Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 

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Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.

Kosaka, H.Hoseki, J.Nakagawa, N.Kuramitsu, S.Masui, R.

(2007) J Mol Biol 373: 839-850

  • DOI: https://doi.org/10.1016/j.jmb.2007.08.022
  • Primary Citation of Related Structures:  
    2D3Y, 2DDG, 2DEM

  • PubMed 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.

  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
uracil-DNA glycosylase219Thermus thermophilus HB8Mutation(s): 0 
Gene Names: ttUDGB
EC: 3.2.2
Find proteins for Q5SJ65 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJ65 
Go to UniProtKB:  Q5SJ65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJ65
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.18α = 90
b = 62.35β = 90
c = 63.04γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations