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Transcription/DNA PDB id
2bop
Jmol
Contents
Protein chain
85 a.a. *
DNA/RNA
Metals
_YB ×2
Waters ×121
* Residue conservation analysis
PDB id:
2bop
Name: Transcription/DNA
Title: Crystal structure at 1.7 angstroms of the bovine papillomavirus-1 e2 DNA-binding domain bound to its DNA target
Structure: DNA (5'- d( Cp Cp Gp Ap Cp Cp Gp Ap Cp Gp Tp Cp Gp Gp Tp Cp G )-3'). Chain: b. Engineered: yes. Protein (e2). Chain: a. Engineered: yes
Source: Synthetic: yes. Bovine papillomavirus type 1. Organism_taxid: 10559. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.70Å     R-factor:   0.201    
Authors: R.S.Hegde,S.R.Grossman,L.A.Laimins,P.B.Sigler
Key ref: R.S.Hegde et al. (1992). Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature, 359, 505-512. PubMed id: 1328886 DOI: 10.1038/359505a0
Date:
13-Jan-94     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03122  (VE2_BPV1) -  Regulatory protein E2
Seq:
Struc: 		410 a.a.
85 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     host cell nucleus   1 term 
  Biological process     regulation of DNA replication   2 terms 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1038/359505a0 Nature 359:505-512 (1992)
PubMed id: 1328886  
 
 
Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target.
R.S.Hegde, S.R.Grossman, L.A.Laimins, P.B.Sigler.
 
  ABSTRACT  
 
The dominant transcriptional regulator of the papillomaviruses, E2, binds to its specific DNA target through a previously unobserved dimeric antiparallel beta-barrel. The DNA is severely but smoothly bent over the barrel by the interaction of successive major grooves with a pair of symmetrically disposed alpha-helices. The specific interface is an 'interwoven' network of interactions where the identifying base pairs of the target contact more than one amino-acid side chain and the discriminating amino acids interact with more than one base pair.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21274725 B.Akgül, R.García-Escudero, C.Ekechi, G.Steger, H.Navsaria, H.Pfister, and A.Storey (2011).
The E2 protein of human papillomavirus type 8 increases the expression of matrix metalloproteinase-9 in human keratinocytes and organotypic skin cultures.
  Med Microbiol Immunol, 200, 127-135.  
21131281 C.Brown, K.Campos-León, M.Strickland, C.Williams, V.Fairweather, R.L.Brady, M.P.Crump, and K.Gaston (2011).
Protein flexibility directs DNA recognition by the papillomavirus E2 proteins.
  Nucleic Acids Res, 39, 2969-2980.  
20334529 R.Rohs, X.Jin, S.M.West, R.Joshi, B.Honig, and R.S.Mann (2010).
Origins of specificity in protein-DNA recognition.
  Annu Rev Biochem, 79, 233-269.  
20484563 S.J.Han, J.Hu, B.Pierce, Z.Weng, and R.Renne (2010).
Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins.
  J Gen Virol, 91, 2203-2215.  
20185566 Z.Xi, Y.Zhang, R.S.Hegde, Z.Shakked, and D.M.Crothers (2010).
Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA.
  Nucleic Acids Res, 38, 3827-3833.  
19156829 D.E.Wetzler, M.Gallo, R.Melis, T.Eliseo, A.D.Nadra, D.U.Ferreiro, M.Paci, I.E.Sánchez, D.O.Cicero, and G.de Prat Gay (2009).
A strained DNA binding helix is conserved for site recognition, folding nucleation, and conformational modulation.
  Biopolymers, 91, 432-443.  
19264634 E.Q.Wu, X.Zha, X.H.Yu, G.N.Zhang, Y.G.Wu, Y.Fan, Y.Ren, L.Q.Kong, and W.Kong (2009).
Profile of physical status and gene variation of human papillomavirus 58 genome in cervical cancer.
  J Gen Virol, 90, 1229-1237.  
19244617 J.W.Locasale, A.A.Napoli, S.Chen, H.M.Berman, and C.L.Lawson (2009).
Signatures of protein-DNA recognition in free DNA binding sites.
  J Mol Biol, 386, 1054-1065.
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19129441 L.R.Dresang, D.T.Vereide, and B.Sugden (2009).
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  J Virol, 83, 2930-2940.  
19865164 R.Rohs, S.M.West, A.Sosinsky, P.Liu, R.S.Mann, and B.Honig (2009).
The role of DNA shape in protein-DNA recognition.
  Nature, 461, 1248-1253.  
18664582 D.U.Ferreiro, I.E.Sánchez, and G.de Prat Gay (2008).
Transition state for protein-DNA recognition.
