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PDBsum entry 1tbd

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protein links
DNA-binding protein PDB id
1tbd
Jmol PyMol
Contents
Protein chain
134 a.a. *
* Residue conservation analysis
PDB id:
1tbd
Name: DNA-binding protein
Title: Solution structure of the origin DNA binding domain of sv40 t-antigen, nmr, minimized average structure
Structure: Sv40 t-antigen. Chain: a. Fragment: DNA binding domain. Engineered: yes
Source: Simian virus 40. Organism_taxid: 10633. Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 1 models
Authors: X.Luo,D.G.Sanford,P.A.Bullock,W.W.Bachovchin
Key ref: X.Luo et al. (1996). Solution structure of the origin DNA-binding domain of SV40 T-antigen. Nat Struct Biol, 3, 1034-1039. PubMed id: 8946857
Date:
04-Nov-96     Release date:   12-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03070  (LT_SV40) -  Large T antigen
Seq:
Struc:
 
Seq:
Struc:
708 a.a.
134 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   1 term 
  Biochemical function     DNA replication origin binding     1 term  

 

 
Nat Struct Biol 3:1034-1039 (1996)
PubMed id: 8946857  
 
 
Solution structure of the origin DNA-binding domain of SV40 T-antigen.
X.Luo, D.G.Sanford, P.A.Bullock, W.W.Bachovchin.
 
