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PDBsum entry 1s9h
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protein Protein-protein interface(s) links
Replication PDB id
1s9h

 

 

 

 

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Contents
Protein chains
268 a.a. *
199 a.a. *
Waters ×357
* Residue conservation analysis
PDB id:
1s9h
Name: Replication
Title: Crystal structure of adeno-associated virus type 2 rep40
Structure: Rep 40 protein. Chain: a, b, c. Synonym: DNA replication protein, non-capsid protein. Engineered: yes
Source: Adeno-associated virus - 2. Organism_taxid: 10804. Gene: rep. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.227     R-free:   0.293
Authors: J.A.James,C.R.Escalante,M.Yoon-Robarts,T.A.Edwards,R.M.Linden, A.K.Aggarwal
Key ref:
J.A.James et al. (2003). Crystal structure of the SF3 helicase from adeno-associated virus type 2. Structure, 11, 1025-1035. PubMed id: 12906833 DOI: 10.1016/S0969-2126(03)00152-7
Date:
04-Feb-04     Release date:   25-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03132  (REP68_AAV2S) -  Protein Rep68 from Adeno-associated virus 2 (isolate Srivastava/1982)
Seq:
Struc: 		 
Seq:
Struc: 		536 a.a.
268 a.a.*
Protein chain
Pfam   ArchSchema ?
P03132  (REP68_AAV2S) -  Protein Rep68 from Adeno-associated virus 2 (isolate Srivastava/1982)
Seq:
Struc: 		 
Seq:
Struc: 		536 a.a.
199 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: 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    
 
 
DOI no: 10.1016/S0969-2126(03)00152-7 Structure 11:1025-1035 (2003)
PubMed id: 12906833  
 
 
Crystal structure of the SF3 helicase from adeno-associated virus type 2.
J.A.James, C.R.Escalante, M.Yoon-Robarts, T.A.Edwards, R.M.Linden, A.K.Aggarwal.
 