  Proc Natl Acad Sci U S A, 105, 10797-10802.  
18337573 E.E.Hernandez-Ramon, J.E.Burns, W.Zhang, H.F.Walker, S.Allen, A.A.Antson, and N.J.Maitland (2008).
Dimerization of the human papillomavirus type 16 E2 N terminus results in DNA looping within the upstream regulatory region.
  J Virol, 82, 4853-4861.  
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Kinetically driven refolding of the hyperstable EBNA1 origin DNA-binding dimeric beta-barrel domain into amyloid-like spherical oligomers.
  Proteins, 70, 450-461.  
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  Protein Sci, 17, 299-312.  
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Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites.
  Nucleic Acids Res, 36, 2268-2283.  
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MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation.
  Biophys J, 95, 1108-1117.  
18687692 N.Gupta, and S.W.Ragsdale (2008).
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  J Biol Chem, 283, 28721-28728.  
18478582 P.Poulain, A.Saladin, B.Hartmann, and C.Prévost (2008).
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  J Comput Chem, 29, 2582-2592.  
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  Nucleic Acids Res, 35, 3525-3534.  
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  Nucleic Acids Res, 35, 3504-3515.
PDB codes: 2jeu 2jex
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  BMC Struct Biol, 7, 4.  
  17241456 J.Keller, N.Leulliot, C.Cambillau, V.Campanacci, S.Porciero, D.Prangishvilli, P.Forterre, D.Cortez, S.Quevillon-Cheruel, and H.van Tilbeurgh (2007).
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  Virology, 360, 191-198.  
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Molecular dynamics of the DNA-binding domain of the papillomavirus E2 transcriptional regulator uncover differential properties for DNA target accommodation.
  FEBS J, 274, 2385-2395.  
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  Plasmid, 58, 1.  
17392356 S.M.Horner, and D.DiMaio (2007).
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  J Virol, 81, 6254-6264.  
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  Nucleic Acids Res, 34, e125.  
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Human papillomaviruses: basic mechanisms of pathogenesis and oncogenicity.
  Rev Med Virol, 16, 83-97.  
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Mechanism of DNA recognition at a viral replication origin.
  J Biol Chem, 281, 26893-26903.  
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  EMBO J, 25, 5961-5969.
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Essential elements of a licensed, mammalian plasmid origin of DNA synthesis.
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  Biophys J, 89, 2542-2551.  
16099158 D.J.McCance (2005).
Transcriptional regulation by human papillomaviruses.
  Curr Opin Genet Dev, 15, 515-519.  
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Free energy contributions to direct readout of a DNA sequence.
  J Biol Chem, 280, 32480-32484.  
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Crosstalk between the human papillomavirus E2 transcriptional activator and the E6 oncoprotein.
  Oncogene, 24, 5149-5164.  
16216581 R.Rohs, H.Sklenar, and Z.Shakked (2005).
Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites.
  Structure, 13, 1499-1509.  
14755572 D.Djuranovic, and B.Hartmann (2004).
DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations.
  Biopolymers, 73, 356-368.  
  14725771 G.Paillard, and R.Lavery (2004).
Analyzing protein-DNA recognition mechanisms.
  Structure, 12, 113-122.  
14755573 K.S.Byun, and D.L.Beveridge (2004).
Molecular dynamics simulations of papilloma virus E2 DNA sequences: dynamical models for oligonucleotide structures in solution.
  Biopolymers, 73, 369-379.  
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Positive contribution of hydration on DNA binding by E2c protein from papillomavirus.
  J Biol Chem, 279, 47968-47974.  
15187189 M.S.Longworth, and L.A.Laimins (2004).
Pathogenesis of human papillomaviruses in differentiating epithelia.
  Microbiol Mol Biol Rev, 68, 362-372.  
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Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus.
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PDB codes: 1pvp 1pvq 1pvr
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12582248 T.D.Schaal, W.G.Mallet, D.L.McMinn, N.V.Nguyen, M.M.Sopko, S.John, and B.S.Parekh (2003).
Inhibition of human papilloma virus E2 DNA binding protein by covalently linked polyamides.
  Nucleic Acids Res, 31, 1282-1291.  
11988474 R.S.Hegde (2002).
The papillomavirus E2 proteins: structure, function, and biology.
  Annu Rev Biophys Biomol Struct, 31, 343-360.  
11160670 C.D.Newhouse, and S.J.Silverstein (2001).
Orientation of a novel DNA binding site affects human papillomavirus-mediated transcription and replication.
  J Virol, 75, 1722-1735.  
15989521 F.X.Wilson (2001).
Emerging therapies for human papillomavirus infection.
  Expert Opin Emerg Drugs, 6, 199-207.  
