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PDBsum entry 1msf
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protein dna_rna links
DNA binding protein/DNA PDB id
1msf

 

 

 

 

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Contents
Protein chain
105 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1msf
Name: DNA binding protein/DNA
Title: Solution structure of a specific DNA complex of the myb DNA-binding domain with cooperative recognition helices
Structure: DNA (5'-d( Cp Cp Tp Ap Ap Cp Tp Gp Ap Cp Ap Cp Ap Cp Ap T)- 3'). Chain: a. Engineered: yes. DNA (5'-d( Ap Tp Gp Tp Gp Tp Gp Tp Cp Ap Gp Tp Tp Ap Gp G)- 3'). Chain: b. Engineered: yes. C-myb DNA-binding domain.
Source: Synthetic: yes. Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 25 models
Authors: K.Ogata,S.Morikawa,H.Nakamura,A.Sekikawa,T.Inoue,H.Kanai,A.Sarai, S.Ishii,Y.Nishimura
Key ref: K.Ogata et al. (1994). Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell, 79, 639-648. PubMed id: 7954830 DOI: 10.1016/0092-8674(94)90549-5
Date:
24-Jan-95     Release date:   31-Mar-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06876  (MYB_MOUSE) -  Transcriptional activator Myb from Mus musculus
Seq:
Struc: 		 
Seq:
Struc: 		636 a.a.
105 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains
  C-C-T-A-A-C-T-G-A-C-A 11 bases
  T-G-T-C-A-G-T-T-A-G-G 11 bases

 

 
DOI no: 10.1016/0092-8674(94)90549-5 Cell 79:639-648 (1994)
PubMed id: 7954830  
 
 
Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices.
K.Ogata, S.Morikawa, H.Nakamura, A.Sekikawa, T.Inoue, H.Kanai, A.Sarai, S.Ishii, Y.Nishimura.
 
  ABSTRACT  
 
The DNA-binding region of Myb consists of three imperfect tandem repeats (R1, R2, and R3). We have determined the solution structure of a specific DNA complex of the minimum DNA-binding domain (R2R3) by heteronuclear multidimensional NMR. Both R2 and R3 contain three helices, and the third helix in each is found to be a recognition helix. R2 and R3 are closely packed in the major groove, so that the two recognition helices contact each other directly to bind to the specific base sequence, AACNG cooperatively; this is a significant arrangement of recognition helices. The three key base pairs in this sequence are specifically recognized by Asn-183 (R3), Lys-182 (R3), and Lys-128 (R2). In contrast, R1 has no specific interactions with DNA from our NMR study of the DNA complex of the full DNA-binding domain (R1R2R3).
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525927 K.Yamada, T.D.Frouws, B.Angst, D.J.Fitzgerald, C.DeLuca, K.Schimmele, D.F.Sargent, and T.J.Richmond (2011).
Structure and mechanism of the chromatin remodelling factor ISW1a.
  Nature, 472, 448-453.
PDB codes: 2y9y 2y9z
20823231 C.Soza-Ried, I.Hess, N.Netuschil, M.Schorpp, and T.Boehm (2010).
Essential role of c-myb in definitive hematopoiesis is evolutionarily conserved.
  Proc Natl Acad Sci U S A, 107, 17304-17308.  
20360860 K.M.Evans-Roberts, C.Breuer, M.K.Wall, K.Sugimoto-Shirasu, and A.Maxwell (2010).
Arabidopsis thaliana GYRB3 does not encode a DNA gyrase subunit.
  PLoS One, 5, e9899.  
20717979 T.Nagata, E.Niyada, N.Fujimoto, Y.Nagasaki, K.Noto, Y.Miyanoiri, J.Murata, K.Hiratsuka, and M.Katahira (2010).
Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation.
  Proteins, 78, 3033-3047.
PDB codes: 2ebi 2jmw
19839711 B.R.Linger, and C.M.Price (2009).
Conservation of telomere protein complexes: shuffling through evolution.
  Crit Rev Biochem Mol Biol, 44, 434-446.  
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
19151329 H.M.Hsu, S.J.Ong, M.C.Lee, and J.H.Tai (2009).
Transcriptional regulation of an iron-inducible gene by differential and alternate promoter entries of multiple Myb proteins in the protozoan parasite Trichomonas vaginalis.