  ABSTRACT  
 
We report here the crystal structure of an SF3 DNA helicase, Rep40, from adeno-associated virus 2 (AAV2). We show that AAV2 Rep40 is structurally more similar to the AAA(+) class of cellular proteins than to DNA helicases from other superfamilies. The structure delineates the expected Walker A and B motifs, but also reveals an unexpected "arginine finger" that directly implies the requirement of Rep40 oligomerization for ATP hydrolysis and helicase activity. Further, the Rep40 AAA(+) domain is novel in that it is unimodular as opposed to bimodular. Altogether, the structural connection to AAA(+) proteins defines the general architecture of SF3 DNA helicases, a family that includes simian virus 40 (SV40) T antigen, as well as provides a conceptual framework for understanding the role of Rep proteins during AAV DNA replication, packaging, and site-specific integration.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structure and Topology of AAV2 Rep40(A) Ribbon representation of the AAV2 Rep40 structure. The N-terminal a-helical domain is shown in blue. The C-terminal a/b (vAAA^+) domain is colored gold. The a helices (a1-a11) are labeled sequentially from the N to the C terminus. b strands are labeled according to their belonging to the central b core (b1-b5) or to the b hairpins (ba-bd).(B) Topology diagrams of representative members of helicase and AAA^+ superfamilies. Gold, NTPase cores; green, extra functional domains; blue, Rep40 N-terminal domain. NSF-D2, D2 domain of N-ethylmaleimide-sensitive fusion protein; PcrA, DNA helicase from B. stereothermophilus; HCV, hepatitis C virus nonstructural protein 3 protease-helicase; T7gp4, bacteriophage T7 gene 4 primase-helicase.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1025-1035) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20219935 E.A.Niskanen, T.O.Ihalainen, O.Kalliolinna, M.M.Häkkinen, and M.Vihinen-Ranta (2010).
Effect of ATP binding and hydrolysis on dynamics of canine parvovirus NS1.
  J Virol, 84, 5391-5403.  
  21212830 E.Henckaerts, and R.M.Linden (2010).
Adeno-associated virus: a key to the human genome?
  Future Virol, 5, 555-574.  
19889770 K.D.Farris, and D.J.Pintel (2010).
Adeno-associated virus type 5 utilizes alternative translation initiation to encode a small Rep40-like protein.
  J Virol, 84, 1193-1197.  
20944244 N.Papageorgiou, B.Coutard, V.Lantez, E.Gautron, O.Chauvet, C.Baronti, H.Norder, X.de Lamballerie, V.Heresanu, N.Ferté, S.Veesler, A.E.Gorbalenya, and B.Canard (2010).
The 2C putative helicase of echovirus 30 adopts a hexameric ring-shaped structure.
  Acta Crystallogr D Biol Crystallogr, 66, 1116-1120.  
19939914 X.Liu, and A.Stenlund (2010).
Mutations in Sensor 1 and Walker B in the bovine papillomavirus E1 initiator protein mimic the nucleotide-bound state.
  J Virol, 84, 1912-1919.  
19593381 J.Mansilla-Soto, M.Yoon-Robarts, W.J.Rice, S.Arya, C.R.Escalante, and R.M.Linden (2009).
DNA structure modulates the oligomerization properties of the AAV initiator protein Rep68.
  PLoS Pathog, 5, e1000513.  
19759129 N.Dutheil, E.Henckaerts, E.Kohlbrenner, and R.M.Linden (2009).
Transcriptional analysis of the adeno-associated virus integration site.
  J Virol, 83, 12512-12525.  
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.  
17881379 C.M.Sanders, O.V.Kovalevskiy, D.Sizov, A.A.Lebedev, M.N.Isupov, and A.A.Antson (2007).
Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors.
  Nucleic Acids Res, 35, 6451-6457.
PDB code: 2v9p
17766252 H.Ren, S.X.Dou, P.Rigolet, Y.Yang, P.Y.Wang, M.Amor-Gueret, and X.G.Xi (2007).
The arginine finger of the Bloom syndrome protein: its structural organization and its role in energy coupling.
  Nucleic Acids Res, 35, 6029-6041.  
17093187 K.A.Boyle, L.Arps, and P.Traktman (2007).
Biochemical and genetic analysis of the vaccinia virus d5 protein: Multimerization-dependent ATPase activity is required to support viral DNA replication.
  J Virol, 81, 844-859.  
17151120 N.Yamamoto, M.Suzuki, M.A.Kawano, T.Inoue, R.U.Takahashi, H.Tsukamoto, T.Enomoto, Y.Yamaguchi, T.Wada, and H.Handa (2007).
Adeno-associated virus site-specific integration is regulated by TRP-185.
  J Virol, 81, 1990-2001.  
16594962 C.Weigel, and H.Seitz (2006).
Bacteriophage replication modules.
  FEMS Microbiol Rev, 30, 321-381.  
16943286 D.Clérot, and F.Bernardi (2006).
DNA helicase activity is associated with the replication initiator protein rep of tomato yellow leaf curl geminivirus.
  J Virol, 80, 11322-11330.  
16689629 J.P.Erzberger, and J.M.Berger (2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
  Annu Rev Biophys Biomol Struct, 35, 93.  
17142233 N.R.Choudhury, P.S.Malik, D.K.Singh, M.N.Islam, K.Kaliappan, and S.K.Mukherjee (2006).
The oligomeric Rep protein of Mungbean yellow mosaic India virus (MYMIV) is a likely replicative helicase.
  Nucleic Acids Res, 34, 6362-6377.  
16160148 D.L.Glauser, O.Saydam, N.A.Balsiger, I.Heid, R.M.Linden, M.Ackermann, and C.Fraefel (2005).
Four-dimensional visualization of the simultaneous activity of alternative adeno-associated virus replication origins.
  J Virol, 79, 12218-12230.  
15681453 S.Bleker, F.Sonntag, and J.A.Kleinschmidt (2005).
Mutational analysis of narrow pores at the fivefold symmetry axes of adeno-associated virus type 2 capsids reveals a dual role in genome packaging and activation of phospholipase A2 activity.
  J Virol, 79, 2528-2540.  
14967147 A.B.Hickman, D.R.Ronning, Z.N.Perez, R.M.Kotin, and F.Dyda (2004).
The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces.
  Mol Cell, 13, 403-414.
PDB codes: 1rz9 1uut
15371437 M.Yoon-Robarts, A.G.Blouin, S.Bleker, J.A.Kleinschmidt, A.K.Aggarwal, C.R.Escalante, and R.M.Linden (2004).
Residues within the B' motif are critical for DNA binding by the superfamily 3 helicase Rep40 of adeno-associated virus type 2.
  J Biol Chem, 279, 50472-50481.  
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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