PDBsum entry 2d3y

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Hydrolase PDB id
Protein chain
219 a.a. *
ACT ×2
Waters ×210
* Residue conservation analysis
PDB id:
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.
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
04-Oct-05     Release date:   17-Oct-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q5SJ65  (Q5SJ65_THET8) -  Uracil-DNA glycosylase
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.
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.  
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