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DNA binding protein/DNA
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PDB id
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1hrz
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* Residue conservation analysis
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Gene Ontology (GO) functional annotation
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Cellular component
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nucleus
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1 term
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Biological process
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male sex determination
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1 term
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Biochemical function
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protein binding
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3 terms
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DOI no:
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Cell
81:705-714
(1995)
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PubMed id:
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Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex.
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M.H.Werner,
J.R.Huth,
A.M.Gronenborn,
G.M.Clore.
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ABSTRACT
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The solution structure of the specific complex between the high mobility group
(HMG) domain of SRY (hSRY-HMG), the protein encoded by the human
testis-determining gene, and its DNA target site in the promoter of the
müllerian inhibitory substance gene has been determined by multidimensional NMR
spectroscopy. hSRY-HMG has a twisted L shape that presents a concave surface
(made up of three helices and the N- and C-terminal strands) to the DNA for
sequence-specific recognition. Binding of hSRY-HMG to its specific target site
occurs exclusively in the minor groove and induces a large conformational change
in the DNA. The DNA in the complex has an overall 70 degrees-80 degrees bend and
is helically unwound relative to classical A- and B-DNA. The structure of the
complex reveals the origin of sequence-specific binding within the HMG-1/HMG-2
family and provides a framework for understanding the effects of point mutations
that cause 46X,Y sex reversal at the atomic level.
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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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|
E.Ntini,
and
E.A.Wimmer
(2011).
Unique establishment of procephalic head segments is supported by the identification of cis-regulatory elements driving segment-specific segment polarity gene expression in Drosophila.
|
| |
Dev Genes Evol, 221,
1.
|
|
|
|
|
|
|
M.Firczuk,
M.Wojciechowski,
H.Czapinska,
and
M.Bochtler
(2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
|
| |
Nucleic Acids Res, 39,
744-754.
|
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|
PDB code:
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|
C.Murata,
F.Yamada,
N.Kawauchi,
Y.Matsuda,
and
A.Kuroiwa
(2010).
Multiple copies of SRY on the large Y chromosome of the Okinawa spiny rat, Tokudaia muenninki.
|
| |
Chromosome Res, 18,
623-634.
|
|
|
|
|
|
|
M.L.Harris,
L.L.Baxter,
S.K.Loftus,
and
W.J.Pavan
(2010).
Sox proteins in melanocyte development and melanoma.
|
| |
Pigment Cell Melanoma Res, 23,
496-513.
|
|
|
|
|
|
|
T.Martin,
S.W.Lu,
H.van Tilbeurgh,
D.R.Ripoll,
C.Dixelius,
B.G.Turgeon,
and
R.Debuchy
(2010).
Tracing the origin of the fungal α1 domain places its ancestor in the HMG-box superfamily: implication for fungal mating-type evolution.
|
| |
PLoS One, 5,
e15199.
|
|
|
|
|
|
|
W.Xu,
and
J.Y.Li
(2010).
SOX11 expression in mantle cell lymphoma.
|
| |
Leuk Lymphoma, 51,
1962-1967.
|
|
|
|
|
|
|
C.Gontan,
T.Güttler,
E.Engelen,
J.Demmers,
M.Fornerod,
F.G.Grosveld,
D.Tibboel,
D.Görlich,
R.A.Poot,
and
R.J.Rottier
(2009).
Exportin 4 mediates a novel nuclear import pathway for Sox family transcription factors.
|
| |
J Cell Biol, 185,
27-34.
|
|
|
|
|
|
|
G.M.Clore,
and
J.Iwahara
(2009).
Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.
|
| |
Chem Rev, 109,
4108-4139.
|
|
|
|
|
|
|
J.A.Hanover,
D.C.Love,
and
W.A.Prinz
(2009).
Calmodulin-driven Nuclear Entry: Trigger for Sex Determination and Terminal Differentiation.
|
| |
J Biol Chem, 284,
12593-12597.
|
|
|
|
|
|
|
J.B.Wu,
K.Chen,
Y.Li,
Y.F.Lau,
and
J.C.Shih
(2009).