  Eukaryot Cell, 8, 362-372.  
19273607 M.Pinskaya, A.Nair, D.Clynes, A.Morillon, and J.Mellor (2009).
Nucleosome remodeling and transcriptional repression are distinct functions of Isw1 in Saccharomyces cerevisiae.
  Mol Cell Biol, 29, 2419-2430.  
19345190 X.Yang, L.M.Figueiredo, A.Espinal, E.Okubo, and B.Li (2009).
RAP1 is essential for silencing telomeric variant surface glycoprotein genes in Trypanosoma brucei.
  Cell, 137, 99.  
19246540 Y.C.Lou, S.Y.Wei, M.Rajasekaran, C.C.Chou, H.M.Hsu, J.H.Tai, and C.Chen (2009).
NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis.
  Nucleic Acids Res, 37, 2381-2394.
PDB codes: 2k9n 2kdz
18765672 C.Kanei-Ishii, T.Nomura, T.Takagi, N.Watanabe, K.I.Nakayama, and S.Ishii (2008).
Fbxw7 Acts as an E3 Ubiquitin Ligase That Targets c-Myb for Nemo-like Kinase (NLK)-induced Degradation.
  J Biol Chem, 283, 30540-30548.  
18840288 E.R.Ko, D.Ko, C.Chen, and J.S.Lipsick (2008).
A conserved acidic patch in the Myb domain is required for activation of an endogenous target gene and for chromatin binding.
  Mol Cancer, 7, 77.  
18548008 T.Yamauchi, T.Ishidao, T.Nomura, T.Shinagawa, Y.Tanaka, S.Yonemura, and S.Ishii (2008).
A B-Myb complex containing clathrin and filamin is required for mitotic spindle function.
  EMBO J, 27, 1852-1862.  
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
17959653 O.Ivanova, D.Braas, and K.H.Klempnauer (2007).
Oncogenic point mutations in the Myb DNA-binding domain alter the DNA-binding properties of Myb at a physiological target gene.
  Nucleic Acids Res, 35, 7237-7247.  
17202137 S.J.Ong, H.M.Hsu, H.W.Liu, C.H.Chu, and J.H.Tai (2007).
Activation of multifarious transcription of an adhesion protein ap65-1 gene by a novel Myb2 protein in the protozoan parasite Trichomonas vaginalis.
  J Biol Chem, 282, 6716-6725.  
17242210 Y.Nakata, S.Shetzline, C.Sakashita, A.Kalota, R.Rallapalli, S.I.Rudnick, Y.Zhang, S.G.Emerson, and A.M.Gewirtz (2007).
c-Myb contributes to G2/M cell cycle transition in human hematopoietic cells by direct regulation of cyclin B1 expression.
  Mol Cell Biol, 27, 2048-2058.  
16231315 K.Y.Kim, J.W.Lee, M.S.Park, M.H.Jung, G.A.Jeon, and M.J.Nam (2006).
Expression of a thioredoxin-related protein-1 is induced by prostaglandin E(2).
  Int J Cancer, 118, 1670-1679.  
16467479 S.J.Ong, H.M.Hsu, H.W.Liu, C.H.Chu, and J.H.Tai (2006).
Multifarious transcriptional regulation of adhesion protein gene ap65-1 by a novel Myb1 protein in the protozoan parasite Trichomonas vaginalis.
  Eukaryot Cell, 5, 391-399.  
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.  
15837933 A.Codina, J.D.Love, Y.Li, M.A.Lazar, D.Neuhaus, and J.W.Schwabe (2005).
Structural insights into the interaction and activation of histone deacetylase 3 by nuclear receptor corepressors.
  Proc Natl Acad Sci U S A, 102, 6009-6014.
PDB code: 1xc5
15923618 B.Li, A.Espinal, and G.A.Cross (2005).
Trypanosome telomeres are protected by a homologue of mammalian TRF2.
  Mol Cell Biol, 25, 5011-5021.  
16299514 C.Qian, Q.Zhang, S.Li, L.Zeng, M.J.Walsh, and M.M.Zhou (2005).
Structure and chromosomal DNA binding of the SWIRM domain.
  Nat Struct Mol Biol, 12, 1078-1085.
PDB codes: 2aqe 2aqf
15606792 G.Lang, W.M.Gombert, and H.J.Gould (2005).
A transcriptional regulatory element in the coding sequence of the human Bcl-2 gene.