11297428 H.Matsuno, K.Niikura, and Y.Okahata (2001).
Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A.T base pairs of oligonucleotides immobilized on a 27 mhz quartz crystal microbalance.
  Biochemistry, 40, 3615-3622.  
11438706 J.Hizver, H.Rozenberg, F.Frolow, D.Rabinovich, and Z.Shakked (2001).
DNA bending by an adenine--thymine tract and its role in gene regulation.
  Proc Natl Acad Sci U S A, 98, 8490-8495.
PDB code: 1ilc
11602702 J.M.Bashaw, and J.L.Yates (2001).
Replication from oriP of Epstein-Barr virus requires exact spacing of two bound dimers of EBNA1 which bend DNA.
  J Virol, 75, 10603-10611.  
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Streptococcus pneumonia YlxR at 1.35 A shows a putative new fold.
  Acta Crystallogr D Biol Crystallogr, 57, 1747-1751.
PDB code: 1g2r
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Crystallization and secondary-structure determination of a protein of the Lrp/AsnC family from a hyperthermophilic archaeon.
  Acta Crystallogr D Biol Crystallogr, 57, 469-471.  
11226172 P.Kapoor, K.Shire, and L.Frappier (2001).
Reconstitution of Epstein-Barr virus-based plasmid partitioning in budding yeast.
  EMBO J, 20, 222-230.  
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Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus.
  EMBO J, 20, 990-997.
PDB code: 1i1g
11461997 S.Bellanger, C.Demeret, S.Goyat, and F.Thierry (2001).
Stability of the human papillomavirus type 18 E2 protein is regulated by a proteasome degradation pathway through its amino-terminal transactivation domain.
  J Virol, 75, 7244-7251.  
10590112 A.Gonzalez, C.Bazaldua-Hernandez, M.West, K.Woytek, and V.G.Wilson (2000).
Identification of a short, hydrophilic amino acid sequence critical for origin recognition by the bovine papillomavirus E1 protein.
  J Virol, 74, 245-253.  
10799567 D.F.Ceccarelli, and L.Frappier (2000).
Functional analyses of the EBNA1 origin DNA binding protein of Epstein-Barr virus.
  J Virol, 74, 4939-4948.  
11087426 D.U.Ferreiro, L.M.Lima, A.D.Nadra, L.G.Alonso, F.A.Goldbaum, and G.de Prat-Gay (2000).
Distinctive cognate sequence discrimination, bound DNA conformation, and binding modes in the E2 C-terminal domains from prototype human and bovine papillomaviruses.
  Biochemistry, 39, 14692-14701.  
10856250 E.Gillitzer, G.Chen, and A.Stenlund (2000).
Separate domains in E1 and E2 proteins serve architectural and productive roles for cooperative DNA binding.
  EMBO J, 19, 3069-3079.  
10949036 E.J.Enemark, G.Chen, D.E.Vaughn, A.Stenlund, and L.Joshua-Tor (2000).
Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus.
  Mol Cell, 6, 149-158.
PDB code: 1f08
10713596 E.R.Leight, and B.Sugden (2000).
EBNA-1: a protein pivotal to latent infection by Epstein-Barr virus.
  Rev Med Virol, 10, 83.  
10627562 G.Chen, and A.Stenlund (2000).
Two patches of amino acids on the E2 DNA binding domain define the surface for interaction with E1.
  J Virol, 74, 1506-1512.  
10821674 J.L.Baber, D.Levens, D.Libutti, and N.Tjandra (2000).
Chemical shift mapped DNA-binding sites and 15N relaxation analysis of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K.
  Biochemistry, 39, 6022-6032.  
10712935 J.L.Keck, and J.M.Berger (2000).
DNA replication at high resolution.
  Chem Biol, 7, R63-R71.  
11060774 K.A.Alexander, and W.C.Phelps (2000).
Recent advances in diagnosis and therapy of human papillomaviruses.
  Expert Opin Investig Drugs, 9, 1753-1765.  
10617590 K.Webster, J.Parish, M.Pandya, P.L.Stern, A.R.Clarke, and K.Gaston (2000).
The human papillomavirus (HPV) 16 E2 protein induces apoptosis in the absence of other HPV proteins and via a p53-dependent pathway.
  J Biol Chem, 275, 87-94.  
11114179 L.M.Lima, D.Foguel, and J.L.Silva (2000).
DNA tightens the dimeric DNA-binding domain of human papillomavirus E2 protein without changes in volume.
  Proc Natl Acad Sci U S A, 97, 14289-14294.  
  11104519 N.M.Luscombe, S.E.Austin, H.M.Berman, and J.M.Thornton (2000).
An overview of the structures of protein-DNA complexes.