Regulation of monoamine oxidase A by the SRY gene on the Y chromosome.
|
| |
FASEB J, 23,
4029-4038.
|
|
|
|
|
|
|
P.L.Privalov,
A.I.Dragan,
and
C.Crane-Robinson
(2009).
The cost of DNA bending.
|
| |
Trends Biochem Sci, 34,
464-470.
|
|
|
|
|
|
|
T.A.Gangelhoff,
P.S.Mungalachetty,
J.C.Nix,
and
M.E.Churchill
(2009).
Structural analysis and DNA binding of the HMG domains of the human mitochondrial transcription factor A.
|
| |
Nucleic Acids Res, 37,
3153-3164.
|
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PDB code:
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M.Morín,
A.Viñuela,
T.Rivera,
M.Villamar,
M.A.Moreno-Pelayo,
F.Moreno,
and
I.del Castillo
(2008).
A de novo missense mutation in the gene encoding the SOX10 transcription factor in a Spanish sporadic case of Waardenburg syndrome type IV.
|
| |
Am J Med Genet A, 146,
1032-1037.
|
|
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|
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S.Ek,
M.Dictor,
M.Jerkeman,
K.Jirström,
and
C.A.Borrebaeck
(2008).
Nuclear expression of the non B-cell lineage Sox11 transcription factor identifies mantle cell lymphoma.
|
| |
Blood, 111,
800-805.
|
|
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|
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F.A.Atcha,
A.Syed,
B.Wu,
N.P.Hoverter,
N.N.Yokoyama,
J.H.Ting,
J.E.Munguia,
H.J.Mangalam,
J.L.Marsh,
and
M.L.Waterman
(2007).
A unique DNA binding domain converts T-cell factors into strong Wnt effectors.
|
| |
Mol Cell Biol, 27,
8352-8363.
|
|
|
|
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|
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G.Gimelli,
S.Gimelli,
N.Dimasi,
R.Bocciardi,
E.Di Battista,
T.Pramparo,
and
O.Zuffardi
(2007).
Identification and molecular modelling of a novel familial mutation in the SRY gene implicated in the pure gonadal dysgenesis.
|
| |
Eur J Hum Genet, 15,
76-80.
|
|
|
|
|
|
|
V.Lefebvre,
B.Dumitriu,
A.Penzo-Méndez,
Y.Han,
and
B.Pallavi
(2007).
Control of cell fate and differentiation by Sry-related high-mobility-group box (Sox) transcription factors.
|
| |
Int J Biochem Cell Biol, 39,
2195-2214.
|
|
|
|
|
|
|
Y.Xu,
R.Tashiro,
and
H.Sugiyama
(2007).
Photochemical determination of different DNA structures.
|
| |
Nat Protoc, 2,
78-87.
|
|
|
|
|
|
|
A.L.Donner,
and
T.Williams
(2006).
Frontal nasal prominence expression driven by Tcfap2a relies on a conserved binding site for STAT proteins.
|
| |
Dev Dyn, 235,
1358-1370.
|
|
|
|
|
|
|
S.Teletchéa,
S.Komeda,
J.M.Teuben,
M.A.Elizondo-Riojas,
J.Reedijk,
and
J.Kozelka
(2006).
A pyrazolato-bridged dinuclear platinum(II) complex induces only minor distortions upon DNA-binding.
|
| |
Chemistry, 12,
3741-3753.
|
|
|
|
|
|
|
S.Wissmüller,
T.Kosian,
M.Wolf,
M.Finzsch,
and
M.Wegner
(2006).
The high-mobility-group domain of Sox proteins interacts with DNA-binding domains of many transcription factors.
|
| |
Nucleic Acids Res, 34,
1735-1744.
|
|
|
|
|
|
|
Y.Xu,
and
H.Sugiyama
(2006).
Photochemical approach to probing different DNA structures.
|
| |
Angew Chem Int Ed Engl, 45,
1354-1362.
|
|
|
|
|
|
|
B.Pils,
R.R.Copley,
and
J.Schultz
(2005).
