1YD0

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

• PDB DOI:  https://doi.org/10.2210/pdb1YD0/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-23 Released: 2005-03-01 
• Deposition Author(s): Truglio, J.J., Rhau, B., Croteau, D.L., Wang, L., Skorvaga, M., Karakas, E., DellaVecchia, M.J., Wang, H., Van Houten, B., Kisker, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.185 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

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

• PubMed: 15692561 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.69 kDa 
• Atom Count: 880 
• Modelled Residue Count: 89 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UvrABC system protein C	A	96	Thermotoga maritima	Mutation(s): 0
UniProt
Find proteins for Q9WYA3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYA3  Go to UniProtKB:  Q9WYA3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	B [auth A], C [auth A], D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 55.009	α = 90
b = 55.009	β = 90
c = 109.025	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Truglio, J.J., Rhau, B., Croteau, D.L., Wang, L., Skorvaga, M., Karakas, E., DellaVecchia, M.J., Wang, H., Van Houten, B., Kisker, C.

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: Non-polymer description, Version format compliance