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PDBsum entry 1hmf
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* Residue conservation analysis
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Embo J
12:1311-1319
(1993)
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PubMed id:
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Structure of the HMG box motif in the B-domain of HMG1.
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H.M.Weir,
P.J.Kraulis,
C.S.Hill,
A.R.Raine,
E.D.Laue,
J.O.Thomas.
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ABSTRACT
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The conserved, abundant chromosomal protein HMG1 consists of two highly
homologous, folded, basic DNA-binding domains, each of approximately 80 amino
acid residues, and an acidic C-terminal tail. Each folded domain represents an
'HMG box', a sequence motif recently recognized in certain sequence-specific
DNA-binding proteins and which also occurs in abundant HMG1-like proteins that
bind to DNA without sequence specificity. The HMG box is defined by a set of
highly conserved residues (most distinctively aromatic and basic) and appears to
define a novel DNA-binding structural motif. We have expressed the HMG box
region of the B-domain of rat HMG1 (residues 88-164 of the intact protein) in
Escherichia coli and we describe here the determination of its structure by 2D
1H-NMR spectroscopy. There are three alpha-helices (residues 13-29, 34-48 and
50-74), which together account for approximately 75% of the total residues and
contain many of the conserved basic and aromatic residues. Strikingly, the
molecule is L-shaped, the angle of approximately 80 degrees between the two arms
being defined by a cluster of conserved, predominantly aromatic, residues. The
distinctive shape of the HMG box motif, which is distinct from hitherto
characterized DNA-binding motifs, may be significant in relation to its
recognition of four-way DNA junctions.
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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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D.Musumeci,
E.M.Bucci,
G.N.Roviello,
R.Sapio,
M.Valente,
M.Moccia,
M.E.Bianchi,
and
C.Pedone
(2011).
DNA-based strategies for blocking HMGB1 cytokine activity: design, synthesis and preliminary in vitro/in vivo assays of DNA and DNA-like duplexes.
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Mol Biosyst,
7,
1742-1752.
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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.
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PLoS One,
5,
e15199.
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W.Gong,
Y.Zheng,
F.Chao,
Y.Li,
Z.Xu,
G.Huang,
X.Gao,
S.Li,
and
F.He
(2010).
The anti-inflammatory activity of HMGB1 A box is enhanced when fused with C-terminal acidic tail.
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J Biomed Biotechnol,
2010,
915234.
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Y.Liu,
R.Prasad,
and
S.H.Wilson
(2010).
HMGB1: roles in base excision repair and related function.
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Biochim Biophys Acta,
1799,
119-130.
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A.Hayashi,
H.Nagafuchi,
I.Ito,
K.Hirota,
M.Yoshida,
and
S.Ozaki
(2009).
Lupus antibodies to the HMGB1 chromosomal protein: epitope mapping and association with disease activity.
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Mod Rheumatol,
19,
283-292.
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M.Thompson
(2009).
Polybromo-1: the chromatin targeting subunit of the PBAF complex.
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Biochimie,
91,
309-319.
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N.T.Sebastian,
E.M.Bystry,
N.A.Becker,
and
L.J.Maher
(2009).
Enhancement of DNA flexibility in vitro and in vivo by HMGB box A proteins carrying box B residues.
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Biochemistry,
48,
2125-2134.
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S.Zhang,
J.Zhong,
P.Yang,
F.Gong,
and
C.Y.Wang
(2009).
HMGB1, an innate alarmin, in the pathogenesis of type 1 diabetes.
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Int J Clin Exp Pathol,
3,
24-38.
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Y.Liu,
G.Y.Chen,
and
P.Zheng
(2009).
CD24-Siglec G/10 discriminates danger- from pathogen-associated molecular patterns.
|
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Trends Immunol,
30,
557-561.
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J.R.Klune,
R.Dhupar,
J.Cardinal,
T.R.Billiar,
and
A.Tsung
(2008).
HMGB1: endogenous danger signaling.
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Mol Med,
14,
476-484.
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K.Kasahara,
S.Ki,
K.Aoyama,
H.Takahashi,
and
T.Kokubo
(2008).
Saccharomyces cerevisiae HMO1 interacts with TFIID and participates in start site selection by RNA polymerase II.
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Nucleic Acids Res,
36,
1343-1357.
