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PDBsum entry 2zja

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protein ligands links
Hydrolase PDB id
2zja
Jmol
Contents
Protein chain
700 a.a. *
Ligands
ACP
Waters ×65
* Residue conservation analysis
PDB id:
2zja
Name: Hydrolase
Title: Archaeal DNA helicase hjm complexed with amppcp in form 2
Structure: Putative ski2-type helicase. Chain: a. Synonym: DNA helicase. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.70Å     R-factor:   0.231     R-free:   0.294
Authors: T.Oyama,H.Oka,R.Fujikane,Y.Ishino,K.Morikawa
Key ref: T.Oyama et al. (2009). Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm. BMC Struct Biol, 9, 2-2. PubMed id: 19159486
Date:
29-Feb-08     Release date:   10-Feb-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O73946  (HELS_PYRFU) -  ATP-dependent DNA helicase Hel308
Seq:
Struc:
 
Seq:
Struc:
720 a.a.
700 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     response to DNA damage stimulus   2 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    reference    
 
 
BMC Struct Biol 9:2-2 (2009)
PubMed id: 19159486  
 
 
Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm.
T.Oyama, H.Oka, K.Mayanagi, T.Shirai, K.Matoba, R.Fujikane, Y.Ishino, K.Morikawa.
 
  ABSTRACT  
 
BACKGROUND: Pyrococcus furiosus Hjm (PfuHjm) is a structure-specific DNA helicase that was originally identified by in vitro screening for Holliday junction migration activity. It belongs to helicase superfamily 2, and shares homology with the human DNA polymerase Theta (PolTheta), HEL308, and Drosophila Mus308 proteins, which are involved in DNA repair. Previous biochemical and genetic analyses revealed that PfuHjm preferentially binds to fork-related Y-structured DNAs and unwinds their double-stranded regions, suggesting that this helicase is a functional counterpart of the bacterial RecQ helicase, which is essential for genome maintenance. Elucidation of the DNA unwinding and translocation mechanisms by PfuHjm will require its three-dimensional structure at atomic resolution. RESULTS: We determined the crystal structures of PfuHjm, in two apo-states and two nucleotide bound forms, at resolutions of 2.0-2.7 A. The overall structures and the local conformations around the nucleotide binding sites are almost the same, including the side-chain conformations, irrespective of the nucleotide-binding states. The architecture of Hjm was similar to that of Archaeoglobus fulgidus Hel308 complexed with DNA. An Hjm-DNA complex model, constructed by fitting the five domains of Hjm onto the corresponding Hel308 domains, indicated that the interaction of Hjm with DNA is similar to that of Hel308. Notably, sulphate ions bound to Hjm lie on the putative DNA binding surfaces. Electron microscopic analysis of an Hjm-DNA complex revealed substantial flexibility of the double stranded region of DNA, presumably due to particularly weak protein-DNA interactions. Our present structures allowed reasonable homology model building of the helicase region of human PolTheta, indicating the strong conformational conservation between archaea and eukarya. CONCLUSION: The detailed comparison between our DNA-free PfuHjm structure and the structure of Hel308 complexed with DNA suggests similar DNA unwinding and translocation mechanisms, which could be generalized to all of the members in the same family. Structural comparison also implied a minor rearrangement of the five domains during DNA unwinding reaction. The unexpected small contact between the DNA duplex region and the enzyme appears to be advantageous for processive helicase activity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20512115 H.Walbott, S.Mouffok, R.Capeyrou, S.Lebaron, O.Humbert, H.van Tilbeurgh, Y.Henry, and N.Leulliot (2010).
Prp43p contains a processive helicase structural architecture with a specific regulatory domain.
  EMBO J, 29, 2194-2204.
PDB code: 2xau
20512111 R.N.Jackson, A.A.Klauer, B.J.Hintze, H.Robinson, A.van Hoof, and S.J.Johnson (2010).
The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing.
  EMBO J, 29, 2205-2216.
PDB code: 3l9o
20168331 Y.He, G.R.Andersen, and K.H.Nielsen (2010).
Structural basis for the function of DEAH helicases.
  EMBO Rep, 11, 180-186.
PDB code: 3kx2
19525970 L.Zhang, T.Xu, C.Maeder, L.O.Bud, J.Shanks, J.Nix, C.Guthrie, J.A.Pleiss, and R.Zhao (2009).
Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2.
  Nat Struct Mol Biol, 16, 731-739.
PDB code: 3hib
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.