PDBsum entry 2w9m

Go to PDB code: 
protein metals Protein-protein interface(s) links
DNA replication PDB id
Protein chains
541 a.a. *
_ZN ×7
_HG ×2
Waters ×77
* Residue conservation analysis
PDB id:
Name: DNA replication
Title: Structure of family x DNA polymerase from deinococcus radiodurans
Structure: Polymerase x. Chain: a, b. Engineered: yes
Source: Deinococcus radiodurans. Organism_taxid: 1299. Expressed in: escherichia coli. Expression_system_taxid: 562
2.46Å     R-factor:   0.206     R-free:   0.249
Authors: N.Leulliot,L.Cladiere,F.Lecointe,D.Durand,U.Hubscher, H.Van Tilbeurgh
Key ref:
N.Leulliot et al. (2009). The family X DNA polymerase from Deinococcus radiodurans adopts a non-standard extended conformation. J Biol Chem, 284, 11992-11999. PubMed id: 19251692 DOI: 10.1074/jbc.M809342200
27-Jan-09     Release date:   10-Feb-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9RX48  (Q9RX48_DEIRA) -  Uncharacterized protein
572 a.a.
541 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA biosynthetic process   3 terms 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1074/jbc.M809342200 J Biol Chem 284:11992-11999 (2009)
PubMed id: 19251692  
The family X DNA polymerase from Deinococcus radiodurans adopts a non-standard extended conformation.
N.Leulliot, L.Cladière, F.Lecointe, D.Durand, U.Hübscher, H.van Tilbeurgh.
Deinococcus radiodurans is an extraordinarily radioresistant bacterium that is able to repair hundreds of radiation-induced double-stranded DNA breaks. One of the players in this pathway is an X family DNA polymerase (PolX(Dr)). Deletion of PolX(Dr) has been shown to decrease the rate of repair of double-stranded DNA breaks and increase cell sensitivity to gamma-rays. A 3'-->5' exonuclease activity that stops cutting close to DNA loops has also been demonstrated. The present crystal structure of PolX(Dr) solved at 2.46-A resolution reveals that PolX(Dr) has a novel extended conformation in stark contrast to the closed "right hand" conformation commonly observed for DNA polymerases. This extended conformation is stabilized by the C-terminal PHP domain, whose putative nuclease active site is obstructed by its interaction with the polymerase domain. The overall conformation and the presence of non standard residues in the active site of the polymerase X domain makes PolX(Dr) the founding member of a novel class of polymerases involved in DNA repair but whose detailed mode of action still remains enigmatic.
  Selected figure(s)  
Figure 1.
Structure of PolX[Dr]. A, schematic and surface representation (B) of Polλ in complex with gapped DNA. Domains are colored dark green, light green, light blue, dark blue, for the thumb, palm, fingers, and 8-kDa domains, respectively (PDB code 2BCR). C, schematic and surface representation (D) of PolX[Dr]. The same coloring scheme as in panel A is adopted. The PolX[Dr] PHP domain is colored red, and its linker to the thumb domain is yellow. The orientations of Polλ and PolX[Dr] in views A and B are superposed on the thumb and palm domains. The DNA substrate has been modeled on the structure of PolX[Dr] using the Polλ complex as a template (bottom). Two models were generated: one by superposing with the palm/thumb and the second with the fingers/8-kDa domains. Both are represented on the bottom schematic, clearly showing that the DNA binding sites are on opposite sides of the molecule. E, schematic representation of PolX[Dr] rotated 90° compared with panel B, showing the stretched conformation of the polymerase domain. F, schematic representation of PolX[Dr] palm (green) and fingers (blue) domains with the palm and fingers domain of Polλ superposed on the palm domains. The β4–β5 loop in Polλ is much longer than in PolX[Dr], which results in a sterical clash with the fingers domain in the stretched conformation.
Figure 2.
Comparison of the active sites of PolX[Dr] and Polβ. Stereo representation of PolX[Dr] (A) and Polβ (B) active sites. Polβ is in complex with incoming nucleotide and DNA. The DNA, fingers, and 8-kDa domains have been omitted for clarity. The incoming nucleotide is in sticks. The two magnesium atoms bound to the two catalytic aspartates are shown as yellow spheres.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 11992-11999) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20974932 B.Baños, L.Villar, M.Salas, and Vega (2010).
Intrinsic apurinic/apyrimidinic (AP) endonuclease activity enables Bacillus subtilis DNA polymerase X to recognize, incise, and further repair abasic sites.
  Proc Natl Acad Sci U S A, 107, 19219-19224.  
19542005 N.P.Khairnar, and H.S.Misra (2009).
DNA polymerase X from Deinococcus radiodurans implicated in bacterial tolerance to DNA damage is characterized as a short patch base excision repair polymerase.
  Microbiology, 155, 3005-3014.  
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.