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PDBsum entry 2d3y

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protein ligands links
Hydrolase PDB id
2d3y
Jmol
Contents
Protein chain
219 a.a. *
Ligands
ACT ×2
SF4
_DU
Waters ×210
* Residue conservation analysis
PDB id:
2d3y
Name: Hydrolase
Title: Crystal structure of uracil-DNA glycosylase from thermus the hb8
Structure: Uracil-DNA glycosylase. Chain: a. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: ttudgb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.55Å     R-factor:   0.186     R-free:   0.210
Authors: H.Kosaka,N.Nakagawa,R.Masui,S.Kuramitsu,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
H.Kosaka et al. (2007). Crystal structure of family 5 uracil-DNA glycosylase bound to DNA. J Mol Biol, 373, 839-850. PubMed id: 17870091 DOI: 10.1016/j.jmb.2007.08.022
Date:
04-Oct-05     Release date:   17-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SJ65  (Q5SJ65_THET8) -  Uracil-DNA glycosylase
Seq:
Struc:
219 a.a.
220 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     iron-sulfur cluster binding     3 terms  

 

 
DOI no: 10.1016/j.jmb.2007.08.022 J Mol Biol 373:839-850 (2007)
PubMed id: 17870091  
 
 
Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.
H.Kosaka, J.Hoseki, N.Nakagawa, S.Kuramitsu, R.Masui.
 
  ABSTRACT  
 
Uracil-DNA glycosylase (UDG) removes uracil generated by the deamination of cytosine or misincorporation of deoxyuridine monophosphate. Within the UDG superfamily, a fifth UDG family lacks a polar residue in the active-site motif, which mediates the hydrolysis of the glycosidic bond by activation of a water molecule in UDG families 1-4. We have determined the crystal structure of a novel family 5 UDG from Thermus thermophilus HB8 complexed with DNA containing an abasic site. The active-site structure suggests this enzyme uses both steric force and water activation for its excision reaction. A conserved asparagine residue acts as a ligand to the catalytic water molecule. The structure also implies that another water molecule acts as a barrier during substrate recognition. Based on no significant open-closed conformational change upon binding to DNA, we propose a "slide-in" mechanism for initial damage recognition.
 
  Selected figure(s)  
 
Figure 6.
Fig. 6. Hydrogen-bonding interaction of the putative catalytic water molecule (blue spheres) in the structure of human UNG–DNA complex (a) and TtUDGB–DNA complex (b).
Figure 9.
Fig. 9. The proposed mechanism of substrate recognition. A red circle represents the lesion in DNA. The αI helix is represented as a cylinder.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 373, 839-850) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20981145 R.Morita, S.Nakane, A.Shimada, M.Inoue, H.Iino, T.Wakamatsu, K.Fukui, N.Nakagawa, R.Masui, and S.Kuramitsu (2010).
Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems.
  J Nucleic Acids, 2010, 179594.  
18562313 S.Kiyonari, M.Uchimura, T.Shirai, and Y.Ishino (2008).
Physical and functional interactions between uracil-DNA glycosylase and proliferating cell nuclear antigen from the euryarchaeon Pyrococcus furiosus.
  J Biol Chem, 283, 24185-24193.  
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.