  ABSTRACT  
 
The structure of the domain from simian virus 40 (SV40) large T-antigen that binds to the SV40 origin of DNA replication (T-ag-OBD131-260) has been determined by nuclear magnetic resonance spectroscopy. The overall fold, consisting of a central five-stranded antiparallel beta-sheet flanked by two alpha-helices on one side and one alpha-helix and one 3(10)-helix on the other, is a new one. Previous mutational analyses have identified two elements, termed A (approximately 152-155) and B2 (203-207), as essential for origin-specific recognition. These elements form two closely juxtaposed loops that define a continuous surface on the protein. The addition of a duplex oligonucleotide containing the origin recognition pentanucleotide GAGGC induces chemical shift changes and slows amide proton exchange in resonances from this region, indicating that this surface directly contacts the DNA.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21636896 G.Meinke, P.Phelan, A.Fradet-Turcotte, J.Archambault, and P.A.Bullock (2011).
Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain.
  Acta Crystallogr D Biol Crystallogr, 67, 560-567.
PDB code: 3qn2
20219473 I.Cuesta, R.Núñez-Ramírez, S.H.Scheres, D.Gai, X.S.Chen, E.Fanning, and J.M.Carazo (2010).
Conformational rearrangements of SV40 large T antigen during early replication events.
  J Mol Biol, 397, 1276-1286.  
20357093 S.Bialasiewicz, R.Rockett, D.W.Whiley, Y.Abed, T.Allander, M.Binks, G.Boivin, A.C.Cheng, J.Y.Chung, P.E.Ferguson, N.M.Gilroy, A.J.Leach, C.Lindau, J.W.Rossen, T.C.Sorrell, M.D.Nissen, and T.P.Sloots (2010).
Whole-genome characterization and genotyping of global WU polyomavirus strains.
  J Virol, 84, 6229-6234.  
19625393 A.Hermannstädter, C.Ziegler, M.Kühl, W.Deppert, and G.V.Tolstonog (2009).
Wild-type p53 enhances efficiency of simian virus 40 large-T-antigen-induced cellular transformation.
  J Virol, 83, 10106-10118.  
19101707 E.Fanning, and K.Zhao (2009).
SV40 DNA replication: from the A gene to a nanomachine.
  Virology, 384, 352-359.  
19144705 W.Wang, and D.T.Simmons (2009).
Simian virus 40 large T antigen can specifically unwind the central palindrome at the origin of DNA replication.
  J Virol, 83, 3312-3322.  
18579587 A.Kumar, W.S.Joo, G.Meinke, S.Moine, E.N.Naumova, and P.A.Bullock (2008).
Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses.
  J Virol, 82, 8849-8862.  
18400864 W.B.Greenleaf, J.Shen, D.Gai, and X.S.Chen (2008).
Systematic study of the functions for the residues around the nucleotide pocket in simian virus 40 AAA+ hexameric helicase.
  J Virol, 82, 6017-6023.  
18353955 X.Zhao, R.J.Madden-Fuentes, B.X.Lou, J.M.Pipas, J.Gerhardt, C.J.Rigell, and E.Fanning (2008).
Ataxia telangiectasia-mutated damage-signaling kinase- and proteasome-dependent destruction of Mre11-Rad50-Nbs1 subunits in Simian virus 40-infected primate cells.
  J Virol, 82, 5316-5328.  
17596312 A.Fradet-Turcotte, C.Vincent, S.Joubert, P.A.Bullock, and J.Archambault (2007).
Quantitative analysis of the binding of simian virus 40 large T antigen to DNA.
  J Virol, 81, 9162-9174.  
17287270 A.Kumar, G.Meinke, D.K.Reese, S.Moine, P.J.Phelan, A.Fradet-Turcotte, J.Archambault, A.Bohm, and P.A.Bullock (2007).
Model for T-antigen-dependent melting of the simian virus 40 core origin based on studies of the interaction of the beta-hairpin with DNA.
  J Virol, 81, 4808-4818.  
17253903 G.Meinke, P.Phelan, S.Moine, E.Bochkareva, A.Bochkarev, P.A.Bullock, and A.Bohm (2007).
The crystal structure of the SV40 T-antigen origin binding domain in complex with DNA.
  PLoS Biol, 5, e23.
PDB codes: 2if9 2ntc
17301125 W.Wang, D.Manna, and D.T.Simmons (2007).
Role of the hydrophilic channels of simian virus 40 T-antigen helicase in DNA replication.
  J Virol, 81, 4510-4519.  
17005644 D.K.Reese, G.Meinke, A.Kumar, S.Moine, K.Chen, J.L.Sudmeier, W.Bachovchin, A.Bohm, and P.A.Bullock (2006).
Analyses of the interaction between the origin binding domain from simian virus 40 T antigen and single-stranded DNA provide insights into DNA unwinding and initiation of DNA replication.
  J Virol, 80, 12248-12259.  
17139255 E.Bochkareva, D.Martynowski, A.Seitova, and A.Bochkarev (2006).
Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA.
  EMBO J, 25, 5961-5969.
PDB codes: 2ipr 2itj 2itl 2nl8
16611889 G.Meinke, P.A.Bullock, and A.Bohm (2006).
Crystal structure of the simian virus 40 large T-antigen origin-binding domain.
  J Virol, 80, 4304-4312.
PDB code: 2fuf
16537620 R.Johne, W.Wittig, D.Fernández-de-Luco, U.Höfle, and H.Müller (2006).
Characterization of two novel polyomaviruses of birds by using multiply primed rolling-circle amplification of their genomes.
  J Virol, 80, 3523-3531.  
16840329 S.Schuck, and A.Stenlund (2006).
Surface mutagenesis of the bovine papillomavirus E1 DNA binding domain reveals residues required for multiple functions related to DNA replication.
  J Virol, 80, 7491-7499.  
17110927 X.Jiang, V.Klimovich, A.I.Arunkumar, E.B.Hysinger, Y.Wang, R.D.Ott, G.D.Guler, B.Weiner, W.J.Chazin, and E.Fanning (2006).
Structural mechanism of RPA loading on DNA during activation of a simple pre-replication complex.
  EMBO J, 25, 5516-5526.  
15793585 A.I.Arunkumar, V.Klimovich, X.Jiang, R.D.Ott, L.Mizoue, E.Fanning, and W.J.Chazin (2005).
Insights into hRPA32 C-terminal domain--mediated assembly of the simian virus 40 replisome.
  Nat Struct Mol Biol, 12, 332-339.
PDB code: 1z1d
16043636 C.J.Park, J.H.Lee, and B.S.Choi (2005).
Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen.
  Nucleic Acids Res, 33, 4172-4181.
PDB code: 1ynx
16027112 L.M.Iyer, E.V.Koonin, D.D.Leipe, and L.Aravind (2005).
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members.
  Nucleic Acids Res, 33, 3875-3896.  
15767419 T.M.Love, R.de Jesus, J.A.Kean, Q.Sheng, A.Leger, and B.Schaffhausen (2005).
Activation of CREB/ATF sites by polyomavirus large T antigen.
  J Virol, 79, 4180-4190.  
15247252 D.Gai, D.Li, C.V.Finkielstein, R.D.Ott, P.Taneja, E.Fanning, and X.S.Chen (2004).
Insights into the oligomeric states, conformational changes, and helicase activities of SV40 large tumor antigen.
  J Biol Chem, 279, 38952-38959.  
14990710 D.K.Reese, K.R.Sreekumar, and P.A.Bullock (2004).
Interactions required for binding of simian virus 40 T antigen to the viral origin and molecular modeling of initial assembly events.
  J Virol, 78, 2921-2934.  
15289463 E.A.Abbate, J.M.Berger, and M.R.Botchan (2004).
The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2.
  Genes Dev, 18, 1981-1996.
PDB code: 1tue
15247253 K.Weisshart, S.Friedl, P.Taneja, H.P.Nasheuer, B.Schlott, F.Grosse, and E.Fanning (2004).
Partial proteolysis of simian virus 40 T antigen reveals intramolecular contacts between domains and conformation changes upon hexamer assembly.
  J Biol Chem, 279, 38943-38951.  
15564510 V.Srinivasan, T.Komatsu, M.E.Ballestas, and K.M.Kaye (2004).
Definition of sequence requirements for latency-associated nuclear antigen 1 binding to Kaposi's sarcoma-associated herpesvirus DNA.
  J Virol, 78, 14033-14038.  
15298926 W.Li, Y.Zhang, and J.Skolnick (2004).
Application of sparse NMR restraints to large-scale protein structure prediction.
  Biophys J, 87, 1241-1248.  
12574131 A.Stenlund (2003).
E1 initiator DNA binding specificity is unmasked by selective inhibition of non-specific DNA binding.
  EMBO J, 22, 954-963.  
12774115 D.Li, R.Zhao, W.Lilyestrom, D.Gai, R.Zhang, J.A.DeCaprio, E.Fanning, A.Jochimiak, G.Szakonyi, and X.S.Chen (2003).
Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen.
  Nature, 423, 512-518.
PDB code: 1n25
14633980 M.G.Gomez-Lorenzo, M.Valle, J.Frank, C.Gruss, C.O.Sorzano, X.S.Chen, L.E.Donate, and J.M.Carazo (2003).
Large T antigen on the simian virus 40 origin of replication: a 3D snapshot prior to DNA replication.
  EMBO J, 22, 6205-6213.  
12941889 R.Roy, P.Trowbridge, Z.Yang, J.J.Champoux, and D.T.Simmons (2003).
The cap region of topoisomerase I binds to sites near both ends of simian virus 40 T antigen.
  J Virol, 77, 9809-9816.  
12692254 S.Titolo, E.Welchner, P.W.White, and J.Archambault (2003).
Characterization of the DNA-binding properties of the origin-binding domain of simian virus 40 large T antigen by fluorescence anisotropy.
  J Virol, 77, 5512-5518.  
12191478 A.B.Hickman, D.R.Ronning, R.M.Kotin, and F.Dyda (2002).
Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep.