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M.M.Abhyankar,
A.E.Hochreiter,
J.Hershey,
C.Evans,
Y.Zhang,
O.Crasta,
B.W.Sobral,
B.J.Mann,
W.A.Petri,
and
C.A.Gilchrist
(2008).
Characterization of an Entamoeba histolytica high-mobility-group box protein induced during intestinal infection.
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Eukaryot Cell,
7,
1565-1572.
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N.A.Becker,
J.D.Kahn,
and
L.J.Maher
(2008).
Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation.
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Nucleic Acids Res,
36,
4009-4021.
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Q.Zhang,
and
Y.Wang
(2008).
High mobility group proteins and their post-translational modifications.
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Biochim Biophys Acta,
1784,
1159-1166.
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R.K.Aneja,
A.Tsung,
H.Sjodin,
J.V.Gefter,
R.L.Delude,
T.R.Billiar,
and
M.P.Fink
(2008).
Preconditioning with high mobility group box 1 (HMGB1) induces lipopolysaccharide (LPS) tolerance.
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J Leukoc Biol,
84,
1326-1334.
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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.
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Nucleic Acids Res,
36,
3655-3666.
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I.Ito,
J.Fukazawa,
and
M.Yoshida
(2007).
Post-translational methylation of high mobility group box 1 (HMGB1) causes its cytoplasmic localization in neutrophils.
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J Biol Chem,
282,
16336-16344.
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J.K.Sabo,
D.W.Keizer,
Z.P.Feng,
J.L.Casey,
K.Parisi,
A.M.Coley,
M.Foley,
and
R.S.Norton
(2007).
Mimotopes of apical membrane antigen 1: Structures of phage-derived peptides recognized by the inhibitory monoclonal antibody 4G2dc1 and design of a more active analogue.
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Infect Immun,
75,
61-73.
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K.Kasahara,
K.Ohtsuki,
S.Ki,
K.Aoyama,
H.Takahashi,
T.Kobayashi,
K.Shirahige,
and
T.Kokubo
(2007).
Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae.
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Mol Cell Biol,
27,
6686-6705.
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S.Briquet,
C.Boschet,
M.Gissot,
E.Tissandié,
E.Sevilla,
J.F.Franetich,
I.Thiery,
Z.Hamid,
C.Bourgouin,
and
C.Vaquero
(2006).
High-mobility-group box nuclear factors of Plasmodium falciparum.
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Eukaryot Cell,
5,
672-682.
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U.Camenisch,
R.Dip,
S.B.Schumacher,
B.Schuler,
and
H.Naegeli
(2006).
Recognition of helical kinks by xeroderma pigmentosum group A protein triggers DNA excision repair.
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Nat Struct Mol Biol,
13,
278-284.
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M.Novoseler,
G.Hershkovits,
and
D.J.Katcoff
(2005).
Functional domains of the yeast chromatin protein Sin1p/Spt2p can bind four-way junction and crossing DNA structures.
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J Biol Chem,
280,
5169-5177.
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N.Kasai,
Y.Tsunaka,
I.Ohki,
S.Hirose,
K.Morikawa,
and
S.Tate
(2005).
Solution structure of the HMG-box domain in the SSRP1 subunit of FACT.
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J Biomol NMR,
32,
83-88.
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PDB code:
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R.Kellermayer,
L.Halvax,
M.Czakó,
M.Shahid,
V.S.Dhillon,
S.A.Husain,
N.Süle,
E.Gömöri,
M.Mammel,
and
G.Kosztolányi
(2005).
A novel frame shift mutation in the HMG box of the SRY gene in a patient with complete 46,XY pure gonadal dysgenesis.
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Diagn Mol Pathol,
14,
159-163.
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Y.Dai,
B.Wong,
Y.M.Yen,
M.A.Oettinger,
J.Kwon,
and
R.C.Johnson
(2005).
Determinants of HMGB proteins required to promote RAG1/2-recombination signal sequence complex assembly and catalysis during V(D)J recombination.
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Mol Cell Biol,
25,
4413-4425.
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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.
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J Biol Chem,
279,
55234-55240.
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H.J.Huttunen,
and
H.Rauvala
(2004).
Amphoterin as an extracellular regulator of cell motility: from discovery to disease.
