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PDBsum entry 2eze
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DNA binding protein/DNA
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PDB id
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2eze
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Nat Struct Biol
4:657-665
(1997)
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PubMed id:
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The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif.
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J.R.Huth,
C.A.Bewley,
M.S.Nissen,
J.N.Evans,
R.Reeves,
A.M.Gronenborn,
G.M.Clore.
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ABSTRACT
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The solution structure of a complex between a truncated form of HMG-I(Y),
consisting of the second and third DNA binding domains (residues 51-90), and a
DNA dodecamer containing the PRDII site of the interferon-beta promoter has been
solved by multidimensional nuclear magnetic resonance spectroscopy. The
stoichiometry of the complex is one molecule of HMG-I(Y) to two molecules of
DNA. The structure reveals a new architectural minor groove binding motif which
stabilizes B-DNA, thereby facilitating the binding of other transcription
factors in the opposing major groove. The interactions involve a central
Arg-Gly-Arg motif together with two other modules that participate in extensive
hydrophobic and polar contracts. The absence of one of these modules in the
third DNA binding domain accounts for its-100 fold reduced affinity relative to
the second one.
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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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P.L.Privalov,
A.I.Dragan,
and
C.Crane-Robinson
(2011).
Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components.
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| |
Nucleic Acids Res,
39,
2483-2491.
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V.N.Uversky
(2011).
Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes.
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Chem Soc Rev,
40,
1623-1634.
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B.Chen,
J.Young,
and
F.Leng
(2010).
DNA bending by the mammalian high-mobility group protein AT hook 2.
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Biochemistry,
49,
1590-1595.
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B.R.Gordon,
Y.Li,
L.Wang,
A.Sintsova,
H.van Bakel,
S.Tian,
W.W.Navarre,
B.Xia,
and
J.Liu
(2010).
Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis.
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| |
Proc Natl Acad Sci U S A,
107,
5154-5159.
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PDB code:
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G.Perales,
A.I.Burguete-García,
J.Dimas,
M.Bahena-Román,
V.H.Bermúdez-Morales,
J.Moreno,
and
V.Madrid-Marina
(2010).
A polymorphism in the AT-hook motif of the transcriptional regulator AKNA is a risk factor for cervical cancer.
|
| |
Biomarkers,
15,
470-474.
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R.M.Baron,
S.Lopez-Guzman,
D.F.Riascos,
A.A.Macias,
M.D.Layne,
G.Cheng,
C.Harris,
S.W.Chung,
R.Reeves,
U.H.von Andrian,
and
M.A.Perrella
(2010).
Distamycin A inhibits HMGA1-binding to the P-selectin promoter and attenuates lung and liver inflammation during murine endotoxemia.
|
| |
PLoS One,
5,
e10656.
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R.Reeves
(2010).
Nuclear functions of the HMG proteins.
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Biochim Biophys Acta,
1799,
3.
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B.Zhang,
J.Chang,
M.Fu,
J.Huang,
R.Kashyap,
E.Salavaggione,
S.Jain,
K.Shashikant,
M.A.Deardorff,
M.L.Uzielli,
D.Dorsett,
D.C.Beebe,
P.Y.Jay,
R.O.Heuckeroth,
I.Krantz,
and
J.Milbrandt
(2009).
Dosage effects of cohesin regulatory factor PDS5 on mammalian development: implications for cohesinopathies.
|
| |
PLoS ONE,
4,
e5232.
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F.García-Heras,
S.Padmanabhan,
F.J.Murillo,
and
M.Elías-Arnanz
(2009).
Functional equivalence of HMGA- and histone H1-like domains in a bacterial transcriptional factor.
|
| |
Proc Natl Acad Sci U S A,
106,
13546-13551.
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G.Gerlitz,
R.Hock,
T.Ueda,
and
M.Bustin
(2009).
The dynamics of HMG protein-chromatin interactions in living cells.
|
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Biochem Cell Biol,
87,
127-137.
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G.Singh,
S.Aras,
A.H.Zea,
S.Koochekpour,
and
A.Aiyar
(2009).
Optimal transactivation by Epstein-Barr nuclear antigen 1 requires the UR1 and ATH1 domains.
|
| |
J Virol,
83,
4227-4235.
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H.Summer,
O.Li,
Q.Bao,
L.Zhan,
S.Peter,
P.Sathiyanathan,
D.Henderson,
T.Klonisch,
S.D.Goodman,
and
P.Dröge
(2009).
HMGA2 exhibits dRP/AP site cleavage activity and protects cancer cells from DNA-damage-induced cytotoxicity during chemotherapy.
|
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Nucleic Acids Res,
37,
4371-4384.
