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PDBsum entry 1mbj
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DNA binding protein
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PDB id
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1mbj
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Contents |
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* Residue conservation analysis
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PDB id:
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DNA binding protein
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Title:
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MousE C-myb DNA-binding domain repeat 3
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Structure:
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Myb proto-oncogene protein. Chain: a. Other_details: genE C-myb, nmr, minimized average structure. Engineered
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090
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NMR struc:
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1 models
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Authors:
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K.Ogata,S.Morikawa,H.Nakamura,H.Hojo,S.Yoshimura,R.Zhang,S.Aimoto, Y.Ametani,Z.Hirata,A.Sarai,S.Ishii,Y.Nishimura
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Key ref:
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K.Ogata
et al.
(1995).
Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb.
Nat Struct Biol,
2,
309-320.
PubMed id:
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Date:
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19-May-95
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Release date:
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31-Jul-95
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PROCHECK
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Headers
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References
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P06876
(MYB_MOUSE) -
Transcriptional activator Myb from Mus musculus
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Seq:
Struc:
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636 a.a.
53 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Nat Struct Biol
2:309-320
(1995)
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PubMed id:
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Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb.
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K.Ogata,
S.Morikawa,
H.Nakamura,
H.Hojo,
S.Yoshimura,
R.Zhang,
S.Aimoto,
Y.Ametani,
Z.Hirata,
A.Sarai.
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ABSTRACT
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The DNA-binding domain of c-Myb consists of three imperfect tandem repeats (R1,
R2 and R3). The three repeats have similar overall architectures, each
containing a helix-turn-helix variation motif. The three conserved tryptophans
in each repeat participate in forming a hydrophobic core. Comparison of the
three repeat structures indicated that cavities are found in the hydrophobic
core of R2, which is thermally unstable. On complexation with DNA, the
orientations of R2 and R3 are fixed by tight binding and their conformations are
slightly changed. No significant changes occur in the chemical shifts of R1
consistent with its loose interaction with DNA.
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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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Y.Chen,
J.Liu,
H.Xu,
Z.Luo,
and
C.Zhang
(2011).
Overexpression of the c-Myb but not its leukemogenic mutant DNA-binding domain increased adipogenic differentiation in mesenchymal stem cells.
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Biochem Biophys Res Commun,
407,
202-206.
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C.Dubos,
R.Stracke,
E.Grotewold,
B.Weisshaar,
C.Martin,
and
L.Lepiniec
(2010).
MYB transcription factors in Arabidopsis.
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Trends Plant Sci,
15,
573-581.
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C.Y.Yang,
K.H.Chin,
M.T.Yang,
A.H.Wang,
and
S.H.Chou
(2009).
Crystal structure of RecX: a potent regulatory protein of RecA from Xanthomonas campestris.
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Proteins,
74,
530-537.
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PDB code:
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J.T.Matus,
F.Aquea,
and
P.Arce-Johnson
(2008).
Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes.
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BMC Plant Biol,
8,
83.
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S.Ko,
S.H.Jun,
H.Bae,
J.S.Byun,
W.Han,
H.Park,
S.W.Yang,
S.Y.Park,
Y.H.Jeon,
C.Cheong,
W.T.Kim,
W.Lee,
and
H.S.Cho
(2008).
Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins.
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Nucleic Acids Res,
36,
2739-2755.
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PDB code:
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J.R.Horton,
S.J.Elgar,
S.I.Khan,
X.Zhang,
P.A.Wade,
and
X.Cheng
(2007).
Structure of the SANT domain from the Xenopus chromatin remodeling factor ISWI.
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Proteins,
67,
1198-1202.
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PDB code:
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C.Barrero,
L.M.Muñiz,
E.Gómez,
G.Hueros,
and
J.Royo
(2006).
Molecular dissection of the interaction between the transcriptional activator ZmMRP-1 and the promoter of BETL-1.
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Plant Mol Biol,
62,
655-668.
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C.E.Stevenson,
N.Burton,
M.M.Costa,
U.Nath,
R.A.Dixon,
E.S.Coen,
and
D.M.Lawson
(2006).
Crystal structure of the MYB domain of the RAD transcription factor from Antirrhinum majus.
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Proteins,
65,
1041-1045.