  Immunology, 114, 25-36.  
15601869 O.Chayka, J.Kintscher, D.Braas, and K.H.Klempnauer (2005).
v-Myb mediates cooperation of a cell-specific enhancer with the mim-1 promoter.
  Mol Cell Biol, 25, 499-511.  
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.  
16055500 T.Kurahashi, T.Nomura, C.Kanei-Ishii, Y.Shinkai, and S.Ishii (2005).
The Wnt-NLK signaling pathway inhibits A-Myb activity by inhibiting the association with coactivator CBP and methylating histone H3.
  Mol Biol Cell, 16, 4705-4713.  
15929795 X.Gao, K.A.Vander Velden, D.F.Voytas, and X.Gu (2005).
SplitTester: software to identify domains responsible for functional divergence in protein family.
  BMC Bioinformatics, 6, 137.  
15666348 X.de la Cruz, S.Lois, S.Sánchez-Molina, and M.A.Martínez-Balbás (2005).
Do protein motifs read the histone code?
  Bioessays, 27, 164-175.  
16162816 Y.Morita, C.Kanei-Ishii, T.Nomura, and S.Ishii (2005).
TRAF7 sequesters c-Myb to the cytoplasm by stimulating its sumoylation.
  Mol Biol Cell, 16, 5433-5444.  
15239831 C.Jiang, X.Gu, and T.Peterson (2004).
Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica.
  Genome Biol, 5, R46.  
15082531 C.Kanei-Ishii, J.Ninomiya-Tsuji, J.Tanikawa, T.Nomura, T.Ishitani, S.Kishida, K.Kokura, T.Kurahashi, E.Ichikawa-Iwata, Y.Kim, K.Matsumoto, and S.Ishii (2004).
Wnt-1 signal induces phosphorylation and degradation of c-Myb protein via TAK1, HIPK2, and NLK.
  Genes Dev, 18, 816-829.  
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.  
14966271 C.Li, G.A.Harding, J.Parise, K.J.McNamara-Schroeder, and W.E.Stumph (2004).
Architectural arrangement of cloned proximal sequence element-binding protein subunits on Drosophila U1 and U6 snRNA gene promoters.
  Mol Cell Biol, 24, 1897-1906.  
15237103 G.F.Heine, J.M.Hernandez, and E.Grotewold (2004).
Two cysteines in plant R2R3 MYB domains participate in REDOX-dependent DNA binding.
  J Biol Chem, 279, 37878-37885.  
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.  
15347654 J.M.Hernandez, G.F.Heine, N.G.Irani, A.Feller, M.G.Kim, T.Matulnik, V.L.Chandler, and E.Grotewold (2004).
Different mechanisms participate in the R-dependent activity of the R2R3 MYB transcription factor C1.
  J Biol Chem, 279, 48205-48213.  
15584962 J.Preston, J.Wheeler, J.Heazlewood, S.F.Li, and R.W.Parish (2004).
AtMYB32 is required for normal pollen development in Arabidopsis thaliana.
  Plant J, 40, 979-995.  
15509555 J.Tanikawa, T.Nomura, E.M.Macmillan, T.Shinagawa, W.Jin, K.Kokura, D.Baba, M.Shirakawa, T.J.Gonda, and S.Ishii (2004).
p53 suppresses c-Myb-induced trans-activation and transformation by recruiting the corepressor mSin3A.
  J Biol Chem, 279, 55393-55400.  
15040448 L.A.Boyer, R.R.Latek, and C.L.Peterson (2004).
The SANT domain: a unique histone-tail-binding module?
  Nat Rev Mol Cell Biol, 5, 158-163.  
15527501 O.Nordgård, T.Ã.˜.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.  
12456674 K.B.Andersson, E.Kowenz-Leutz, E.M.Brendeford, A.H.Tygsett, A.Leutz, and O.S.Gabrielsen (2003).
Phosphorylation-dependent down-regulation of c-Myb DNA binding is abrogated by a point mutation in the v-myb oncogene.
  J Biol Chem, 278, 3816-3824.  
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.  
12482983 S.Muratoglu, S.Georgieva, G.Pápai, E.Scheer, I.Enünlü, O.Komonyi, I.Cserpán, L.Lebedeva, E.Nabirochkina, A.Udvardy, L.Tora, and I.Boros (2003).
Two different Drosophila ADA2 homologues are present in distinct GCN5 histone acetyltransferase-containing complexes.
  Mol Cell Biol, 23, 306-321.  
14536084 T.Grüne, J.Brzeski, A.Eberharter, C.R.Clapier, D.F.Corona, P.B.Becker, and C.W.Müller (2003).
Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI.
  Mol Cell, 12, 449-460.
PDB code: 1ofc
12631292 Ã.˜.Dahle, T.Ã.˜.Andersen, O.Nordgård, V.Matre, G.Del Sal, and O.S.Gabrielsen (2003).
Transactivation properties of c-Myb are critically dependent on two SUMO-1 acceptor sites that are conjugated in a PIASy enhanced manner.
  Eur J Biochem, 270, 1338-1348.  
11741916 C.D.Tsai, H.W.Liu, and J.H.Tai (2002).
Characterization of an iron-responsive promoter in the protozoan pathogen Trichomonas vaginalis.
  J Biol Chem, 277, 5153-5162.  
12421304 C.H.Sun, D.Palm, A.G.McArthur, S.G.Svärd, and F.D.Gillin (2002).
A novel Myb-related protein involved in transcriptional activation of encystation genes in Giardia lamblia.
  Mol Microbiol, 46, 971-984.  
11777910 D.E.Sterner, X.Wang, M.H.Bloom, G.M.Simon, and S.L.Berger (2002).
The SANT domain of Ada2 is required for normal acetylation of histones by the yeast SAGA complex.
  J Biol Chem, 277, 8178-8186.  
12228710 H.Yang, P.D.Jeffrey, J.Miller, E.Kinnucan, Y.Sun, N.H.Thoma, N.Zheng, P.L.Chen, W.H.Lee, and N.P.Pavletich (2002).
BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.
  Science, 297, 1837-1848.
PDB codes: 1iyj 1miu 1mje
12032301 J.R.Manak, N.Mitiku, and J.S.Lipsick (2002).
Mutation of the Drosophila homologue of the Myb protooncogene causes genomic instability.
  Proc Natl Acad Sci U S A, 99, 7438-7443.  
12419236 L.A.Boyer, M.R.Langer, K.A.Crowley, S.Tan, J.M.Denu, and C.L.Peterson (2002).
Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes.
  Mol Cell, 10, 935-942.  
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.  
11847115 M.Okada, H.Akimaru, D.X.Hou, T.Takahashi, and S.Ishii (2002).
Myb controls G(2)/M progression by inducing cyclin B expression in the Drosophila eye imaginal disc.
  EMBO J, 21, 675-684.  
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
11139623 B.Pinson, E.M.Brendeford, O.S.Gabrielsen, and B.Daignan-Fornier (2001).
Highly conserved features of DNA binding between two divergent members of the Myb family of transcription factors.
  Nucleic Acids Res, 29, 527-535.  
11676925 J.Kanoh, and F.Ishikawa (2001).
spRap1 and spRif1, recruited to telomeres by Taz1, are essential for telomere function in fission yeast.
  Curr Biol, 11, 1624-1630.  
11545737 L.Fairall, L.Chapman, H.Moss, T.de Lange, and D.Rhodes (2001).
Structure of the TRFH dimerization domain of the human telomeric proteins TRF1 and TRF2.
  Mol Cell, 8, 351-361.
PDB codes: 1h6o 1h6p
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.  
11571752 R.Haw, A.D.Yarragudi, and H.Uemura (2001).
Isolation of a Candida glabrata homologue of RAP1, a regulator of transcription and telomere function in Saccharomyces cerevisiae.
  Yeast, 18, 1277-1284.  
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.  
11600718 T.Berge, S.L.Bergholtz, K.B.Andersson, and O.S.Gabrielsen (2001).
A novel yeast system for in vivo selection of recognition sequences: defining an optimal c-Myb-responsive element.
  Nucleic Acids Res, 29, E99.  
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
11726497 Y.Tanaka, O.Nureki, H.Kurumizaka, S.Fukai, S.Kawaguchi, M.Ikuta, J.Iwahara, T.Okazaki, and S.Yokoyama (2001).
Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.
  EMBO J, 20, 6612-6618.
PDB code: 1hlv
10850490 B.Li, S.Oestreich, and T.de Lange (2000).
Identification of human Rap1: implications for telomere evolution.
  Cell, 101, 471-483.  
10679372 D.J.Segal, and C.F.Barbas (2000).
Design of novel sequence-specific DNA-binding proteins.
  Curr Opin Chem Biol, 4, 34-39.  
11095727 E.Grotewold, M.B.Sainz, L.Tagliani, J.M.Hernandez, B.Bowen, and V.L.Chandler (2000).
Identification of the residues in the Myb domain of maize C1 that specify the interaction with the bHLH cofactor R.
  Proc Natl Acad Sci U S A, 97, 13579-13584.  
10660576 G.G.Ying, P.Proost, J.van Damme, M.Bruschi, M.Introna, and J.Golay (2000).
Nucleolin, a novel partner for the Myb transcription factor family that regulates their activity.
  J Biol Chem, 275, 4152-4158.  
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.  
10613862 P.Manna, R.P.Nieder, and M.R.Schaefer (2000).
DNA-Binding properties of the Fremyella diplosiphon RpbA repressor.
  J Bacteriol, 182, 51-56.  
10523316 A.Bianchi, R.M.Stansel, L.Fairall, J.D.Griffith, D.Rhodes, and T.de Lange (1999).
TRF1 binds a bipartite telomeric site with extreme spatial flexibility.
  EMBO J, 18, 5735-5744.  
  10364339 D.M.Wang, J.W.Dubendorff, C.H.Woo, and J.S.Lipsick (1999).
Functional analysis of carboxy-terminal deletion mutants of c-Myb.
  J Virol, 73, 5875-5886.  
10097068 E.J.Park, D.J.Schroen, M.Yang, H.Li, L.Li, and J.D.Chen (1999).
SMRTe, a silencing mediator for retinoid and thyroid hormone receptors-extended isoform that is more related to the nuclear receptor corepressor.
  Proc Natl Acad Sci U S A, 96, 3519-3524.  
10393910 J.Yang, H.S.Malik, and T.H.Eickbush (1999).
Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements.
  Proc Natl Acad Sci U S A, 96, 7847-7852.  
10419522 K.B.Andersson, T.Berge, V.Matre, and O.S.Gabrielsen (1999).
Sequence selectivity of c-Myb in vivo. Resolution of a DNA target specificity paradox.
  J Biol Chem, 274, 21986-21994.  
10336605 L.Liu, M.J.White, and T.H.MacRae (1999).
Transcription factors and their genes in higher plants functional domains, evolution and regulation.
  Eur J Biochem, 262, 247-257.  
10026273 L.Zargarian, V.Le Tilly, N.Jamin, A.Chaffotte, O.S.Gabrielsen, F.Toma, and B.Alpert (1999).
Myb-DNA recognition: role of tryptophan residues and structural changes of the minimal DNA binding domain of c-Myb.
  Biochemistry, 38, 1921-1929.  
  10471724 P.D.Rabinowicz, E.L.Braun, A.D.Wolfe, B.Bowen, and E.Grotewold (1999).
Maize R2R3 Myb genes: Sequence analysis reveals amplification in the higher plants.
  Genetics, 153, 427-444.  
10393303 T.H.Tahirov, H.Morii, H.Uedaira, A.Sarai, and K.Ogata (1999).
Crystallization and preliminary X-ray analysis of wild-type and V103L mutant Myb R2 DNA-binding domain.
  Acta Crystallogr D Biol Crystallogr, 55, 1345-1347.  
  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.  
  9512517 A.L.Katzen, J.Jackson, B.P.Harmon, S.M.Fung, G.Ramsay, and J.M.Bishop (1998).
Drosophila myb is required for the G2/M transition and maintenance of diploidy.
  Genes Dev, 12, 831-843.  
9427759 B.Ganter, S.Fu, and J.S.Lipsick (1998).
D-type cyclins repress transcriptional activation by the v-Myb but not the c-Myb DNA-binding domain.
  EMBO J, 17, 255-268.  
9705508 B.Pinson, I.Sagot, F.Borne, O.S.Gabrielsen, and B.Daignan-Fornier (1998).
Mutations in the yeast Myb-like protein Bas1p resulting in discrimination between promoters in vivo but notin vitro.
  Nucleic Acids Res, 26, 3977-3985.  
  9658130 C.H.Woo, L.Sopchak, and J.S.Lipsick (1998).
Overexpression of an alternatively spliced form of c-Myb results in increases in transactivation and transforms avian myelomonoblasts.
  J Virol, 72, 6813-6821.  
  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.  
  9620859 H.Otsuka, and P.J.Van Haastert (1998).
A novel Myb homolog initiates Dictyostelium development by induction of adenylyl cyclase expression.
  Genes Dev, 12, 1738-1748.  
9628022 I.Romero, A.Fuertes, M.J.Benito, J.M.Malpica, A.Leyva, and J.Paz-Ares (1998).
More than 80R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana.
  Plant J, 14, 273-284.  
9659917 J.D.Leverson, and S.A.Ness (1998).
Point mutations in v-Myb disrupt a cyclophilin-catalyzed negative regulatory mechanism.
  Mol Cell, 1, 203-211.  
9451007 J.Iwahara, T.Kigawa, K.Kitagawa, H.Masumoto, T.Okazaki, and S.Yokoyama (1998).
A helix-turn-helix structure unit in human centromere protein B (CENP-B).
  EMBO J, 17, 827-837.
PDB code: 1bw6
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.  
  9488476 K.Inoue, and C.J.Sherr (1998).
Gene expression and cell cycle arrest mediated by transcription factor DMP1 is antagonized by D-type cyclins through a cyclin-dependent-kinase-independent mechanism.
  Mol Cell Biol, 18, 1590-1600.  
9774480 M.Lehmann, T.Siegmund, K.G.Lintermann, and G.Korge (1998).
The pipsqueak protein of Drosophila melanogaster binds to GAGA sequences through a novel DNA-binding domain.
  J Biol Chem, 273, 28504-28509.  
  9418884 M.W.Wong, R.W.Henry, B.Ma, R.Kobayashi, N.Klages, P.Matthias, M.Strubin, and N.Hernandez (1998).
The large subunit of basal transcription factor SNAPc is a Myb domain protein that interacts with Oct-1.
  Mol Cell Biol, 18, 368-377.  
9657674 P.B.McIntosh, T.A.Frenkiel, U.Wollborn, J.E.McCormick, K.H.Klempnauer, J.Feeney, and M.D.Carr (1998).
Solution structure of the B-Myb DNA-binding domain: a possible role for conformational instability of the protein in DNA binding and control of gene expression.
  Biochemistry, 37, 9619-9629.
PDB code: 1a5j
9512546 P.König, L.Fairall, and D.Rhodes (1998).
Sequence-specific DNA recognition by the myb-like domain of the human telomere binding protein TRF1: a model for the protein-DNA complex.
  Nucleic Acids Res, 26, 1731-1740.  
9665700 P.K.Radha, P.K.Patel, and R.V.Hosur (1998).
NMR structure of the extended Myb cognate sequence and modeling studies on specific DNA-Myb complexes.
  Biochemistry, 37, 9952-9963.
PDB code: 1bdz
  9632794 R.Ohi, A.Feoktistova, S.McCann, V.Valentine, A.T.Look, J.S.Lipsick, and K.L.Gould (1998).
Myb-related Schizosaccharomyces pombe cdc5p is structurally and functionally conserved in eukaryotes.
  Mol Cell Biol, 18, 4097-4108.  
9657154 R.Schaffer, N.Ramsay, A.Samach, S.Corden, J.Putterill, I.A.Carré, and G.Coupland (1998).
The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering.
  Cell, 93, 1219-1229.  
10384275 R.W.Henry, E.Ford, R.Mital, V.Mittal, and N.Hernandez (1998).
Crossing the line between RNA polymerases: transcription of human snRNA genes by RNA polymerases II and III.
  Cold Spring Harb Symp Quant Biol, 63, 111-120.  
9724717 S.Rhee, R.G.Martin, J.L.Rosner, and D.R.Davies (1998).
A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator.
  Proc Natl Acad Sci U S A, 95, 10413-10418.
PDB code: 1bl0
9458036 T.Hunter (1998).
Prolyl isomerases and nuclear function.
  Cell, 92, 141-143.  
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
  9539422 W.C.Shen, J.Wieser, T.H.Adams, and D.J.Ebbole (1998).
The Neurospora rca-1 gene complements an Aspergillus flbD sporulation mutant but has no identifiable role in Neurospora sporulation.
