spacer
spacer

PDBsum entry 1mbe

Go to PDB code: 
protein links
DNA binding protein PDB id
1mbe
Jmol
Contents
Protein chain
53 a.a. *
* Residue conservation analysis
PDB id:
1mbe
Name: DNA binding protein
Title: MousE C-myb DNA-binding domain repeat 1
Structure: Myb proto-oncogene protein. Chain: a. Other_details: genE C-myb, nmr, minimized average structure engineered
Source: Mus musculus. House mouse. Organism_taxid: 10090
NMR struc: 1 models
Authors: K.Ogata,S.Morikawa,H.Nakamura,H.Hojo,S.Yoshimura,R.Zhang,S.A Y.Ametani,Z.Hirata,A.Sarai,S.Ishii,Y.Nishimura
Key ref: 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: 7796266
Date:
19-May-95     Release date:   31-Jul-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06876  (MYB_MOUSE) -  Transcriptional activator Myb
Seq:
Struc:
 
Seq:
Struc:
636 a.a.
53 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     chromatin binding     2 terms  

 

 
Nat Struct Biol 2:309-320 (1995)
PubMed id: 7796266  
 
 
Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb.
K.Ogata, S.Morikawa, H.Nakamura, H.Hojo, S.Yoshimura, R.Zhang, S.Aimoto, Y.Ametani, Z.Hirata, A.Sarai.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21376705 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.
  Biochem Biophys Res Commun, 407, 202-206.  
20674465 C.Dubos, R.Stracke, E.Grotewold, B.Weisshaar, C.Martin, and L.Lepiniec (2010).
MYB transcription factors in Arabidopsis.
  Trends Plant Sci, 15, 573-581.  
19003992 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.
  Proteins, 74, 530-537.
PDB code: 3dfg
18647406 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.
  BMC Plant Biol, 8, 83.  
18367475 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.
  Nucleic Acids Res, 36, 2739-2755.
PDB code: 2ckx
17377988 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.
  Proteins, 67, 1198-1202.
PDB code: 2nog
17001496 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.
  Plant Mol Biol, 62, 655-668.  
17044043 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.
  Proteins, 65, 1041-1045.
PDB code: 2cjj
16463103 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.
  Plant Mol Biol, 60, 107-124.  
16490360 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.
  J Am Soc Mass Spectrom, 17, 611-620.  
15653371 S.Akashi, R.Osawa, and Y.Nishimura (2005).
Evaluation of protein-DNA binding affinity by electrospray ionization mass spectrometry.
  J Am Soc Mass Spectrom, 16, 116-125.  
15608118 S.Hanaoka, A.Nagadoi, and Y.Nishimura (2005).
Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities.
  Protein Sci, 14, 119-130.
PDB codes: 1vf9 1vfc
16284201 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.
  Nucleic Acids Res, 33, 6461-6468.  
15308626 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.
  J Biol Chem, 279, 44582-44589.  
15361138 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.
  Plant J, 40, 22-34.  
15527501 O.Nordgård, T...Andersen, and O.S.Gabrielsen (2004).
Selective inhibition of c-Myb DNA-binding by RNA polymers.
  BMC Biochem, 5, 15.  
14761981 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.
  J Biol Chem, 279, 16715-16726.  
12581658 K.Ogata, K.Sato, T.H.Tahirov, and T.Tahirov (2003).
Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar.
  Curr Opin Struct Biol, 13, 40-48.  
12354778 L.Mohrmann, A.J.Kal, and C.P.Verrijzer (2002).
Characterization of the extended Myb-like DNA-binding domain of trithorax group protein Zeste.
  J Biol Chem, 277, 47385-47392.  
12202384 S.Kumar, and R.Nussinov (2002).
Relationship between ion pair geometries and electrostatic strengths in proteins.
  Biophys J, 83, 1595-1612.  
11792321 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.
  Cell, 108, 57-70.
PDB codes: 1h88 1h89 1h8a
11536365 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.
  Proteins, 45, 96.  
11522824 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.
  Nucleic Acids Res, 29, 3546-3556.  
11340660 S.Kumar, and R.Nussinov (2001).
Fluctuations in ion pairs and their stabilities in proteins.
  Proteins, 43, 433-454.  
11738049 T.Nishikawa, H.Okamura, A.Nagadoi, P.König, D.Rhodes, and Y.Nishimura (2001).
Solution structure of a telomeric DNA complex of human TRF1.
  Structure, 9, 1237-1251.
PDB codes: 1ity 1iv6
10656266 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.
  Proteins, 38, 197-209.  
10886361 M.Oda, and H.Nakamura (2000).
Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition.
  Genes Cells, 5, 319-326.  
10545119 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).
  EMBO J, 18, 6084-6094.
PDB code: 1c20
  10409726 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.
  Mol Cell Biol, 19, 5352-5362.  
10497154 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.
  J Biol Chem, 274, 28067-28070.  
  9528796 G.Cutler, K.M.Perry, and R.Tjian (1998).
Adf-1 is a nonmodular transcription factor that contains a TAF-binding Myb-like motif.
  Mol Cell Biol, 18, 2252-2261.  
9565750 J.P.Schneider, A.Lombardi, and W.F.DeGrado (1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
  Fold Des, 3, R29-R40.  
9601636 T.Graf (1998).
Leukemogenesis: small differences in Myb have large effects.
  Curr Biol, 8, R353-R355.  
9739097 T.Nishikawa, A.Nagadoi, S.Yoshimura, S.Aimoto, and Y.Nishimura (1998).
Solution structure of the DNA-binding domain of human telomeric protein, hTRF1.
  Structure, 6, 1057-1065.
PDB code: 1ba5
9312061 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.
  EMBO J, 16, 6044-6054.
PDB code: 1tc3
9218422 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.
  J Biol Chem, 272, 17966-17971.  
9006933 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.
  J Biol Chem, 272, 2889-2895.  
9468617 R.V.Hosur, P.K.Radha, A.Madan, and L.C.Padhy (1997).
Biophysical investigations on the myb-DNA system.
  Biophys Chem, 68, 147-159.  
8918802 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.
  Nucleic Acids Res, 24, 3990-3995.  
8783394 H.Nakamura (1996).
Roles of electrostatic interaction in proteins.
  Q Rev Biophys, 29, 1.  
8942977 K.Furukawa, M.Oda, and H.Nakamura (1996).
A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy.
  Proc Natl Acad Sci U S A, 93, 13583-13588.
PDB codes: 1idy 1idz
8654422 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.
  Eur J Biochem, 235, 721-735.  
8604322 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.
  Nucleic Acids Res, 24, 766-774.  
9011176 S.A.Ness (1996).
The Myb oncoprotein: regulating a regulator.
  Biochim Biophys Acta, 1288, F123-F139.  
8591032 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.
  Structure, 3, 1217-1224.
PDB codes: 1pru 1prv
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.