  Mol Cell, 10, 327-337.
PDB code: 1m55
12370317 G.Chen, and A.Stenlund (2002).
Sequential and ordered assembly of E1 initiator complexes on the papillomavirus origin of DNA replication generates progressive structural changes related to melting.
  Mol Cell Biol, 22, 7712-7720.  
12130667 R.Campos-Olivas, J.M.Louis, D.Clerot, B.Gronenborn, and A.M.Gronenborn (2002).
The structure of a replication initiator unites diverse aspects of nucleic acid metabolism.
  Proc Natl Acad Sci U S A, 99, 10310-10315.
PDB codes: 1l2m 1l5i
11413306 J.D.Purviance, A.E.Prack, B.Barbaro, and P.A.Bullock (2001).
In the simian virus 40 in vitro replication system, start site selection by the polymerase alpha-primase complex is not significantly altered by changes in the concentration of ribonucleotides.
  J Virol, 75, 6392-6401.  
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.  
10954562 B.A.Barbaro, K.R.Sreekumar, D.R.Winters, A.E.Prack, and P.A.Bullock (2000).
Phosphorylation of simian virus 40 T antigen on Thr 124 selectively promotes double-hexamer formation on subfragments of the viral core origin.
  J Virol, 74, 8601-8613.  
10799598 D.Gai, R.Roy, C.Wu, and D.T.Simmons (2000).
Topoisomerase I associates specifically with simian virus 40 large-T-antigen double hexamer-origin complexes.
  J Virol, 74, 5224-5232.  
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
10712935 J.L.Keck, and J.M.Berger (2000).
DNA replication at high resolution.
  Chem Biol, 7, R63-R71.  
10954561 K.R.Sreekumar, A.E.Prack, D.R.Winters, B.A.Barbaro, and P.A.Bullock (2000).
The simian virus 40 core origin contains two separate sequence modules that support T-antigen double-hexamer assembly.
  J Virol, 74, 8589-8600.  
10594006 M.Valle, C.Gruss, L.Halmer, J.M.Carazo, and L.E.Donate (2000).
Large T-antigen double hexamers imaged at the simian virus 40 origin of replication.
  Mol Cell Biol, 20, 34-41.  
11118619 P.C.Zuzarte, I.K.Farrance, P.C.Simpson, and A.G.Wildeman (2000).
Tumor cell splice variants of the transcription factor TEF-1 induced by SV40 T-antigen transformation.
  Biochim Biophys Acta, 1517, 82-90.  
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
  10438844 H.Y.Kim, B.A.Barbaro, W.S.Joo, A.E.Prack, K.R.Sreekumar, and P.A.Bullock (1999).
Sequence requirements for the assembly of simian virus 40 T antigen and the T-antigen origin binding domain on the viral core origin of replication.
  J Virol, 73, 7543-7555.  
  9971803 K.Weisshart, P.Taneja, A.Jenne, U.Herbig, D.T.Simmons, and E.Fanning (1999).
Two regions of simian virus 40 T antigen determine cooperativity of double-hexamer assembly on the viral origin of DNA replication and promote hexamer interactions during bidirectional origin DNA unwinding.
  J Virol, 73, 2201-2211.  
  9882311 U.Herbig, K.Weisshart, P.Taneja, and E.Fanning (1999).
Interaction of the transcription factor TFIID with simian virus 40 (SV40) large T antigen interferes with replication of SV40 DNA in vitro.
  J Virol, 73, 1099-1107.  
9519296 A.M.Edwards, A.Bochkarev, and L.Frappier (1998).
Origin DNA-binding proteins.
  Curr Opin Struct Biol, 8, 49-53.  
  9811712 K.Weisshart, P.Taneja, and E.Fanning (1998).
The replication protein A binding site in simian virus 40 (SV40) T antigen and its role in the initial steps of SV40 DNA replication.
  J Virol, 72, 9771-9781.  
  9620396 R.D.Smith, J.H.Galla, K.Skahan, P.Anderson, C.C.Linnemann, G.S.Ault, C.F.Ryschkewitsch, and G.L.Stoner (1998).
Tubulointerstitial nephritis due to a mutant polyomavirus BK virus strain, BKV(Cin), causing end-stage renal disease.
  J Clin Microbiol, 36, 1660-1665.  
  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.  
  9343233 L.Chen, W.S.Joo, P.A.Bullock, and D.T.Simmons (1997).
The N-terminal side of the origin-binding domain of simian virus 40 large T antigen is involved in A/T untwisting.
  J Virol, 71, 8743-8749.  
  9444478 P.A.Bullock (1997).
The initiation of simian virus 40 DNA replication in vitro.
  Crit Rev Biochem Mol Biol, 32, 503-568.  
  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.  
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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