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J Intern Med,
255,
351-366.
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S.Matsutani
(2004).
Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III.
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BMC Evol Biol,
4,
26.
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G.Zhang,
T.Kobayashi,
W.Kamitani,
S.Komoto,
M.Yamashita,
S.Baba,
H.Yanai,
K.Ikuta,
and
K.Tomonaga
(2003).
Borna disease virus phosphoprotein represses p53-mediated transcriptional activity by interference with HMGB1.
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J Virol,
77,
12243-12251.
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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.
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Nucleic Acids Res,
31,
2852-2864.
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J.Li,
R.Kokkola,
S.Tabibzadeh,
R.Yang,
M.Ochani,
X.Qiang,
H.E.Harris,
C.J.Czura,
H.Wang,
L.Ulloa,
H.Wang,
H.S.Warren,
L.L.Moldawer,
M.P.Fink,
U.Andersson,
K.J.Tracey,
and
H.Yang
(2003).
Structural basis for the proinflammatory cytokine activity of high mobility group box 1.
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Mol Med,
9,
37-45.
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Y.Matsushima,
K.Matsumura,
S.Ishii,
H.Inagaki,
T.Suzuki,
Y.Matsuda,
K.Beck,
and
Y.Kitagawa
(2003).
Functional domains of chicken mitochondrial transcription factor A for the maintenance of mitochondrial DNA copy number in lymphoma cell line DT40.
|
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J Biol Chem,
278,
31149-31158.
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A.Dintilhac,
and
J.Bernués
(2002).
HMGB1 interacts with many apparently unrelated proteins by recognizing short amino acid sequences.
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J Biol Chem,
277,
7021-7028.
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D.Subramanian,
and
J.D.Griffith
(2002).
Interactions between p53, hMSH2-hMSH6 and HMG I(Y) on Holliday junctions and bulged bases.
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Nucleic Acids Res,
30,
2427-2434.
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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.
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J Biol Chem,
277,
11957-11964.
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S.Veilleux,
and
G.Boissonneault
(2002).
Dynamics of reporter gene stimulation by HMG box proteins.
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DNA Cell Biol,
21,
199-212.
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J.O.Thomas,
and
A.A.Travers
(2001).
HMG1 and 2, and related 'architectural' DNA-binding proteins.
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Trends Biochem Sci,
26,
167-174.
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L.Dailey,
and
C.Basilico
(2001).
Coevolution of HMG domains and homeodomains and the generation of transcriptional regulation by Sox/POU complexes.
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J Cell Physiol,
186,
315-328.
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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.
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Biochemistry,
40,
4769-4779.
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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.
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Protein Sci,
10,
83-98.
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PDB code:
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A.Travers
(2000).
Recognition of distorted DNA structures by HMG domains.
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Curr Opin Struct Biol,
10,
102-109.
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F.V.Murphy,
and
M.E.Churchill
(2000).
Nonsequence-specific DNA recognition: a structural perspective.
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Structure,
8,
R83-R89.
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H.Xin,
S.Taudte,
N.R.Kallenbach,
M.P.Limbach,
and
R.S.Zitomer
(2000).
DNA binding by single HMG box model proteins.
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Nucleic Acids Res,
28,
4044-4050.
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J.M.Benevides,
G.Chan,
X.J.Lu,
W.K.Olson,
M.A.Weiss,
and
G.J.Thomas
(2000).
Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal.
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Biochemistry,
39,
537-547.
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K.B.Ellwood,
Y.M.Yen,
R.C.Johnson,
and
M.Carey
(2000).
Mechanism for specificity by HMG-1 in enhanceosome assembly.
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Mol Cell Biol,
20,
4359-4370.
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L.K.Dow,
D.N.Jones,
S.A.Wolfe,
G.L.Verdine,
and
M.E.Churchill
(2000).
Structural studies of the high mobility group globular domain and basic tail of HMG-D bound to disulfide cross-linked DNA.
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Biochemistry,
39,
9725-9736.
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M.Stros,
D.Cherny,
and
T.M.Jovin
(2000).
HMG1 protein stimulates DNA end joining by promoting association of DNA molecules via their ends.
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Eur J Biochem,
267,
4088-4097.
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C.Ferrándiz,
S.Pelaz,
and
M.F.Yanofsky
(1999).
