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PDBsum entry 2nl8

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protein dna_rna links
DNA binding protein/DNA PDB id
2nl8
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Contents
Protein chain
117 a.a. *
DNA/RNA
Waters ×82
* Residue conservation analysis
PDB id:
2nl8
Name: DNA binding protein/DNA
Title: The origin binding domain of the sv40 large t antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)
Structure: 18-nt pen element of the sv40 DNA origin. Chain: w. Engineered: yes. Other_details: p2 pentamer replaced with atcat. Large t antigen. Chain: a. Fragment: origin binding domain (residues 131-259). Engineered: yes. Mutation: yes
Source: Synthetic: yes. Simian virus 40. Organism_taxid: 10633. Strain: 776. Gene: large t antigen. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.30Å     R-factor:   0.240     R-free:   0.299
Authors: D.Martynowski,E.Bochkareva,A.Bochkarev
Key ref:
E.Bochkareva et al. (2006). Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA. EMBO J, 25, 5961-5969. PubMed id: 17139255 DOI: 10.1038/sj.emboj.7601452
Date:
19-Oct-06     Release date:   12-Dec-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q98ZP7  (Q98ZP7_SV40) -  Truncated large tumor antigen
Seq:
Struc:
 
Seq:
Struc:
537 a.a.
117 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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

 

 
DOI no: 10.1038/sj.emboj.7601452 EMBO J 25:5961-5969 (2006)
PubMed id: 17139255  
 
 
Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA.
E.Bochkareva, D.Martynowski, A.Seitova, A.Bochkarev.
 
  ABSTRACT  
 
The large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori) in simian virus 40 (SV40). Here, we determined the crystal structures of the T-ag origin-binding domain (OBD) in apo form, and bound to either a 17 bp palindrome (sites 1 and 3) or a 23 bp ori DNA palindrome comprising all four GAGGC binding sites for OBD. The T-ag OBDs were shown to interact with the DNA through a loop comprising Ser147-Thr155 (A1 loop), a combination of a DNA-binding helix and loop (His203-Asn210), and Asn227. The A1 loop traveled back-and-forth along the major groove and accounted for most of the sequence-determining contacts with the DNA. Unexpectedly, in both T-ag-DNA structures, the T-ag OBDs bound DNA independently and did not make direct protein-protein contacts. The T-ag OBD was also captured bound to a non-consensus site ATGGC even in the presence of its canonical site GAGGC. Our observations taken together with the known biochemical and structural features of the T-ag-origin interaction suggest a model for origin unwinding.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Structural details of T-ag interaction with DNA bases in the PEN-2 and PEN-4 structures. (A) Sequence-specific interaction of Arg 154 with G1 (the first G in the GAGGC pentamer) in the PEN-4 structure. A representative electron density map (shown in blue) is superimposed on the model. (B) Nonspecific interaction of Arg 154 with A1 (A in position of G1) in the PEN-2 structure. A representative electron density is superimposed on Arg 154. (C) Sequence-specific interaction of Ser 152 with A2. (D) Nonspecific interaction of Ser 152 with the T2 in the PEN-2 structure. Sequence-specific interactions, which involve (E) the G3 and Asn 153, (F) the G4 and Asn 153, and (G) the G (complementary to C5) with Arg 204. The protein and DNA are shown as stick models and colored by atom type; yellow for carbon, blue for nitrogen, red for oxygen, and purple for phosphorus. A representative electron density as captured from 2F[o]-F[c] map is shown with contours drawn at the 1.25 level. Hydrogen bonds are indicated with red dashed lines, and the length of the bonds is indicated in Å.
Figure 5.
Figure 5 Molecular model of an initial step in the SV40 DNA replication. The PEN-4 structure is shown in black, two hexameric helicase domains are in blue (PDB Id: 1N25), modeled DNA is shown as a stick model and colored per atom type (carbon in yellow, oxygen in red, nitrogen in blue, and phosphorus in purple). Position of the initially melted 8 nt fragment of EP with respect to the PEN box is highlighted with a yellow rectangle. Relative positions of the C-terminus in the OBD (aa 253) and N-terminus in the helicase domain (aa 266) are indicated. See text for more detail.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 5961-5969) copyright 2006.  
  Figures were selected by the author.  

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
19440202 D.R.Boer, J.A.Ruíz-Masó, J.R.López-Blanco, A.G.Blanco, M.Vives-Llàcer, P.Chacón, I.Usón, F.X.Gomis-Rüth, M.Espinosa, O.Llorca, G.del Solar, and M.Coll (2009).
Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains.
  EMBO J, 28, 1666-1678.
PDB codes: 3dkx 3dky
19101707 E.Fanning, and K.Zhao (2009).
SV40 DNA replication: from the A gene to a nanomachine.
  Virology, 384, 352-359.  
19946136 M.L.Bochman, and A.Schwacha (2009).
The Mcm complex: unwinding the mechanism of a replicative helicase.
  Microbiol Mol Biol Rev, 73, 652-683.  
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.  
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.  
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.  
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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