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PDB code:
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C.Yanhui,
Y.Xiaoyuan,
H.Kun,
L.Meihua,
L.Jigang,
G.Zhaofeng,
L.Zhiqiang,
Z.Yunfei,
W.Xiaoxiao,
Q.Xiaoming,
S.Yunping,
Z.Li,
D.Xiaohui,
L.Jingchu,
D.Xing-Wang,
C.Zhangliang,
G.Hongya,
and
Q.Li-Jia
(2006).
The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family.
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Plant Mol Biol,
60,
107-124.
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X.Shi,
Y.Nishimura,
S.Akashi,
A.Takamizawa,
and
K.Hiraoka
(2006).
Evaluation of binding affinity of protein-mutant DNA complexes in solution by laser spray mass spectrometry.
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J Am Soc Mass Spectrom,
17,
611-620.
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S.Akashi,
R.Osawa,
and
Y.Nishimura
(2005).
Evaluation of protein-DNA binding affinity by electrospray ionization mass spectrometry.
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J Am Soc Mass Spectrom,
16,
116-125.
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S.Hanaoka,
A.Nagadoi,
and
Y.Nishimura
(2005).
Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities.
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Protein Sci,
14,
119-130.
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PDB codes:
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S.M.Christensen,
A.Bibillo,
and
T.H.Eickbush
(2005).
Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction.
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Nucleic Acids Res,
33,
6461-6468.
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C.Kanei-Ishii,
T.Nomura,
J.Tanikawa,
E.Ichikawa-Iwata,
and
S.Ishii
(2004).
Differential sensitivity of v-Myb and c-Myb to Wnt-1-induced protein degradation.
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J Biol Chem,
279,
44582-44589.
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I.M.Zimmermann,
M.A.Heim,
B.Weisshaar,
and
J.F.Uhrig
(2004).
Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins.
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Plant J,
40,
22-34.
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O.Nordgård,
T.Ã.˜.Andersen,
and
O.S.Gabrielsen
(2004).
Selective inhibition of c-Myb DNA-binding by RNA polymers.
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BMC Biochem,
5,
15.
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T.Nomura,
J.Tanikawa,
H.Akimaru,
C.Kanei-Ishii,
E.Ichikawa-Iwata,
M.M.Khan,
H.Ito,
and
S.Ishii
(2004).
Oncogenic activation of c-Myb correlates with a loss of negative regulation by TIF1beta and Ski.
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J Biol Chem,
279,
16715-16726.
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K.Ogata,
K.Sato,
T.H.Tahirov,
and
T.Tahirov
(2003).
Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar.
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Curr Opin Struct Biol,
13,
40-48.
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L.Mohrmann,
A.J.Kal,
and
C.P.Verrijzer
(2002).
Characterization of the extended Myb-like DNA-binding domain of trithorax group protein Zeste.
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J Biol Chem,
277,
47385-47392.
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S.Kumar,
and
R.Nussinov
(2002).
Relationship between ion pair geometries and electrostatic strengths in proteins.
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Biophys J,
83,
1595-1612.
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T.H.Tahirov,
K.Sato,
E.Ichikawa-Iwata,
M.Sasaki,
T.Inoue-Bungo,
M.Shiina,
K.Kimura,
S.Takata,
A.Fujikawa,
H.Morii,
T.Kumasaka,
M.Yamamoto,
S.Ishii,
and
K.Ogata
(2002).
Mechanism of c-Myb-C/EBP beta cooperation from separated sites on a promoter.
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Cell,
108,
57-70.
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PDB codes:
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M.W.Lassalle,
H.Yamada,
H.Morii,
K.Ogata,
A.Sarai,
and
K.Akasaka
(2001).
Filling a cavity dramatically increases pressure stability of the c-Myb R2 subdomain.
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Proteins,
45,
96.
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S.Bergholtz,
T.O.Andersen,
K.B.Andersson,
J.Borrebaek,
B.Lüscher,
and
O.S.Gabrielsen
(2001).
The highly conserved DNA-binding domains of A-, B- and c-Myb differ with respect to DNA-binding, phosphorylation and redox properties.
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Nucleic Acids Res,
29,
3546-3556.
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S.Kumar,
and
R.Nussinov
(2001).
Fluctuations in ion pairs and their stabilities in proteins.
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Proteins,
43,
433-454.
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T.Nishikawa,
H.Okamura,
A.Nagadoi,
P.König,
D.Rhodes,
and
Y.Nishimura
(2001).
Solution structure of a telomeric DNA complex of human TRF1.
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Structure,
9,
1237-1251.
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PDB codes:
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H.Kono,
M.Saito,
and
A.Sarai
(2000).
Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations.
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Proteins,
38,
197-209.
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M.Oda,
and
H.Nakamura
(2000).
Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition.
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Genes Cells,
5,
319-326.
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J.Iwahara,
and
R.T.Clubb
(1999).
Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID).
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EMBO J,
18,
6084-6094.
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PDB code:
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W.H.McDonald,
R.Ohi,
N.Smelkova,
D.Frendewey,
and
K.L.Gould
(1999).
Myb-related fission yeast cdc5p is a component of a 40S snRNP-containing complex and is essential for pre-mRNA splicing.
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Mol Cell Biol,
19,
5352-5362.
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Y.Tanaka,
N.P.Patestos,
T.Maekawa,
and
S.Ishii
(1999).
B-myb is required for inner cell mass formation at an early stage of development.
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J Biol Chem,
274,
28067-28070.
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G.Cutler,
K.M.Perry,
and
R.Tjian
(1998).
Adf-1 is a nonmodular transcription factor that contains a TAF-binding Myb-like motif.
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Mol Cell Biol,
18,
2252-2261.
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J.P.Schneider,
A.Lombardi,
and
W.F.DeGrado
(1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
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Fold Des,
3,
R29-R40.
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T.Graf
(1998).
Leukemogenesis: small differences in Myb have large effects.
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Curr Biol,
8,
R353-R355.
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T.Nishikawa,
A.Nagadoi,
S.Yoshimura,
S.Aimoto,
and
Y.Nishimura
(1998).
Solution structure of the DNA-binding domain of human telomeric protein, hTRF1.
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Structure,
6,
1057-1065.
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PDB code:
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G.van Pouderoyen,
R.F.Ketting,
A.Perrakis,
R.H.Plasterk,
and
T.K.Sixma
(1997).
Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA.
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EMBO J,
16,
6044-6054.
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PDB code:
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M.Oda,
K.Furukawa,
K.Ogata,
A.Sarai,
S.Ishii,
Y.Nishimura,
and
H.Nakamura
(1997).
Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence.
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J Biol Chem,
272,
17966-17971.
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R.Solano,
A.Fuertes,
L.Sánchez-Pulido,
A.Valencia,
and
J.Paz-Ares
(1997).
A single residue substitution causes a switch from the dual DNA binding specificity of plant transcription factor MYB.Ph3 to the animal c-MYB specificity.
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J Biol Chem,
272,
2889-2895.
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R.V.Hosur,
P.K.Radha,
A.Madan,
and
L.C.Padhy
(1997).
Biophysical investigations on the myb-DNA system.
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Biophys Chem,
68,
147-159.
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A.B.Hegvold,
and
O.S.Gabrielsen
(1996).
The importance of the linker connecting the repeats of the c-Myb oncoprotein may be due to a positioning function.
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Nucleic Acids Res,
24,
3990-3995.
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H.Nakamura
(1996).
Roles of electrostatic interaction in proteins.
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Q Rev Biophys,
29,
1.
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K.Furukawa,
M.Oda,
and
H.Nakamura
(1996).
A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy.
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Proc Natl Acad Sci U S A,
93,
13583-13588.
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PDB codes:
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M.D.Carr,
U.Wollborn,
P.B.McIntosh,
T.A.Frenkiel,
J.E.McCormick,
C.J.Bauer,
K.H.Klempnauer,
and
J.Feeney
(1996).
Structure of the B-Myb DNA-binding domain in solution and evidence for multiple conformations in the region of repeat-2 involved in DNA binding: implications for sequence-specific DNA binding by Myb proteins.
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Eur J Biochem,
235,
721-735.
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Q.L.Deng,
S.Ishii,
and
A.Sarai
(1996).
Binding site analysis of c-Myb: screening of potential binding sites by using the mutation matrix derived from systematic binding affinity measurements.
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Nucleic Acids Res,
24,
766-774.
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S.A.Ness
(1996).
The Myb oncoprotein: regulating a regulator.
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Biochim Biophys Acta,
1288,
F123-F139.
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A.Nagadoi,
S.Morikawa,
H.Nakamura,
M.Enari,
K.Kobayashi,
H.Yamamoto,
G.Sampei,
K.Mizobuchi,
M.A.Schumacher,
and
R.G.Brennan
(1995).
Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain.
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Structure,
3,
1217-1224.
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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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Links