Variation in structural location and amino acid conservation of functional sites in protein domain families.
|
| |
BMC Bioinformatics, 6,
210.
|
|
|
|
|
|
|
C.Y.Chen,
T.P.Ko,
T.W.Lin,
C.C.Chou,
C.J.Chen,
and
A.H.Wang
(2005).
Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d.
|
| |
Nucleic Acids Res, 33,
430-438.
|
|
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PDB codes:
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M.Wegner
(2005).
Secrets to a healthy Sox life: lessons for melanocytes.
|
| |
Pigment Cell Res, 18,
74-85.
|
|
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|
|
|
|
E.Kamau,
K.T.Bauerle,
and
A.Grove
(2004).
The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains.
|
| |
J Biol Chem, 279,
55234-55240.
|
|
|
|
|
|
|
S.Matsutani
(2004).
Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III.
|
| |
BMC Evol Biol, 4,
26.
|
|
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|
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A.Argentaro,
H.Sim,
S.Kelly,
S.Preiss,
A.Clayton,
D.A.Jans,
and
V.R.Harley
(2003).
A SOX9 defect of calmodulin-dependent nuclear import in campomelic dysplasia/autosomal sex reversal.
|
| |
J Biol Chem, 278,
33839-33847.
|
|
|
|
|
|
|
A.Irrthum,
K.Devriendt,
D.Chitayat,
G.Matthijs,
C.Glade,
P.M.Steijlen,
J.P.Fryns,
M.A.Van Steensel,
and
M.Vikkula
(2003).
Mutations in the transcription factor gene SOX18 underlie recessive and dominant forms of hypotrichosis-lymphedema-telangiectasia.
|
| |
Am J Hum Genet, 72,
1470-1478.
|
|
|
|
|
|
|
A.Reményi,
K.Lins,
L.J.Nissen,
R.Reinbold,
H.R.Schöler,
and
M.Wilmanns
(2003).
Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers.
|
| |
Genes Dev, 17,
2048-2059.
|
|
|
PDB code:
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|
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|
|
C.Beloin,
J.Jeusset,
B.Revet,
G.Mirambeau,
F.Le Hégarat,
and
E.Le Cam
(2003).
Contribution of DNA conformation and topology in right-handed DNA wrapping by the Bacillus subtilis LrpC protein.
|
| |
J Biol Chem, 278,
5333-5342.
|
|
|
|
|
|
|
C.L.Li,
L.I.Hor,
Z.F.Chang,
L.C.Tsai,
W.Z.Yang,
and
H.S.Yuan
(2003).
DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site.
|
| |
EMBO J, 22,
4014-4025.
|
|
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PDB codes:
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D.Serban,
J.M.Benevides,
and
G.J.Thomas
(2003).
HU protein employs similar mechanisms of minor-groove recognition in binding to different B-DNA sites: demonstration by Raman spectroscopy.
|
| |
Biochemistry, 42,
7390-7399.
|
|
|
|
|
|
|
E.O'Flaherty,
and
J.Kaye
(2003).
TOX defines a conserved subfamily of HMG-box proteins.
|
| |
BMC Genomics, 4,
13.
|
|
|
|
|
|
|
H.N.Cinar,
K.L.Richards,
K.S.Oommen,
and
A.P.Newman
(2003).
The EGL-13 SOX domain transcription factor affects the uterine pi cell lineages in Caenorhabditis elegans.
|
| |
Genetics, 165,
1623-1628.
|
|
|
|
|
|
|
I.Gómez-Pinto,
V.Marchán,
F.Gago,
A.Grandas,
and
C.González
(2003).
Solution structure and stability of tryptophan-containing nucleopeptide duplexes.
|
| |
Chembiochem, 4,
40-49.
|
|
|
PDB code:
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|
|
J.G.Luz,
C.A.Hassig,
C.Pickle,
A.Godzik,
B.J.Meyer,
and
I.A.Wilson
(2003).
XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators.
|
| |
Genes Dev, 17,
977-990.
|
|
|
PDB code:
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|
|
J.Klass,
F.V.Murphy,
S.Fouts,
M.Serenil,
A.Changela,
J.Siple,
and
M.E.Churchill
(2003).