  Genome Biol, 1, REVIEWS001.  
  10794423 Y.K.Mok, L.G.Alonso, L.M.Lima, M.Bycroft, and G.de Prat-Gay (2000).
Folding of a dimeric beta-barrel: residual structure in the urea denatured state of the human papillomavirus E2 DNA binding domain.
  Protein Sci, 9, 799-811.  
10569923 A.Claiborne, J.I.Yeh, T.C.Mallett, J.Luba, E.J.Crane, V.Charrier, and D.Parsonage (1999).
Protein-sulfenic acids: diverse roles for an unlikely player in enzyme catalysis and redox regulation.
  Biochemistry, 38, 15407-15416.  
9988734 B.A.Fox, V.C.Yee, L.C.Pedersen, I.Le Trong, P.D.Bishop, R.E.Stenkamp, and D.C.Teller (1999).
Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography.
  J Biol Chem, 274, 4917-4923.
PDB codes: 1bl2 1ggu 1ggy 1qrk
10651283 D.J.Rigden, and M.Carneiro (1999).
A structural model for the rolA protein and its interaction with DNA.
  Proteins, 37, 697-708.  
10469640 H.Komori, F.Matsunaga, Y.Higuchi, M.Ishiai, C.Wada, and K.Miki (1999).
Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution.
  EMBO J, 18, 4597-4607.
PDB code: 1rep
  10647173 J.Janin (1999).
Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition.
  Structure, 7, R277-R279.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
  10233926 R.Kurg, J.Parik, E.Juronen, T.Sedman, A.Abroi, I.Liiv, U.Langel, and M.Ustav (1999).
Effect of bovine papillomavirus E2 protein-specific monoclonal antibodies on papillomavirus DNA replication.
  J Virol, 73, 4670-4677.  
10356398 S.F.Harris, and M.R.Botchan (1999).
Crystal structure of the human papillomavirus type 18 E2 activation domain.
  Science, 284, 1673-1677.
PDB code: 1qqh
10587434 S.Veeraraghavan, C.C.Mello, E.J.Androphy, and J.D.Baleja (1999).
Structural correlates for enhanced stability in the E2 DNA-binding domain from bovine papillomavirus.
  Biochemistry, 38, 16115-16124.
PDB code: 1dbd
9519296 A.M.Edwards, A.Bochkarev, and L.Frappier (1998).
Origin DNA-binding proteins.
  Curr Opin Struct Biol, 8, 49-53.  
9539738 C.W.Lehman, and M.R.Botchan (1998).
Segregation of viral plasmids depends on tethering to chromosomes and is regulated by phosphorylation.
  Proc Natl Acad Sci U S A, 95, 4338-4343.  
  9499046 D.A.Lim, M.Gossen, C.W.Lehman, and M.R.Botchan (1998).
Competition for DNA binding sites between the short and long forms of E2 dimers underlies repression in bovine papillomavirus type 1 DNA replication control.
  J Virol, 72, 1931-1940.  
10089498 D.E.Bussiere, X.Kong, D.A.Egan, K.Walter, T.F.Holzman, F.Lindh, T.Robins, and V.L.Giranda (1998).
Structure of the E2 DNA-binding domain from human papillomavirus serotype 31 at 2.4 A.
  Acta Crystallogr D Biol Crystallogr, 54, 1367-1376.
PDB code: 1a7g
9535893 D.Foguel, J.L.Silva, and G.de Prat-Gay (1998).
Characterization of a partially folded monomer of the DNA-binding domain of human papillomavirus E2 protein obtained at high pressure.
  J Biol Chem, 273, 9050-9057.  
9860938 D.M.Crothers (1998).
DNA curvature and deformation in protein-DNA complexes: a step in the right direction.
  Proc Natl Acad Sci U S A, 95, 15163-15165.  
10089509 D.Rabinovich, H.Rozenberg, and Z.Shakked (1998).
Molecular replacement: the revival of the molecular Fourier transform method.
  Acta Crystallogr D Biol Crystallogr, 54, 1336-1342.  
  9557678 E.C.Goodwin, L.K.Naeger, D.E.Breiding, E.J.Androphy, and D.DiMaio (1998).
Transactivation-competent bovine papillomavirus E2 protein is specifically required for efficient repression of human papillomavirus oncogene expression and for acute growth inhibition of cervical carcinoma cell lines.
  J Virol, 72, 3925-3934.  
9524133 E.L.Beall, and D.C.Rio (1998).
Transposase makes critical contacts with, and is stimulated by, single-stranded DNA at the P element termini in vitro.
  EMBO J, 17, 2122-2136.  
