P.Nguyen,
R.Rebong,
C.Yuan,
L.A.Simeoni,
R.C.Ribeiro,
J.D.Baxter,
P.Webb,
and
F.A.Neves
(2007).
Thyroid hormone response element organization dictates the composition of active receptor.
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| |
J Biol Chem,
282,
12458-12466.
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M.Jakób,
R.Kołodziejczyk,
M.Orłowski,
S.Krzywda,
A.Kowalska,
J.Dutko-Gwóźdź,
T.Gwóźdź,
M.Kochman,
M.Jaskólski,
and
A.Ozyhar
(2007).
Novel DNA-binding element within the C-terminal extension of the nuclear receptor DNA-binding domain.
|
| |
Nucleic Acids Res,
35,
2705-2718.
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PDB code:
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I.H.Chan,
and
M.L.Privalsky
(2006).
Thyroid hormone receptors mutated in liver cancer function as distorted antimorphs.
|
| |
Oncogene,
25,
3576-3588.
|
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|
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|
|
S.C.Roemer,
D.C.Donham,
L.Sherman,
V.H.Pon,
D.P.Edwards,
and
M.E.Churchill
(2006).
Structure of the progesterone receptor-deoxyribonucleic acid complex: novel interactions required for binding to half-site response elements.
|
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Mol Endocrinol,
20,
3042-3052.
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PDB code:
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T.T.Hörkkö,
K.Tuppurainen,
S.M.George,
P.Jernvall,
T.J.Karttunen,
and
M.J.Mäkinen
(2006).
Thyroid hormone receptor beta1 in normal colon and colorectal cancer-association with differentiation, polypoid growth type and K-ras mutations.
|
| |
Int J Cancer,
118,
1653-1659.
|
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J.E.Donald,
and
E.I.Shakhnovich
(2005).
Predicting specificity-determining residues in two large eukaryotic transcription factor families.
|
| |
Nucleic Acids Res,
33,
4455-4465.
|
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K.A.Temple,
R.N.Cohen,
S.R.Wondisford,
C.Yu,
D.Deplewski,
and
F.E.Wondisford
(2005).
An intact DNA-binding domain is not required for peroxisome proliferator-activated receptor gamma (PPARgamma) binding and activation on some PPAR response elements.
|
| |
J Biol Chem,
280,
3529-3540.
|
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|
|
S.C.Perera,
S.Zheng,
Q.L.Feng,
P.J.Krell,
A.Retnakaran,
and
S.R.Palli
(2005).
Heterodimerization of ecdysone receptor and ultraspiracle on symmetric and asymmetric response elements.
|
| |
Arch Insect Biochem Physiol,
60,
55-70.
|
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|
|
|
|
|
Y.Shostak,
and
K.R.Yamamoto
(2005).
Overlapping but separable determinants of DNA binding and nuclear localization map to the C-terminal end of the Caenorhabditis elegans DAF-12 DNA binding domain.
|
| |
J Biol Chem,
280,
6554-6560.
|
|
|
|
|
|
|
A.B.de la Hoz,
F.Pratto,
R.Misselwitz,
C.Speck,
W.Weihofen,
K.Welfle,
W.Saenger,
H.Welfle,
and
J.C.Alonso
(2004).
Recognition of DNA by omega protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats.
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| |
Nucleic Acids Res,
32,
3136-3147.
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|
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|
A.Reményi,
H.R.Schöler,
and
M.Wilmanns
(2004).
Combinatorial control of gene expression.
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| |
Nat Struct Mol Biol,
11,
812-815.
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B.Xu,
and
R.J.Koenig
(2004).
An RNA-binding domain in the thyroid hormone receptor enhances transcriptional activation.
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J Biol Chem,
279,
33051-33056.
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C.Guarnaccia,
B.Raman,
S.Zahariev,
A.Simoncsits,
and
S.Pongor
(2004).
DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains.
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| |
Nucleic Acids Res,
32,
4992-5002.
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P.L.Shaffer,
A.Jivan,
D.E.Dollins,
F.Claessens,
and
D.T.Gewirth
(2004).
