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PDBsum entry 3aaf

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protein dna_rna ligands links
DNA binding protein/DNA PDB id
3aaf
Jmol
Contents
Protein chain
109 a.a. *
DNA/RNA
Ligands
ACT ×2
Waters ×338
* Residue conservation analysis
PDB id:
3aaf
Name: DNA binding protein/DNA
Title: Structure of wrn rqc domain bound to double-stranded DNA
Structure: Werner syndrome atp-dependent helicase. Chain: a, b. Fragment: recq c-terminal (rqc) domain. Synonym: werner syndrome protein, wrn. Engineered: yes. DNA (5'-d( Ap Cp Cp Cp Tp Ap Ap Tp Tp Ap Gp Gp Gp chain: c, d. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
Resolution:
1.90Å     R-factor:   0.213     R-free:   0.244
Authors: K.Kitano,T.Hakoshima
Key ref: K.Kitano et al. (2010). Structural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN. Structure, 18, 177-187. PubMed id: 20159463
Date:
16-Nov-09     Release date:   16-Feb-10    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q14191  (WRN_HUMAN) -  Werner syndrome ATP-dependent helicase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1432 a.a.
109 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
+ H(2)O
= ADP
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   2 terms 
  Biochemical function     ATP-dependent 3'-5' DNA helicase activity     1 term  

 

 
    reference    
 
 
Structure 18:177-187 (2010)
PubMed id: 20159463  
 
 
Structural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN.
K.Kitano, S.Y.Kim, T.Hakoshima.
 
  ABSTRACT  
 
The RecQ family of DNA helicases including WRN (Werner syndrome protein) and BLM (Bloom syndrome protein) protects the genome against deleterious changes. Here we report the cocrystal structure of the RecQ C-terminal (RQC) domain of human WRN bound to a DNA duplex. In the complex, the RQC domain specifically interacted with a blunt end of the duplex and, surprisingly, unpaired a Watson-Crick base pair in the absence of an ATPase domain. The beta wing, an extended hairpin motif that is characteristic of winged-helix motifs, was used as a "separating knife" to wedge between the first and second base pairs, whereas the recognition helix, a principal component of helix-turn-helix motifs that are usually embedded within DNA grooves, was unprecedentedly excluded from the interaction. Our results demonstrate a function of the winged-helix motif central to the helicase reaction, establishing the first structural paradigm concerning the DNA structure-specific activities of the RecQ helicases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265761 I.L.Woodman, and E.L.Bolt (2011).
Winged helix domains with unknown function in Hel308 and related helicases.
  Biochem Soc Trans, 39, 140-144.  
20967027 C.Fernández-Tornero, B.Böttcher, U.J.Rashid, U.Steuerwald, B.Flörchinger, D.P.Devos, D.Lindner, and C.W.Müller (2010).
Conformational flexibility of RNA polymerase III during transcriptional elongation.
  EMBO J, 29, 3762-3772.  
20443122 K.Friedrich, L.Lee, D.F.Leistritz, G.Nürnberg, B.Saha, F.M.Hisama, D.K.Eyman, D.Lessel, P.Nürnberg, C.Li, M.J.Garcia-F-Villalta, C.M.Kets, J.Schmidtke, V.T.Cruz, P.C.Van den Akker, J.Boak, D.Peter, G.Compoginis, K.Cefle, S.Ozturk, N.López, T.Wessel, M.Poot, P.F.Ippel, B.Groff-Kellermann, H.Hoehn, G.M.Martin, C.Kubisch, and J.Oshima (2010).
WRN mutations in Werner syndrome patients: genomic rearrangements, unusual intronic mutations and ethnic-specific alterations.
  Hum Genet, 128, 103-111.  
20639533 Y.M.Kim, and B.S.Choi (2010).
Structure and function of the regulatory HRDC domain from human Bloom syndrome protein.
  Nucleic Acids Res, 38, 7764-7777.
PDB code: 2kv2
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.