  9445001 F.Stubenrauch, H.B.Lim, and L.A.Laimins (1998).
Differential requirements for conserved E2 binding sites in the life cycle of oncogenic human papillomavirus type 31.
  J Virol, 72, 1071-1077.  
9860945 H.Rozenberg, D.Rabinovich, F.Frolow, R.S.Hegde, and Z.Shakked (1998).
Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets.
  Proc Natl Acad Sci U S A, 95, 15194-15199.
PDB codes: 423d 424d 425d
10089541 J.E.Burns, O.V.Moroz, A.A.Antson, C.M.Sanders, K.S.Wilson, and N.J.Maitland (1998).
Expression, crystallization and preliminary X-ray analysis of the E2 transactivation domain from papillomavirus type 16.
  Acta Crystallogr D Biol Crystallogr, 54, 1471-1474.  
  9444994 J.M.Yao, D.E.Breiding, and E.J.Androphy (1998).
Functional interaction of the bovine papillomavirus E2 transactivation domain with TFIIB.
  J Virol, 72, 1013-1019.  
9736626 M.D.Allen, K.Yamasaki, M.Ohme-Takagi, M.Tateno, and M.Suzuki (1998).
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.
  EMBO J, 17, 5484-5496.
PDB codes: 1gcc 2gcc 3gcc
  9499063 M.H.Skiadopoulos, and A.A.McBride (1998).
Bovine papillomavirus type 1 genomes and the E2 transactivator protein are closely associated with mitotic chromatin.
  J Virol, 72, 2079-2088.  
9668115 M.K.Shirra, and U.Hansen (1998).
LSF and NTF-1 share a conserved DNA recognition motif yet require different oligomerization states to form a stable protein-DNA complex.
  J Biol Chem, 273, 19260-19268.  
  9621032 T.G.Gillette, and J.A.Borowiec (1998).
Distinct roles of two binding sites for the bovine papillomavirus (BPV) E2 transactivator on BPV DNA replication.
  J Virol, 72, 5735-5744.  
  9566887 W.S.Joo, H.Y.Kim, J.D.Purviance, K.R.Sreekumar, and P.A.Bullock (1998).
Assembly of T-antigen double hexamers on the simian virus 40 core origin requires only a subset of the available binding sites.
  Mol Cell Biol, 18, 2677-2687.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
  9371593 C.Demeret, C.Desaintes, M.Yaniv, and F.Thierry (1997).
Different mechanisms contribute to the E2-mediated transcriptional repression of human papillomavirus type 18 viral oncogenes.
  J Virol, 71, 9343-9349.  
9034333 C.Desaintes, C.Demeret, S.Goyat, M.Yaniv, and F.Thierry (1997).
Expression of the papillomavirus E2 protein in HeLa cells leads to apoptosis.
  EMBO J, 16, 504-514.  
  9094639 C.W.Lehman, D.S.King, and M.R.Botchan (1997).
A papillomavirus E2 phosphorylation mutant exhibits normal transient replication and transcription but is defective in transformation and plasmid retention.
  J Virol, 71, 3652-3665.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
9032063 J.W.Schwabe (1997).
The role of water in protein-DNA interactions.
  Curr Opin Struct Biol, 7, 126-134.  
9303004 K.Swaminathan, P.Flynn, R.J.Reece, and R.Marmorstein (1997).
Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster.
  Nat Struct Biol, 4, 751-759.
PDB code: 1zme
9235925 L.M.Lima, and G.de Prat-Gay (1997).
Conformational changes and stabilization induced by ligand binding in the DNA-binding domain of the E2 protein from human papillomavirus.
  J Biol Chem, 272, 19295-19303.  
9029152 M.G.Frattini, S.D.Hurst, H.B.Lim, S.Swaminathan, and L.A.Laimins (1997).
Abrogation of a mitotic checkpoint by E2 proteins from oncogenic human papillomaviruses correlates with increased turnover of the p53 tumor suppressor protein.
  EMBO J, 16, 318-331.  
9782775 M.Tateno, K.Yamasaki, N.Amano, J.Kakinuma, H.Koike, M.D.Allen, and M.Suzuki (1997).
DNA recognition by beta-sheets.
  Biopolymers, 44, 335-359.  
  9444478 P.A.Bullock (1997).
The initiation of simian virus 40 DNA replication in vitro.
  Crit Rev Biochem Mol Biol, 32, 503-568.  
  8985425 R.B.Pepinsky, S.S.Prakash, K.Corina, M.J.Grossel, J.Barsoum, and E.J.Androphy (1997).
Sequences flanking the core DNA-binding domain of bovine papillomavirus type 1 E2 contribute to DNA-binding function.
