Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima bound to its catalytic divalent cation: manganese

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

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Structural insights into the first incision reaction during nucleotide excision repair

Truglio, J.J.Rhau, B.Croteau, D.L.Wang, L.Skorvaga, M.Karakas, E.Dellavecchia, M.J.Wang, H.Van Houten, B.Kisker, C.

(2005) EMBO J 24: 885-894

  • DOI: https://doi.org/10.1038/sj.emboj.7600568
  • Primary Citation of Related Structures:  
    1YCZ, 1YD0, 1YD1, 1YD2, 1YD3, 1YD4, 1YD5, 1YD6

  • PubMed Abstract: 

    Nucleotide excision repair is a highly conserved DNA repair mechanism present in all kingdoms of life. The incision reaction is a critical step for damage removal and is accomplished by the UvrC protein in eubacteria. No structural information is so far available for the 3' incision reaction. Here we report the crystal structure of the N-terminal catalytic domain of UvrC at 1.5 A resolution, which catalyzes the 3' incision reaction and shares homology with the catalytic domain of the GIY-YIG family of intron-encoded homing endonucleases. The structure reveals a patch of highly conserved residues surrounding a catalytic magnesium-water cluster, suggesting that the metal binding site is an essential feature of UvrC and all GIY-YIG endonuclease domains. Structural and biochemical data strongly suggest that the N-terminal endonuclease domain of UvrC utilizes a novel one-metal mechanism to cleave the phosphodiester bond.

  • Organizational Affiliation

    Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UvrABC system protein C96Thermotoga maritimaMutation(s): 0 
Find proteins for Q9WYA3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WYA3 
Go to UniProtKB:  Q9WYA3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYA3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.009α = 90
b = 55.009β = 90
c = 109.025γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations