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PDBsum entry 1f08
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protein metals Protein-protein interface(s) links
Replication PDB id
1f08

 

 

 

 

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Contents
Protein chains
148 a.a. *
Metals
_BR ×14
Waters ×100
* Residue conservation analysis
PDB id:
1f08
Name: Replication
Title: Crystal structure of the DNA-binding domain of the replication initiation protein e1 from papillomavirus
Structure: Replication protein e1. Chain: a, b. Fragment: DNA-binding domain. Engineered: yes
Source: Bovine papillomavirus. Organism_taxid: 10571. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.241     R-free:   0.271
Authors: E.J.Enemark,G.Chen,D.E.Vaughn,A.Stenlund,L.Joshua-Tor
Key ref: E.J.Enemark et al. (2000). Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus. Mol Cell, 6, 149-158. PubMed id: 10949036
Date:
15-May-00     Release date:   16-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03116  (VE1_BPV1) -  Replication protein E1 from Bovine papillomavirus type 1
Seq:
Struc: 		 
Seq:
Struc: 		605 a.a.
148 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate + H+
ATP
 + H2O
 = ADP
 + phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Mol Cell 6:149-158 (2000)
PubMed id: 10949036  
 
 
Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus.
E.J.Enemark, G.Chen, D.E.Vaughn, A.Stenlund, L.Joshua-Tor.
 
  ABSTRACT  
 
Papillomaviral infection causes both benign and malignant lesions and is a necessary cause of cervical carcinoma. Replication of this virus requires the replication initiation proteins E1 and E2, which bind cooperatively at the origin of replication (ori) as an (E1)2-(E2)2-DNA complex. This is a precursor to larger E1 complexes that distort and unwind the ori. We present the crystal structure of the E1 DNA binding domain refined to 1.9 A resolution. Residues critical for DNA binding are located on an extended loop and an alpha helix. We identify the E1 dimerization surface by selective mutations at an E1/E1 interface observed in the crystal and propose a model for the (E1)2-DNA complex. These and other observations suggest how the E1 DNA binding domain orchestrates assembly of the hexameric helicase on the ori.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20147403 X.Liu, S.Schuck, and A.Stenlund (2010).
Structure-based mutational analysis of the bovine papillomavirus E1 helicase domain identifies residues involved in the nonspecific DNA binding activity required for double trimer formation.
  J Virol, 84, 4264-4276.  
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
19759150 H.J.Kwun, A.Guastafierro, M.Shuda, G.Meinke, A.Bohm, P.S.Moore, and Y.Chang (2009).
The minimum replication origin of merkel cell polyomavirus has a unique large T-antigen loading architecture and requires small T-antigen expression for optimal replication.
  J Virol, 83, 12118-12128.  
18267969 C.M.Sanders (2008).
A DNA-binding activity in BPV initiator protein E1 required for melting duplex ori DNA but not processive helicase activity initiated on partially single-stranded DNA.
  Nucleic Acids Res, 36, 1891-1899.  
18201744 G.Rosas-Acosta, and V.G.Wilson (2008).
Identification of a nuclear export signal sequence for bovine papillomavirus E1 protein.
  Virology, 373, 149-162.  
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
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
16855583 E.J.Enemark, and L.Joshua-Tor (2006).
Mechanism of DNA translocation in a replicative hexameric helicase.
  Nature, 442, 270-275.
PDB code: 2gxa
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
  16524476 M.R.Lentz, S.M.Stevens, J.Raynes, and N.Elkhoury (2006).
A phosphorylation map of the bovine papillomavirus E1 helicase.
  Virol J, 3, 13.  
16439535 N.Gammoh, H.S.Grm, P.Massimi, and L.Banks (2006).
Regulation of human papillomavirus type 16 E7 activity through direct protein interaction with the E2 transcriptional activator.
  J Virol, 80, 1787-1797.  
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.  
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.  
15956609 S.Schuck, and A.Stenlund (2005).
Role of papillomavirus E1 initiator dimerization in DNA replication.
  J Virol, 79, 8661-8664.  
16285920 S.Schuck, and A.Stenlund (2005).
Assembly of a double hexameric helicase.
  Mol Cell, 20, 377-389.  
14593106 A.S.Auster, and L.Joshua-Tor (2004).
The DNA-binding domain of human papillomavirus type 18 E1. Crystal structure, dimerization, and DNA binding.
  J Biol Chem, 279, 3733-3742.
PDB code: 1r9w
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
15187189 M.S.Longworth, and L.A.Laimins (2004).
Pathogenesis of human papillomaviruses in differentiating epithelia.
  Microbiol Mol Biol Rev, 68, 362-372.  
15342486 R.A.Sclafani, R.J.Fletcher, and X.S.Chen (2004).
Two heads are better than one: regulation of DNA replication by hexameric helicases.
  Genes Dev, 18, 2039-2045.  
12574131 A.Stenlund (2003).
E1 initiator DNA binding specificity is unmasked by selective inhibition of non-specific DNA binding.
  EMBO J, 22, 954-963.  
14504622 A.Stenlund (2003).
Initiation of DNA replication: lessons from viral initiator proteins.
  Nat Rev Mol Cell Biol, 4, 777-785.  
12975364 J.H.Shin, Y.Jiang, B.Grabowski, J.Hurwitz, and Z.Kelman (2003).
Substrate requirements for duplex DNA translocation by the eukaryal and archaeal minichromosome maintenance helicases.
  J Biol Chem, 278, 49053-49062.  
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.  
12692220 S.Titolo, K.Brault, J.Majewski, P.W.White, and J.Archambault (2003).
Characterization of the minimal DNA binding domain of the human papillomavirus e1 helicase: fluorescence anisotropy studies and characterization of a dimerization-defective mutant protein.
  J Virol, 77, 5178-5191.  
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
11889054 E.J.Enemark, A.Stenlund, and L.Joshua-Tor (2002).
Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex.
  EMBO J, 21, 1487-1496.
PDB codes: 1ksx 1ksy
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
11119599 G.Chen, and A.Stenlund (2001).
The E1 initiator recognizes multiple overlapping sites in the papillomavirus origin of DNA replication.
  J Virol, 75, 292-302.  
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.  
11711585 M.West, D.Flanery, K.Woytek, D.Rangasamy, and V.G.Wilson (2001).
Functional mapping of the DNA binding domain of bovine papillomavirus E1 protein.
  J Virol, 75, 11948-11960.  
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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