  J Virol, 71, 828-831.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
  9032076 T.Ellenberger, and A.Landy (1997).
A good turn for DNA: the structure of integration host factor bound to DNA.
  Structure, 5, 153-157.  
  9094674 W.S.Joo, X.Luo, D.Denis, H.Y.Kim, G.J.Rainey, C.Jones, K.R.Sreekumar, and P.A.Bullock (1997).
Purification of the simian virus 40 (SV40) T antigen DNA-binding domain and characterization of its interactions with the SV40 origin.
  J Virol, 71, 3972-3985.  
  8709243 A.Abroi, R.Kurg, and M.Ustav (1996).
Transcriptional and replicational activation functions in the bovine papillomavirus type 1 E2 protein are encoded by different structural determinants.
  J Virol, 70, 6169-6179.  
8625416 A.Bochkarev, J.A.Barwell, R.A.Pfuetzner, E.Bochkareva, L.Frappier, and A.M.Edwards (1996).
Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein, EBNA1, bound to DNA.
  Cell, 84, 791-800.  
8838587 A.Modesti, N.Taddei, F.Chiti, M.Bucciantini, F.Magherini, S.Rigacci, M.Stefani, G.Raugei, and G.Ramponi (1996).
Properties of Cys21-mutated muscle acylphosphatases.
  J Protein Chem, 15, 27-34.  
  8794373 A.Thain, O.Jenkins, A.R.Clarke, and K.Gaston (1996).
CpG methylation directly inhibits binding of the human papillomavirus type 16 E2 protein to specific DNA sequences.
  J Virol, 70, 7233-7235.  
8805327 F.B.Dean, and M.O'Donnell (1996).
Two steps to binding replication origins? DNA-protein interactions.
  Curr Biol, 6, 931-934.  
8548452 G.Guzikevich-Guerstein, and Z.Shakked (1996).
A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein.
  Nat Struct Biol, 3, 32-37.  
8652551 H.Liang, A.M.Petros, R.P.Meadows, H.S.Yoon, D.A.Egan, K.Walter, T.F.Holzman, T.Robins, and S.W.Fesik (1996).
Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: evidence for flexible DNA-binding regions.
  Biochemistry, 35, 2095-2103.
PDB code: 1dhm
  8627680 H.Sakai, T.Yasugi, J.D.Benson, J.J.Dowhanick, and P.M.Howley (1996).
Targeted mutagenesis of the human papillomavirus type 16 E2 transactivation domain reveals separable transcriptional activation and DNA replication functions.
  J Virol, 70, 1602-1611.  
  8754805 J.Dekker, J.A.van Oosterhout, and P.C.van der Vliet (1996).
Two regions within the DNA binding domain of nuclear factor I interact with DNA and stimulate adenovirus DNA replication independently.
  Mol Cell Biol, 16, 4073-4080.  
8756456 J.I.Yeh, A.Claiborne, and W.G.Hol (1996).
Structure of the native cysteine-sulfenic acid redox center of enterococcal NADH peroxidase refined at 2.8 A resolution.
  Biochemistry, 35, 9951-9957.
PDB code: 1joa
8703960 K.A.Alexander, and W.C.Phelps (1996).
A fluorescence anisotropy study of DNA binding by HPV-11 E2C protein: a hierarchy of E2-binding sites.
  Biochemistry, 35, 9864-9872.  
  8551571 M.H.Skiadopoulos, and A.A.McBride (1996).
The bovine papillomavirus type 1 E2 transactivator and repressor proteins use different nuclear localization signals.
  J Virol, 70, 1117-1124.  
  8676438 M.K.Ferguson, and M.R.Botchan (1996).
Genetic analysis of the activation domain of bovine papillomavirus protein E2: its role in transcription and replication.
  J Virol, 70, 4193-4199.  
8663420 M.Kurokawa, T.Tanaka, K.Tanaka, N.Hirano, S.Ogawa, K.Mitani, Y.Yazaki, and H.Hirai (1996).
A conserved cysteine residue in the runt homology domain of AML1 is required for the DNA binding ability and the transforming activity on fibroblasts.
  J Biol Chem, 271, 16870-16876.  
8679533 N.Taddei, M.Stefani, F.Magherini, F.Chiti, A.Modesti, G.Raugei, and G.Ramponi (1996).
Looking for residues involved in the muscle acylphosphatase catalytic mechanism and structural stabilization: role of Asn41, Thr42, and Thr46.
  Biochemistry, 35, 7077-7083.  
  8868083 S.R.Grossman, and L.A.Laimins (1996).
EBNA1 and E2: a new paradigm for origin-binding proteins?
  Trends Microbiol, 4, 87-89.  