Control of carpel and fruit development in Arabidopsis.
|
| |
Annu Rev Biochem,
68,
321-354.
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F.H.Allain,
Y.M.Yen,
J.E.Masse,
P.Schultze,
T.Dieckmann,
R.C.Johnson,
and
J.Feigon
(1999).
Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding.
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EMBO J,
18,
2563-2579.
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PDB code:
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F.V.Murphy,
J.V.Sehy,
L.K.Dow,
Y.G.Gao,
and
M.E.Churchill
(1999).
Co-crystallization and preliminary crystallographic analysis of the high mobility group domain of HMG-D bound to DNA.
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| |
Acta Crystallogr D Biol Crystallogr,
55,
1594-1597.
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F.V.Murphy,
R.M.Sweet,
and
M.E.Churchill
(1999).
The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition.
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EMBO J,
18,
6610-6618.
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PDB code:
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G.C.Banks,
B.Mohr,
and
R.Reeves
(1999).
The HMG-I(Y) A.T-hook peptide motif confers DNA-binding specificity to a structured chimeric protein.
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| |
J Biol Chem,
274,
16536-16544.
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J.R.Wiśniewski,
N.M.Krohn,
E.Heyduk,
K.D.Grasser,
and
T.Heyduk
(1999).
HMG1 proteins from evolutionary distant organisms distort B-DNA conformation in similar way.
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| |
Biochim Biophys Acta,
1447,
25-34.
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J.Ramstein,
D.Locker,
M.E.Bianchi,
and
M.Leng
(1999).
Domain-domain interactions in high mobility group 1 protein (HMG1).
|
| |
Eur J Biochem,
260,
692-700.
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K.Yoshioka,
K.Saito,
T.Tanabe,
A.Yamamoto,
Y.Ando,
Y.Nakamura,
H.Shirakawa,
and
M.Yoshida
(1999).
Differences in DNA recognition and conformational change activity between boxes A and B in HMG2 protein.
|
| |
Biochemistry,
38,
589-595.
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M.Bustin
(1999).
Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins.
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| |
Mol Cell Biol,
19,
5237-5246.
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P.Hindmarsh,
T.Ridky,
R.Reeves,
M.Andrake,
A.M.Skalka,
and
J.Leis
(1999).
HMG protein family members stimulate human immunodeficiency virus type 1 and avian sarcoma virus concerted DNA integration in vitro.
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| |
J Virol,
73,
2994-3003.
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W.Ranatunga,
J.Lebowitz,
B.Axe,
P.Pavlik,
S.R.Kar,
and
W.M.Scovell
(1999).
Reexamination of the high mobility group-1 protein for self-association and characterization of hydrodynamic properties.
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Biochim Biophys Acta,
1432,
1.
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Y.Tang,
and
L.Nilsson
(1999).
Effect of G40R mutation on the binding of human SRY protein to DNA: a molecular dynamics view.
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| |
Proteins,
35,
101-113.
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A.Balaeff,
M.E.Churchill,
and
K.Schulten
(1998).
Structure prediction of a complex between the chromosomal protein HMG-D and DNA.
|
| |
Proteins,
30,
113-135.
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C.Ritt,
R.Grimm,
S.Fernandez,
J.C.Alonso,
and
K.D.Grasser
(1998).
Basic and acidic regions flanking the HMG domain of maize HMGa modulate the interactions with DNA and the self-association of the protein.
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| |
Biochemistry,
37,
2673-2681.
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J.R.P-ohler,
D.G.Norman,
J.Bramham,
M.E.Bianchi,
and
D.M.Lilley
(1998).
HMG box proteins bind to four-way DNA junctions in their open conformation.
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| |
EMBO J,
17,
817-826.
|
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M.G.Prieve,
K.L.Guttridge,
J.Munguia,
and
M.L.Waterman
(1998).
Differential importin-alpha recognition and nuclear transport by nuclear localization signals within the high-mobility-group DNA binding domains of lymphoid enhancer factor 1 and T-cell factor 1.
|
| |
Mol Cell Biol,
18,
4819-4832.
|
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M.Stros
(1998).
DNA bending by the chromosomal protein HMG1 and its high mobility group box domains. Effect of flanking sequences.
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Nucleic Acids Res,
21,
2493-2501.
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