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K.Pfannkuche,
H.Summer,
O.Li,
J.Hescheler,
and
P.Dröge
(2009).
The high mobility group protein HMGA2: a co-regulator of chromatin structure and pluripotency in stem cells?
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Stem Cell Rev Rep,
5,
224-230.
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K.S.Weiler
(2009).
The Multi-AT-Hook Chromosomal Protein of Drosophila melanogaster, D1, Is Dispensable for Viability.
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Genetics,
182,
145-159.
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M.A.Grant,
R.M.Baron,
A.A.Macias,
M.D.Layne,
M.A.Perrella,
and
A.C.Rigby
(2009).
Netropsin improves survival from endotoxaemia by disrupting HMGA1 binding to the NOS2 promoter.
|
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Biochem J,
418,
103-112.
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S.Joynt,
V.Morillo,
and
F.Leng
(2009).
Binding the mammalian high mobility group protein AT-hook 2 to AT-rich deoxyoligonucleotides: enthalpy-entropy compensation.
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Biophys J,
96,
4144-4152.
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T.E.Haran,
and
U.Mohanty
(2009).
The unique structure of A-tracts and intrinsic DNA bending.
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Q Rev Biophys,
42,
41-81.
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Y.Yonetani,
and
H.Kono
(2009).
Sequence dependencies of DNA deformability and hydration in the minor groove.
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Biophys J,
97,
1138-1147.
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A.Abyzov,
A.Uzun,
P.R.Strauss,
and
V.A.Ilyin
(2008).
An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces.
|
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PLoS Comput Biol,
4,
e1000066.
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B.A.Rasala,
C.Ramos,
A.Harel,
and
D.J.Forbes
(2008).
Capture of AT-rich chromatin by ELYS recruits POM121 and NDC1 to initiate nuclear pore assembly.
|
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Mol Biol Cell,
19,
3982-3996.
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C.R.Houchens,
W.Lu,
R.Y.Chuang,
M.G.Frattini,
A.Fuller,
P.Simancek,
and
T.J.Kelly
(2008).
Multiple Mechanisms Contribute to Schizosaccharomyces pombe Origin Recognition Complex-DNA Interactions.
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J Biol Chem,
283,
30216-30224.
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K.S.Lee,
D.Bumbaca,
J.Kosman,
P.Setlow,
and
M.J.Jedrzejas
(2008).
Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species.
|
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Proc Natl Acad Sci U S A,
105,
2806-2811.
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M.Fuxreiter,
P.Tompa,
I.Simon,
V.N.Uversky,
J.C.Hansen,
and
F.J.Asturias
(2008).
Malleable machines take shape in eukaryotic transcriptional regulation.
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Nat Chem Biol,
4,
728-737.
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O.A.Zill,
and
J.Rine
(2008).
Interspecies variation reveals a conserved repressor of alpha-specific genes in Saccharomyces yeasts.
|
| |
Genes Dev,
22,
1704-1716.
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R.Takamiya,
R.M.Baron,
S.F.Yet,
M.D.Layne,
and
M.A.Perrella
(2008).
High mobility group A1 protein mediates human nitric oxide synthase 2 gene expression.
|
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FEBS Lett,
582,
810-814.
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W.Wan,
W.Wang,
and
A.D.Li
(2008).
HMGA1a protein unfolds or refolds synthetic DNA-chromophore hybrid polymers: a chaperone-like behavior.
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Chembiochem,
9,
304-311.
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Y.Miao,
T.Cui,
F.Leng,
and
W.D.Wilson
(2008).
Inhibition of high-mobility-group A2 protein binding to DNA by netropsin: a biosensor-surface plasmon resonance assay.
|
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Anal Biochem,
374,
7.
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D.Panne,
T.Maniatis,
and
S.C.Harrison
(2007).
An atomic model of the interferon-beta enhanceosome.
|
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Cell,
129,
1111-1123.
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PDB codes:
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G.A.Dement,
S.C.Maloney,
and
R.Reeves
(2007).
Nuclear HMGA1 nonhistone chromatin proteins directly influence mitochondrial transcription, maintenance, and function.
|
| |
Exp Cell Res,
313,
77-87.
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G.Cattaruzzi,
S.Altamura,
M.A.Tessari,
A.Rustighi,
V.Giancotti,
C.Pucillo,
and
G.Manfioletti
(2007).
The second AT-hook of the architectural transcription factor HMGA2 is determinant for nuclear localization and function.
|
| |
Nucleic Acids Res,
35,
1751-1760.
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Q.Zhang,
and
Y.Wang
(2007).