  Genetics, 148, 1031-1041.  
  9488474 Y.Wang, and W.E.Stumph (1998).
Identification and topological arrangement of Drosophila proximal sequence element (PSE)-binding protein subunits that contact the PSEs of U1 and U6 small nuclear RNA genes.
  Mol Cell Biol, 18, 1570-1579.  
9130722 A.Bianchi, S.Smith, L.Chong, P.Elias, and T.de Lange (1997).
TRF1 is a dimer and bends telomeric DNA.
  EMBO J, 16, 1785-1794.  
8995298 C.E.Williams, and E.Grotewold (1997).
Differences between plant and animal Myb domains are fundamental for DNA binding activity, and chimeric Myb domains have novel DNA binding specificities.
  J Biol Chem, 272, 563-571.  
9055608 C.Martin, and J.Paz-Ares (1997).
MYB transcription factors in plants.
  Trends Genet, 13, 67-73.  
9326950 D.Broccoli, A.Smogorzewska, L.Chong, and T.de Lange (1997).
Human telomeres contain two distinct Myb-related proteins, TRF1 and TRF2.
  Nat Genet, 17, 231-235.  
9020167 E.M.Brendeford, A.H.Myrset, A.B.Hegvold, M.Lundin, and O.S.Gabrielsen (1997).
Oncogenic point mutations induce altered conformation, redox sensitivity, and DNA binding in the minimal DNA binding domain of avian myeloblastosis virus v-Myb.
  J Biol Chem, 272, 4436-4443.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
9155030 H.C.van Leeuwen, M.J.Strating, M.Rensen, W.de Laat, and P.C.van der Vliet (1997).
Linker length and composition influence the flexibility of Oct-1 DNA binding.
  EMBO J, 16, 2043-2053.  
9153301 J.Chen, S.Pongor, and A.Simoncsits (1997).
Recognition of DNA by single-chain derivatives of the phage 434 repressor: high affinity binding depends on both the contacted and non-contacted base pairs.
  Nucleic Acids Res, 25, 2047-2054.  
9369944 K.Bein, M.Husain, J.A.Ware, M.L.Mucenski, R.D.Rosenberg, and M.Simons (1997).
c-Myb function in fibroblasts.
  J Cell Physiol, 173, 319-326.  
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.  
9391075 M.Shen, C.Haggblom, M.Vogt, T.Hunter, and K.P.Lu (1997).
Characterization and cell cycle regulation of the related human telomeric proteins Pin2 and TRF1 suggest a role in mitosis.
  Proc Natl Acad Sci U S A, 94, 13618-13623.  
9048479 P.König, and D.Rhodes (1997).
Recognition of telomeric DNA.
  Trends Biochem Sci, 22, 43-47.  
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.  
9009844 S.Smith, and T.de Lange (1997).
TRF1, a mammalian telomeric protein.
  Trends Genet, 13, 21-26.  
9045645 T.L.Brandt, D.J.Fraser, S.Leal, P.M.Halandras, A.R.Kroll, and D.J.Kroll (1997).
c-Myb trans-activates the human DNA topoisomerase IIalpha gene promoter.
  J Biol Chem, 272, 6278-6284.  
9032060 Y.Choo, and A.Klug (1997).
Physical basis of a protein-DNA recognition code.
  Curr Opin Struct Biol, 7, 117-125.  
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.  
8646530 D.Shore (1996).
The means to bind the ends.
  Nat Struct Biol, 3, 491-493.  
  8887674 H.Hirai, and C.J.Sherr (1996).
Interaction of D-type cyclins with a novel myb-like transcription factor, DMP1.
  Mol Cell Biol, 16, 6457-6467.  
8783394 H.Nakamura (1996).
Roles of electrostatic interaction in proteins.
  Q Rev Biophys, 29, 1.  
8739852 J.Golay, L.Basilico, L.Loffarelli, S.Songia, V.Broccoli, and M.Introna (1996).
Regulation of hematopoietic cell proliferation and differentiation by the myb oncogene family of transcription factors.
  Int J Clin Lab Res, 26, 24-32.  
  8725565 J.J.Hutton, K.C.Ess, D.P.Witte, and B.J.Aronow (1996).
Winner of the Theodore E. Woodward Award: c-Myb and the coordinate regulation of thymic genes.