Structural basis of androgen receptor binding to selective androgen response elements.
|
| |
Proc Natl Acad Sci U S A,
101,
4758-4763.
|
|
|
PDB code:
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V.S.Melvin,
C.Harrell,
J.S.Adelman,
W.L.Kraus,
M.Churchill,
and
D.P.Edwards
(2004).
The role of the C-terminal extension (CTE) of the estrogen receptor alpha and beta DNA binding domain in DNA binding and interaction with HMGB.
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| |
J Biol Chem,
279,
14763-14771.
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Y.Umemura,
T.Ishiduka,
R.Yamamoto,
and
M.Esaka
(2004).
The Dof domain, a zinc finger DNA-binding domain conserved only in higher plants, truly functions as a Cys2/Cys2 Zn finger domain.
|
| |
Plant J,
37,
741-749.
|
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C.Frank,
M.M.Gonzalez,
C.Oinonen,
T.W.Dunlop,
and
C.Carlberg
(2003).
Characterization of DNA complexes formed by the nuclear receptor constitutive androstane receptor.
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| |
J Biol Chem,
278,
43299-43310.
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G.Mainguy,
P.M.In der Rieden,
E.Berezikov,
J.M.Woltering,
R.H.Plasterk,
and
A.J.Durston
(2003).
A position-dependent organisation of retinoid response elements is conserved in the vertebrate Hox clusters.
|
| |
Trends Genet,
19,
476-479.
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H.Fischer,
S.M.Dias,
M.A.Santos,
A.C.Alves,
N.Zanchin,
A.F.Craievich,
J.W.Apriletti,
J.D.Baxter,
P.Webb,
F.A.Neves,
R.C.Ribeiro,
and
I.Polikarpov
(2003).
Low resolution structures of the retinoid X receptor DNA-binding and ligand-binding domains revealed by synchrotron X-ray solution scattering.
|
| |
J Biol Chem,
278,
16030-16038.
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|
M.A.Lazar
(2003).
Thyroid hormone action: a binding contract.
|
| |
J Clin Invest,
112,
497-499.
|
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M.E.Colosimo,
S.Tran,
and
P.Sengupta
(2003).
The divergent orphan nuclear receptor ODR-7 regulates olfactory neuron gene expression via multiple mechanisms in Caenorhabditis elegans.
|
| |
Genetics,
165,
1779-1791.
|
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M.T.Mizwicki,
and
A.W.Norman
(2003).
Two key proteins of the vitamin D endocrine system come into crystal clear focus: comparison of the X-ray structures of the nuclear receptor for 1alpha,25(OH)2 vitamin D3, the plasma vitamin D binding protein, and their ligands.
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| |
J Bone Miner Res,
18,
795-806.
|
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|
N.Shibusawa,
A.N.Hollenberg,
and
F.E.Wondisford
(2003).
Thyroid hormone receptor DNA binding is required for both positive and negative gene regulation.
|
| |
J Biol Chem,
278,
732-738.
|
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|
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|
|
|
S.Devarakonda,
J.M.Harp,
Y.Kim,
A.Ozyhar,
and
F.Rastinejad
(2003).
Structure of the heterodimeric ecdysone receptor DNA-binding complex.
|
| |
EMBO J,
22,
5827-5840.
|
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PDB codes:
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T.Oosterveen,
P.van Vliet,
J.Deschamps,
and
F.Meijlink
(2003).
The direct context of a hox retinoic acid response element is crucial for its activity.
|
| |
J Biol Chem,
278,
24103-24107.
|
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V.Bloch,
Y.Yang,
E.Margeat,
A.Chavanieu,
M.T.Augé,
B.Robert,
S.Arold,
S.Rimsky,
and
M.Kochoyan
(2003).
The H-NS dimerization domain defines a new fold contributing to DNA recognition.
|
| |
Nat Struct Biol,
10,
212-218.
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PDB code:
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V.Vivat-Hannah,
W.Bourguet,
M.Gottardis,
and
H.Gronemeyer
(2003).
Separation of retinoid X receptor homo- and heterodimerization functions.
|
| |
Mol Cell Biol,
23,
7678-7688.
|
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|
|
|
|
F.D.Urnov
(2002).
