Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 68.94 kDa 
• Atom Count: 4829 
• Modelled Residue Count: 561 
• Deposited Residue Count: 604 
• Unique protein chains: 1

2J6V

Crystal structure of the DNA repair enzyme UV Damage Endonuclease

• PDB DOI: 10.2210/pdb2J6V/pdb

• Classification: LYASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-10-04 Released: 2007-10-16 
• Deposition Author(s): Paspaleva, K., Thomassen, E.A.J., Pannu, N.S., Goossen, N., Abrahams, J.P.

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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 

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

• PubMed: 17937920 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UV ENDONUCLEASE	A, B	301	Thermus thermophilus	Mutation(s): 1
UniProt
Find proteins for Q746K1 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q746K1  Go to UniProtKB:  Q746K1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A, B	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS
KCX	A, B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 47.352	α = 106.14
b = 48.7	β = 94.36
c = 68.763	γ = 114.2

Software Package:

Software Name	Purpose
ARP/wARP	model building
MOSFLM	data reduction
SCALA	data scaling
AFRO	phasing
CRUNCH2	phasing
BP3	phasing
ARP/wARP	phasing
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-04 
• Released Date: 2007-10-16 
Deposition Author(s): Paspaleva, K., Thomassen, E.A.J., Pannu, N.S., Goossen, N., Abrahams, J.P.

Revision History  

• 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