  Trans Am Clin Climatol Assoc, 107, 115-124.  
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
8564545 K.Ogata, C.Kanei-Ishii, M.Sasaki, H.Hatanaka, A.Nagadoi, M.Enari, H.Nakamura, Y.Nishimura, S.Ishii, and A.Sarai (1996).
The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation.
  Nat Struct Biol, 3, 178-187.  
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.  
8980549 N.Quaedvlieg, J.Dockx, G.Keultjes, P.Kock, J.Wilmering, P.Weisbeek, and S.Smeekens (1996).
Identification of a light-regulated MYB gene from an Arabidopsis transcription factor gene collection.
  Plant Mol Biol, 32, 987-993.  
8605176 P.Dumoulin, R.H.Ebright, R.Knegtel, R.Kaptein, M.Granger-Schnarr, and M.Schnarr (1996).
Structure of the LexA repressor-DNA complex probed by affinity cleavage and affinity photo-cross-linking.
  Biochemistry, 35, 4279-4286.  
8620531 P.Konig, R.Giraldo, L.Chapman, and D.Rhodes (1996).
The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA.
  Cell, 85, 125-136.
PDB code: 1ign
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.  
8639738 Q.Lin, W.D.Hamilton, and A.Merryweather (1996).
Cloning and initial characterization of 14 myb-related cDNAs from tomato (Lycopersicon esculentum cv. Ailsa Craig).
  Plant Mol Biol, 30, 1009-1020.  
8882580 R.Aasland, A.F.Stewart, and T.Gibson (1996).
The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB.
  Trends Biochem Sci, 21, 87-88.  
9011176 S.A.Ness (1996).
The Myb oncoprotein: regulating a regulator.
  Biochim Biophys Acta, 1288, F123-F139.  
8614633 T.Bilaud, C.E.Koering, E.Binet-Brasselet, K.Ancelin, A.Pollice, S.M.Gasser, and E.Gilson (1996).
The telobox, a Myb-related telomeric DNA binding motif found in proteins from yeast, plants and human.
  Nucleic Acids Res, 24, 1294-1303.  
8917598 T.Hirayama, and K.Shinozaki (1996).
A cdc5+ homolog of a higher plant, Arabidopsis thaliana.
  Proc Natl Acad Sci U S A, 93, 13371-13376.  
  8575189 A.M.Gronenborn, and G.M.Clore (1995).
Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy.
  Crit Rev Biochem Mol Biol, 30, 351-385.  
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
8524664 B.Lustig, and R.L.Jernigan (1995).
Consistencies of individual DNA base-amino acid interactions in structures and sequences.
  Nucleic Acids Res, 23, 4707-4711.  
  7565722 K.C.Ess, T.L.Whitaker, G.J.Cost, D.P.Witte, J.J.Hutton, and B.J.Aronow (1995).
A central role for a single c-Myb binding site in a thymic locus control region.
  Mol Cell Biol, 15, 5707-5715.  
7796266 K.Ogata, S.Morikawa, H.Nakamura, H.Hojo, S.Yoshimura, R.Zhang, S.Aimoto, Y.Ametani, Z.Hirata, and A.Sarai (1995).
Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb.
  Nat Struct Biol, 2, 309-320.
PDB codes: 1mbe 1mbf 1mbg 1mbh 1mbj 1mbk
  7565749 M.Oelgeschläger, J.Krieg, J.M.Lüscher-Firzlaff, and B.Lüscher (1995).
Casein kinase II phosphorylation site mutations in c-Myb affect DNA binding and transcriptional cooperativity with NF-M.
  Mol Cell Biol, 15, 5966-5974.  
  7737128 R.Solano, C.Nieto, J.Avila, L.Cañas, I.Diaz, and J.Paz-Ares (1995).
Dual DNA binding specificity of a petal epidermis-specific MYB transcription factor (MYB.Ph3) from Petunia hybrida.
  EMBO J, 14, 1773-1784.  
7592692 T.Yasukawa, C.Kanei-Ishii, T.Maekawa, J.Fujimoto, T.Yamamoto, and S.Ishii (1995).
Increase of solubility of foreign proteins in Escherichia coli by coproduction of the bacterial thioredoxin.
  J Biol Chem, 270, 25328-25331.  
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 codes are shown on the right.

 

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