8946857 X.Luo, D.G.Sanford, P.A.Bullock, and W.W.Bachovchin (1996).
Solution structure of the origin DNA-binding domain of SV40 T-antigen.
  Nat Struct Biol, 3, 1034-1039.
PDB codes: 1tbd 2tbd
  8745409 Y.K.Mok, G.de Prat Gay, P.J.Butler, and M.Bycroft (1996).
Equilibrium dissociation and unfolding of the dimeric human papillomavirus strain-16 E2 DNA-binding domain.
  Protein Sci, 5, 310-319.  
8756330 Y.K.Mok, M.Bycroft, and G.de Prat-Gay (1996).
The dimeric DNA binding domain of the human papillomavirus E2 protein folds through a monomeric intermediate which cannot be native-like.
  Nat Struct Biol, 3, 711-717.  
7553871 A.Bochkarev, J.A.Barwell, R.A.Pfuetzner, W.Furey, A.M.Edwards, and L.Frappier (1995).
Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein EBNA 1.
  Cell, 83, 39-46.
PDB code: 1vhi
  7891721 A.H.Swirnoff, and J.Milbrandt (1995).
DNA-binding specificity of NGFI-A and related zinc finger transcription factors.
  Mol Cell Biol, 15, 2275-2287.  
7625690 A.Klug (1995).
Gene regulatory proteins and their interaction with DNA.
  Ann N Y Acad Sci, 758, 143-160.  
7716167 J.Janin (1995).
Elusive affinities.
  Proteins, 21, 30-39.  
7592989 J.S.Liu, S.R.Kuo, T.R.Broker, and L.T.Chow (1995).
The functions of human papillomavirus type 11 E1, E2, and E2C proteins in cell-free DNA replication.
  J Biol Chem, 270, 27283-27291.  
7647248 M.A.Young, G.Ravishanker, D.L.Beveridge, and H.M.Berman (1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
  Biophys J, 68, 2454-2468.  
8749848 M.Suzuki, and M.Gerstein (1995).
Binding geometry of alpha-helices that recognize DNA.
  Proteins, 23, 525-535.  
7610037 M.Suzuki, and N.Yagi (1995).
Stereochemical basis of DNA bending by transcription factors.
  Nucleic Acids Res, 23, 2083-2091.  
  7745726 R.Mendoza, L.Gandhi, and M.R.Botchan (1995).
E1 recognition sequences in the bovine papillomavirus type 1 origin of DNA replication: interaction between half sites of the inverted repeats.
  J Virol, 69, 3789-3798.  
  7760806 R.P.Ryseck, J.Novotny, and R.Bravo (1995).
Characterization of elements determining the dimerization properties of RelB and p50.
  Mol Cell Biol, 15, 3100-3109.  
  8196641 A.E.Uv, C.R.Thompson, and S.J.Bray (1994).
The Drosophila tissue-specific factor Grainyhead contains novel DNA-binding and dimerization domains which are conserved in the human protein CP2.
  Mol Cell Biol, 14, 4020-4031.  
7800477 C.M.Sanders, and N.J.Maitland (1994).
Kinetic and equilibrium binding studies of the human papillomavirus type-16 transcription regulatory protein E2 interacting with core enhancer elements.
  Nucleic Acids Res, 22, 4890-4897.  
  9383374 D.A.Erlanson, and G.L.Verdine (1994).
Falling out of the fold: tumorigenic mutations and p53.
  Chem Biol, 1, 79-84.  
  7866749 E.Cheah, P.D.Carr, P.M.Suffolk, S.G.Vasudevan, N.E.Dixon, and D.L.Ollis (1994).
Structure of the Escherichia coli signal transducing protein PII.
  Structure, 2, 981-990.
PDB code: 1pil
8040616 E.J.Androphy (1994).
Molecular biology of human papillomavirus infection and oncogenesis.
  J Invest Dermatol, 103, 248-256.  
  7933077 F.Stubenrauch, and H.Pfister (1994).
Low-affinity E2-binding site mediates downmodulation of E2 transactivation of the human papillomavirus type 8 late promoter.
  J Virol, 68, 6959-6966.  
  8081746 G.M.Clore, A.Bax, J.G.Omichinski, and A.M.Gronenborn (1994).
Localization of bound water in the solution structure of a complex of the erythroid transcription factor GATA-1 with DNA.
  Structure, 2, 89-94.  
8302865 J.Liu, M.Sodeoka, W.S.Lane, and G.L.Verdine (1994).
Evidence for a non-alpha-helical DNA-binding motif in the Rel homology region.
  Proc Natl Acad Sci U S A, 91, 908-912.  
8041727 L.Nekludova, and C.O.Pabo (1994).
Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes.