Homeodomain-interacting protein kinase-2 (HIPK2) phosphorylates HMGA1a at Ser-35, Thr-52, and Thr-77 and modulates its DNA binding affinity.
|
| |
J Proteome Res,
6,
4711-4719.
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R.Joshi,
J.M.Passner,
R.Rohs,
R.Jain,
A.Sosinsky,
M.A.Crickmore,
V.Jacob,
A.K.Aggarwal,
B.Honig,
and
R.S.Mann
(2007).
Functional specificity of a Hox protein mediated by the recognition of minor groove structure.
|
| |
Cell,
131,
530-543.
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PDB codes:
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R.M.Bannen,
C.A.Bingman,
and
G.N.Phillips
(2007).
Effect of low-complexity regions on protein structure determination.
|
| |
J Struct Funct Genomics,
8,
217-226.
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T.Kubota,
S.Maezawa,
K.Koiwai,
T.Hayano,
and
O.Koiwai
(2007).
Identification of functional domains in TdIF1 and its inhibitory mechanism for TdT activity.
|
| |
Genes Cells,
12,
941-959.
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V.H.Adams,
S.J.McBryant,
P.A.Wade,
C.L.Woodcock,
and
J.C.Hansen
(2007).
Intrinsic disorder and autonomous domain function in the multifunctional nuclear protein, MeCP2.
|
| |
J Biol Chem,
282,
15057-15064.
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C.Crane-Robinson,
A.I.Dragan,
and
P.L.Privalov
(2006).
The extended arms of DNA-binding domains: a tale of tails.
|
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Trends Biochem Sci,
31,
547-552.
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F.Turlure,
G.Maertens,
S.Rahman,
P.Cherepanov,
and
A.Engelman
(2006).
A tripartite DNA-binding element, comprised of the nuclear localization signal and two AT-hook motifs, mediates the association of LEDGF/p75 with chromatin in vivo.
|
| |
Nucleic Acids Res,
34,
1653-1675.
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J.Liu,
N.B.Perumal,
C.J.Oldfield,
E.W.Su,
V.N.Uversky,
and
A.K.Dunker
(2006).
Intrinsic disorder in transcription factors.
|
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Biochemistry,
45,
6873-6888.
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M.Peñalver-Mellado,
F.García-Heras,
S.Padmanabhan,
D.García-Moreno,
F.J.Murillo,
and
M.Elías-Arnanz
(2006).
Recruitment of a novel zinc-bound transcriptional factor by a bacterial HMGA-type protein is required for regulating multiple processes in Myxococcus xanthus.
|
| |
Mol Microbiol,
61,
910-926.
|
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M.Singh,
L.D'Silva,
and
T.A.Holak
(2006).
DNA-binding properties of the recombinant high-mobility-group-like AT-hook-containing region from human BRG1 protein.
|
| |
Biol Chem,
387,
1469-1478.
|
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R.Sgarra,
J.Lee,
M.A.Tessari,
S.Altamura,
B.Spolaore,
V.Giancotti,
M.T.Bedford,
and
G.Manfioletti
(2006).
The AT-hook of the chromatin architectural transcription factor high mobility group A1a is arginine-methylated by protein arginine methyltransferase 6.
|
| |
J Biol Chem,
281,
3764-3772.
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A.K.Dunker,
M.S.Cortese,
P.Romero,
L.M.Iakoucheva,
and
V.N.Uversky
(2005).
Flexible nets. The roles of intrinsic disorder in protein interaction networks.
|
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FEBS J,
272,
5129-5148.
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D.D.Edberg,
J.N.Adkins,
D.L.Springer,
and
R.Reeves
(2005).
Dynamic and differential in vivo modifications of the isoform HMGA1a and HMGA1b chromatin proteins.
|
| |
J Biol Chem,
280,
8961-8973.
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J.E.Adair,
Y.Kwon,
G.A.Dement,
M.J.Smerdon,
and
R.Reeves
(2005).
Inhibition of nucleotide excision repair by high mobility group protein HMGA1.
|
| |
J Biol Chem,
280,
32184-32192.
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V.N.Uversky,
C.J.Oldfield,
and
A.K.Dunker
(2005).
Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling.
|
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J Mol Recognit,
18,
343-384.
|
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P.M.Ayton,
E.H.Chen,
and
M.L.Cleary
(2004).
Binding to nonmethylated CpG DNA is essential for target recognition, transactivation, and myeloid transformation by an MLL oncoprotein.
|
| |
Mol Cell Biol,
24,
10470-10478.
|
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S.Fujimoto,
S.Matsunaga,
M.Yonemura,
S.Uchiyama,
T.Azuma,
and
K.Fukui
(2004).
Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces.
|
| |
Plant Mol Biol,
56,
225-239.
|
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B.Beitzel,
and
F.Bushman
(2003).
Construction and analysis of cells lacking the HMGA gene family.
|
| |
Nucleic Acids Res,
31,
5025-5032.
|
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|
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J.Sears,
J.Kolman,
G.M.Wahl,
and
A.Aiyar
(2003).
Metaphase chromosome tethering is necessary for the DNA synthesis and maintenance of oriP plasmids but is insufficient for transcription activation by Epstein-Barr nuclear antigen 1.
|
| |
J Virol,
77,
11767-11780.
|
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|
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|
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M.L.Cayuela,
M.Elías-Arnanz,
M.Peñalver-Mellado,
S.Padmanabhan,
and
F.J.Murillo
(2003).
The Stigmatella aurantiaca homolog of Myxococcus xanthus high-mobility-group A-type transcription factor CarD: insights into the functional modules of CarD and their distribution in bacteria.
|
| |
J Bacteriol,
185,
3527-3537.
|
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|
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R.Reeves
(2003).
HMGA proteins: flexibility finds a nuclear niche?
|
| |
Biochem Cell Biol,
81,
185-195.
|
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|
S.Vashee,
C.Cvetic,
W.Lu,
P.Simancek,
T.J.Kelly,
and
J.C.Walter
(2003).
Sequence-independent DNA binding and replication initiation by the human origin recognition complex.
|
| |
Genes Dev,
17,
1894-1908.
|
|
|
|
|
|
|
B.Berkowitz,
D.B.Huang,
F.E.Chen-Park,
P.B.Sigler,
and
G.Ghosh
(2002).
The x-ray crystal structure of the NF-kappa B p50.p65 heterodimer bound to the interferon beta -kappa B site.
|
| |
J Biol Chem,
277,
24694-24700.
|
|
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PDB codes:
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C.D.Shaffer,
G.E.Stephens,
B.A.Thompson,
L.Funches,
J.A.Bernat,
C.A.Craig,
and
S.C.Elgin
(2002).
Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin.
|
| |
Proc Natl Acad Sci U S A,
99,
14332-14337.
|
|
|
|
|
|
|
C.R.Escalante,
L.Shen,
D.Thanos,
and
A.K.Aggarwal
(2002).
Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter.
|
| |
Structure,
10,
383-391.
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PDB code:
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C.I.Webster,
L.C.Packman,
and
J.C.Gray
(2001).
HMG-1 enhances HMG-I/Y binding to an A/T-rich enhancer element from the pea plastocyanin gene.
|
| |
Eur J Biochem,
268,
3154-3162.
|
|
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|
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|
|
P.Romero,
Z.Obradovic,
X.Li,
E.C.Garner,
C.J.Brown,
and
A.K.Dunker
(2001).
Sequence complexity of disordered protein.
|
| |
Proteins,
42,
38-48.
|
|
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|
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|
|
P.Thunyakitpisal,
M.Alvarez,
K.Tokunaga,
J.E.Onyia,
J.Hock,
N.Ohashi,
H.Feister,
S.J.Rhodes,
and
J.P.Bidwell
(2001).
Cloning and functional analysis of a family of nuclear matrix transcription factors (NP/NMP4) that regulate type I collagen expression in osteoblasts.
|
| |
J Bone Miner Res,
16,
10-23.
|
|
|
|
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|
|
R.Reeves,
D.D.Edberg,
and
Y.Li
(2001).
Architectural transcription factor HMGI(Y) promotes tumor progression and mesenchymal transition of human epithelial cells.
|
| |
Mol Cell Biol,
21,
575-594.
|
|
|
|
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|
|
S.Padmanabhan,
M.Elías-Arnanz,
E.Carpio,
P.Aparicio,
and
F.J.Murillo
(2001).
Domain architecture of a high mobility group A-type bacterial transcriptional factor.
|
| |
J Biol Chem,
276,
41566-41575.
|
|
|
|
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|
|
W.Ross,
A.Ernst,
and
R.L.Gourse
(2001).
Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove.
|
| |
Genes Dev,
15,
491-506.
|
|
|
|
|
|
|
A.Slama-Schwok,
K.Zakrzewska,
G.Léger,
Y.Leroux,
M.Takahashi,
E.Käs,
and
P.Debey
(2000).
Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence.
|
| |
Biophys J,
78,
2543-2559.
|
|
|
|
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|
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C.I.Webster,
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PDB code:
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J.R.Huth,
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