The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity.
|
| |
Nucleic Acids Res, 31,
2852-2864.
|
|
|
|
|
|
|
L.Baldazzi,
A.Nicoletti,
M.Gennari,
M.Barbaro,
P.Pirazzoli,
A.Cicognani,
E.Cacciari,
and
A.Nicolettic
(2003).
Two new point mutations of the SRY gene identified in two Italian 46,XY females with gonadal dysgenesis.
|
| |
Clin Genet, 64,
258-260.
|
|
|
|
|
|
|
B.Schlierf,
A.Ludwig,
K.Klenovsek,
and
M.Wegner
(2002).
Cooperative binding of Sox10 to DNA: requirements and consequences.
|
| |
Nucleic Acids Res, 30,
5509-5516.
|
|
|
|
|
|
|
E.Kanaya,
N.Nakajima,
and
K.Okada
(2002).
Non-sequence-specific DNA binding by the FILAMENTOUS FLOWER protein from Arabidopsis thaliana is reduced by EDTA.
|
| |
J Biol Chem, 277,
11957-11964.
|
|
|
|
|
|
|
J.Kasparkova,
J.Zehnulova,
N.Farrell,
and
V.Brabec
(2002).
DNA interstrand cross-links of the novel antitumor trinuclear platinum complex BBR3464. Conformation, recognition by high mobility group domain proteins, and nucleotide excision repair.
|
| |
J Biol Chem, 277,
48076-48086.
|
|
|
|
|
|
|
L.M.Budde,
C.Wu,
C.Tilman,
I.Douglas,
and
S.Ghosh
(2002).
Regulation of IkappaBbeta expression in testis.
|
| |
Mol Biol Cell, 13,
4179-4194.
|
|
|
|
|
|
|
M.M.Bharath,
N.R.Chandra,
and
M.R.Rao
(2002).
Prediction of an HMG-box fold in the C-terminal domain of histone H1: insights into its role in DNA condensation.
|
| |
Proteins, 49,
71-81.
|
|
|
|
|
|
|
S.Baud,
E.Margeat,
S.Lumbroso,
F.Paris,
C.Sultan,
C.Royer,
and
N.Poujol
(2002).
Equilibrium binding assays reveal the elevated stoichiometry and salt dependence of the interaction between full-length human sex-determining region on the Y chromosome (SRY) and DNA.
|
| |
J Biol Chem, 277,
18404-18410.
|
|
|
|
|
|
|
U.Narendra,
L.Zhu,
B.Li,
J.Wilken,
and
M.A.Weiss
(2002).
Sex-specific gene regulation. The Doublesex DM motif is a bipartite DNA-binding domain.
|
| |
J Biol Chem, 277,
43463-43473.
|
|
|
|
|
|
|
V.Oleinikov,
A.Sukhanova,
K.Mochalov,
O.Ustinova,
I.Kudelina,
I.Bronstein,
and
I.Nabiev
(2002).
DNA binding induces conformational transition within human DNA topoisomerase I in solution.
|
| |
Biopolymers, 67,
369-375.
|
|
|
|
|
|
|
B.Li,
W.Zhang,
G.Chan,
A.Jancso-Radek,
S.Liu,
and
M.A.Weiss
(2001).
Human sex reversal due to impaired nuclear localization of SRY. A clinical correlation.
|
| |
J Biol Chem, 276,
46480-46484.
|
|
|
|
|
|
|
J.K.Forwood,
V.Harley,
and
D.A.Jans
(2001).
The C-terminal nuclear localization signal of the sex-determining region Y (SRY) high mobility group domain mediates nuclear import through importin beta 1.
|
| |
J Biol Chem, 276,
46575-46582.
|
|
|
|
|
|
|
J.O.Thomas,
and
A.A.Travers
(2001).
HMG1 and 2, and related 'architectural' DNA-binding proteins.
|
| |
Trends Biochem Sci, 26,
167-174.
|
|
|
|
|
|
|
L.Dailey,
and
C.Basilico
(2001).
Coevolution of HMG domains and homeodomains and the generation of transcriptional regulation by Sox/POU complexes.
|
| |
J Cell Physiol, 186,
315-328.
|
|
|
|
|
|
|
M.Stros
(2001).
Two mutations of basic residues within the N-terminus of HMG-1 B domain with different effects on DNA supercoiling and binding to bent DNA.
|
| |
Biochemistry, 40,
4769-4779.
|
|
|
|
|
|
|
P.D.Cary,
C.M.Read,
B.Davis,
P.C.Driscoll,
and
C.Crane-Robinson
(2001).
Solution structure and backbone dynamics of the DNA-binding domain of mouse Sox-5.
|
| |
Protein Sci, 10,
83-98.
|
|
|
PDB code:
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|
|
P.Scaffidi,
and
M.E.Bianchi
(2001).
Spatially precise DNA bending is an essential activity of the sox2 transcription factor.
|
| |
J Biol Chem, 276,
47296-47302.
|
|
|
|
|
|
|
R.Cerdan,
D.Payet,
J.C.Yang,
A.A.Travers,
and
D.Neuhaus
(2001).
HMG-D complexed to a bulge DNA: an NMR model.
|
| |
Protein Sci, 10,
504-518.
|
|
|
PDB code:
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|
|
T.Stockner,
C.Plugariu,
G.Koraimann,
G.Högenauer,
W.Bermel,
S.Prytulla,
and
H.Sterk
(2001).
Solution structure of the DNA-binding domain of TraM.
|
| |
Biochemistry, 40,
3370-3377.
|
|
|
PDB code:
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|
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|
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|
|
X.Yuan,
M.L.Lu,
T.Li,
and
S.P.Balk
(2001).
SRY interacts with and negatively regulates androgen receptor transcriptional activity.
|
| |
J Biol Chem, 276,
46647-46654.
|
|
|
|
|
|
|
Y.Kikuchi,
A.Agathon,
J.Alexander,
C.Thisse,
S.Waldron,
D.Yelon,
B.Thisse,
and
D.Y.Stainier
(2001).
casanova encodes a novel Sox-related protein necessary and sufficient for early endoderm formation in zebrafish.
|
| |
Genes Dev, 15,
1493-1505.
|
|
|
|
|
|
|
A.Travers
(2000).
Recognition of distorted DNA structures by HMG domains.
|
| |
Curr Opin Struct Biol, 10,
102-109.
|
|
|
|
|
|
|
C.Castagné,
E.C.Murphy,
A.M.Gronenborn,
and
M.Delepierre
(2000).
31P NMR analysis of the DNA conformation induced by protein binding SRY/DNA complexes.
|
| |
Eur J Biochem, 267,
1223-1229.
|
|
|
|
|
|
|
E.R.Jamieson,
and
S.J.Lippard
(2000).
Stopped-flow fluorescence studies of HMG-domain protein binding to cisplatin-modified DNA.
|
| |
Biochemistry, 39,
8426-8438.
|
|
|
|
|
|
|
F.V.Murphy,
and
M.E.Churchill
(2000).
Nonsequence-specific DNA recognition: a structural perspective.
|
| |
Structure, 8,
R83-R89.
|
|
|
|
|
|
|
H.Xin,
S.Taudte,
N.R.Kallenbach,
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PDB code:
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PDB code:
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Cisplatin-DNA adducts inhibit ribosomal RNA synthesis by hijacking the transcription factor human upstream binding factor.
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Nat Struct Biol, 5,
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PDB code:
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Y.G.Gao,
S.Y.Su,
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The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.
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Nat Struct Biol, 5,
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PDB codes:
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Nat Struct Biol, 4,
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PDB codes:
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J.R.Wísniewski,
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Structural and functional consequences of mutations within the hydrophobic cores of the HMG1-box domain of the Chironomus high-mobility-group protein 1a.
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Nat Struct Biol, 4,
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PDB code:
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L.H.Pevny,
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Solution structure of the ATF-2 recognition site and its interaction with the ATF-2 peptide.
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Nucleic Acids Res, 25,
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PDB code:
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P.A.Rice
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PDB code:
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PDB code:
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PDB codes:
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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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