  Proc Natl Acad Sci U S A, 91, 6948-6952.  
7809048 M.G.Frattini, and L.A.Laimins (1994).
Binding of the human papillomavirus E1 origin-recognition protein is regulated through complex formation with the E2 enhancer-binding protein.
  Proc Natl Acad Sci U S A, 91, 12398-12402.  
  8137808 M.Lindahl, L.A.Svensson, A.Liljas, S.E.Sedelnikova, I.A.Eliseikina, N.P.Fomenkova, N.Nevskaya, S.V.Nikonov, M.B.Garber, and T.A.Muranova (1994).
Crystal structure of the ribosomal protein S6 from Thermus thermophilus.
  EMBO J, 13, 1249-1254.
PDB code: 1ris
7809040 M.Suzuki, and N.Yagi (1994).
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.
  Proc Natl Acad Sci U S A, 91, 12357-12361.  
  8087558 M.Suzuki (1994).
A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.
  Structure, 2, 317-326.  
  8083999 M.Ushikai, M.J.Lace, Y.Yamakawa, M.Kono, J.Anson, T.Ishiji, S.Parkkinen, N.Wicker, M.E.Valentine, and I.Davidson (1994).
trans activation by the full-length E2 proteins of human papillomavirus type 16 and bovine papillomavirus type 1 in vitro and in vivo: cooperation with activation domains of cellular transcription factors.
  J Virol, 68, 6655-6666.  
7945933 R.B.Pepinsky, E.J.Androphy, K.Corina, R.Brown, and J.Barsoum (1994).
Specific inhibition of a human papillomavirus E2 trans-activator by intracellular delivery of its repressor.
  DNA Cell Biol, 13, 1011-1019.  
  8083979 S.H.Tan, L.E.Leong, P.A.Walker, and H.U.Bernard (1994).
The human papillomavirus type 16 E2 transcription factor binds with low cooperativity to two flanking sites and represses the E6 promoter through displacement of Sp1 and TFIID.
  J Virol, 68, 6411-6420.  
7656043 S.K.Burley (1994).
Plus ça change, plus c'est la même chose.
  Nat Struct Biol, 1, 207-208.  
8052621 S.R.Grossman, E.Johannsen, X.Tong, R.Yalamanchili, and E.Kieff (1994).
The Epstein-Barr virus nuclear antigen 2 transactivator is directed to response elements by the J kappa recombination signal binding protein.
  Proc Natl Acad Sci U S A, 91, 7568-7572.  
  7532533 T.Unge, S.Knight, R.Bhikhabhai, S.Lövgren, Z.Dauter, K.Wilson, and B.Strandberg (1994).
2.2 A resolution structure of the amino-terminal half of HIV-1 reverse transcriptase (fingers and palm subdomains).
  Structure, 2, 953-961.
PDB code: 1har
7937813 V.Gopalakrishnan, and S.A.Khan (1994).
E1 protein of human papillomavirus type 1a is sufficient for initiation of viral DNA replication.
  Proc Natl Acad Sci U S A, 91, 9597-9601.  
  8223472 A.H.Myrset, A.Bostad, N.Jamin, P.N.Lirsac, F.Toma, and O.S.Gabrielsen (1993).
DNA and redox state induced conformational changes in the DNA-binding domain of the Myb oncoprotein.
  EMBO J, 12, 4625-4633.  
8431949 D.E.Fisher, L.A.Parent, and P.A.Sharp (1993).
High affinity DNA-binding Myc analogs: recognition by an alpha helix.
  Cell, 72, 467-476.  
  8230435 J.Z.Lu, Y.N.Sun, R.C.Rose, W.Bonnez, and D.J.McCance (1993).
Two E2 binding sites (E2BS) alone or one E2BS plus an A/T-rich region are minimal requirements for the replication of the human papillomavirus type 11 origin.
  J Virol, 67, 7131-7139.  
  8081741 M.Chiadmi, S.Moréra, I.Lascu, C.Dumas, G.Le Bras, M.Véron, and J.Janin (1993).
Crystal structure of the Awd nucleotide diphosphate kinase from Drosophila.
  Structure, 1, 283-293.
PDB code: 1ndl
  8392621 M.R.Chen, J.M.Middeldorp, and S.D.Hayward (1993).
Separation of the complex DNA binding domain of EBNA-1 into DNA recognition and dimerization subdomains of novel structure.
  J Virol, 67, 4875-4885.  
  8344259 M.Suzuki (1993).
Common features in DNA recognition helices of eukaryotic transcription factors.
  EMBO J, 12, 3221-3226.  
15336020 J.W.Schwabe (1992).
DNA between the sheets.
  Curr Biol, 2, 661-663.  
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