1YD5

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant N88A bound to its catalytic divalent cation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UvrABC system protein CA96Thermotoga maritimaMutation(s): 1 
Find proteins for Q9WYA3 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9WYA3 
Go to UniProtKB:  Q9WYA3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.315α = 90
b = 55.315β = 90
c = 108.711γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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: Advisory, Version format compliance