2J6V

Crystal structure of the DNA repair enzyme UV Damage Endonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the DNA Repair Enzyme Ultraviolet Damage Endonuclease.

Paspaleva, K.Thomassen, E.A.J.Pannu, N.S.Iwai, S.Moolenaar, G.F.Goosen, N.Abrahams, J.P.

(2007) Structure 15: 1316

  • DOI: 10.1016/j.str.2007.05.010
  • Primary Citation of Related Structures:  
    2J6V

  • PubMed Abstract: 
  • The ultraviolet damage endonuclease (UVDE) performs the initial step in an alternative excision repair pathway of UV-induced DNA damage, nicking immediately adjacent to the 5' phosphate of the damaged nucleotides. Unique for a single-protein DNA repair endonuclease, it can detect different types of damage ...

    The ultraviolet damage endonuclease (UVDE) performs the initial step in an alternative excision repair pathway of UV-induced DNA damage, nicking immediately adjacent to the 5' phosphate of the damaged nucleotides. Unique for a single-protein DNA repair endonuclease, it can detect different types of damage. Here we show that Thermus thermophilus UVDE shares some essential structural features with Endo IV, an enzyme from the base excision repair pathway that exclusively nicks at abasic sites. A comparison between the structures indicates how DNA is bound by UVDE, how UVDE may recognize damage, and which of its residues are involved in catalysis. Furthermore, the comparison suggests an elegant explanation of UVDE's potential to recognize different types of damage. Incision assays including point mutants of UVDE confirmed the relevance of these conclusions.


    Organizational Affiliation

    Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UV ENDONUCLEASE AB301Thermus thermophilusMutation(s): 1 
Find proteins for Q746K1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q746K1 
Go to UniProtKB:  Q746K1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
A,BL-PEPTIDE LINKINGC8 H16 N2 O3LYS
KCX
Query on KCX
A,BL-PEPTIDE LINKINGC7 H14 N2 O4LYS
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.352α = 106.14
b = 48.7β = 94.36
c = 68.763γ = 114.2
Software Package:
Software NamePurpose
ARP/wARPmodel building
MOSFLMdata reduction
SCALAdata scaling
AFROphasing
CRUNCH2phasing
BP3phasing
ARP/wARPphasing
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Refinement description