A feel for the template: zinc finger protein transcription factors and chromatin.
|
| |
Biochem Cell Biol,
80,
321-333.
|
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|
|
|
|
J.R.Schultz,
M.A.Loven,
V.M.Melvin,
D.P.Edwards,
and
A.M.Nardulli
(2002).
Differential modulation of DNA conformation by estrogen receptors alpha and beta.
|
| |
J Biol Chem,
277,
8702-8707.
|
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|
J.R.Tata
(2002).
Signalling through nuclear receptors.
|
| |
Nat Rev Mol Cell Biol,
3,
702-710.
|
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|
|
M.Quack,
C.Frank,
and
C.Carlberg
(2002).
Differential nuclear receptor signalling from DR4-type response elements.
|
| |
J Cell Biochem,
86,
601-612.
|
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|
|
P.L.Shaffer,
and
D.T.Gewirth
(2002).
Structural basis of VDR-DNA interactions on direct repeat response elements.
|
| |
EMBO J,
21,
2242-2252.
|
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|
PDB codes:
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|
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|
|
V.S.Melvin,
S.C.Roemer,
M.E.Churchill,
and
D.P.Edwards
(2002).
The C-terminal extension (CTE) of the nuclear hormone receptor DNA binding domain determines interactions and functional response to the HMGB-1/-2 co-regulatory proteins.
|
| |
J Biol Chem,
277,
25115-25124.
|
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|
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|
|
Y.B.Shi,
J.W.Ritchie,
and
P.M.Taylor
(2002).
Complex regulation of thyroid hormone action: multiple opportunities for pharmacological intervention.
|
| |
Pharmacol Ther,
94,
235-251.
|
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|
|
|
|
|
Z.Morávek,
S.Neidle,
and
B.Schneider
(2002).
Protein and drug interactions in the minor groove of DNA.
|
| |
Nucleic Acids Res,
30,
1182-1191.
|
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|
|
D.M.Campisi,
V.Calabro,
and
A.D.Frankel
(2001).
Structure-based design of a dimeric RNA-peptide complex.
|
| |
EMBO J,
20,
178-186.
|
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|
|
|
|
|
F.Rastinejad
(2001).
Retinoid X receptor and its partners in the nuclear receptor family.
|
| |
Curr Opin Struct Biol,
11,
33-38.
|
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|
|
H.Hauksdóttir,
and
M.L.Privalsky
(2001).
DNA recognition by the aberrant retinoic acid receptors implicated in human acute promyelocytic leukemia.
|
| |
Cell Growth Differ,
12,
85-98.
|
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H.Thomassin,
M.Flavin,
M.L.Espinás,
and
T.Grange
(2001).
Glucocorticoid-induced DNA demethylation and gene memory during development.
|
| |
EMBO J,
20,
1974-1983.
|
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|
|
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|
|
I.Grad,
A.Niedziela-Majka,
M.Kochman,
and
A.Ozyhar
(2001).
Analysis of Usp DNA binding domain targeting reveals critical determinants of the ecdysone receptor complex interaction with the response element.
|
| |
Eur J Biochem,
268,
3751-3758.
|
|
|
|
|
|
|
J.J.Kohler,
and
A.Schepartz
(2001).
Kinetic studies of Fos.Jun.DNA complex formation: DNA binding prior to dimerization.
|
| |
Biochemistry,
40,
130-142.
|
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|
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|
|
J.Zhang,
P.Kuehl,
E.D.Green,
J.W.Touchman,
P.B.Watkins,
A.Daly,
S.D.Hall,
P.Maurel,
M.Relling,
C.Brimer,
K.Yasuda,
S.A.Wrighton,
M.Hancock,
R.B.Kim,
S.Strom,
K.Thummel,
C.G.Russell,
J.R.Hudson,
E.G.Schuetz,
and
M.S.Boguski
(2001).
The human pregnane X receptor: genomic structure and identification and functional characterization of natural allelic variants.
|
| |
Pharmacogenetics,
11,
555-572.
|
|
|
|
|
|
|
N.V.Grishin
(2001).
Treble clef finger--a functionally diverse zinc-binding structural motif.
|
| |
Nucleic Acids Res,
29,
1703-1714.
|
|
|
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|
|
P.Rotkiewicz,
W.Sicinska,
A.Kolinski,
and
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