Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.41 kDa 
• Atom Count: 2387 
• Residue Count: 278 
• Unique protein chains: 1

3BZJ

UVDE K229L

• DOI: 10.2210/pdb3BZJ/pdb

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


• Deposited: 2008-01-18 Released: 2008-12-09 
• Deposition Author(s): Meulenbroek, E.M., Paspaleva, K., Thomassen, E.A.J., Abrahams, J.P., Goosen, N., Pannu, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.244 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Involvement of a carboxylated lysine in UV damage endonuclease

Meulenbroek, E.M., Paspaleva, K., Thomassen, E.A., Abrahams, J.P., Goosen, N., Pannu, N.S.

(2009) Protein Sci 18: 549-558

• PubMed: 19241382 
• DOI: 10.1002/pro.54
• Structures With Same Primary Citation


• PubMed Abstract: 
  

UV damage endonuclease is a DNA repair enzyme that can both recognize damage such as UV lesions and introduce a nick directly 5' to them. Recently, the crystal structure of the enzyme from Thermus thermophilus was solved. In the electron density map of this structure, unexplained density near the active site was observed at the tip of Lys229. Based on this finding, it was proposed that Lys229 is post-translationally modified. In this article, we give evidence that this modification is a carboxyl group. By combining activity assays and X-ray crystallography on several point mutants, we show that the carboxyl group assists in metal binding required for catalysis by donating negative charge to the metal-coordinating residue His231. Moreover, functional and structural analysis of the K229R mutant reveals that if His231 shifts away, an increased activity results on both damaged and undamaged DNA. Taken together, the results show that T. thermophilus ultraviolet damage endonuclease is carboxylated and the modified lysine is required for proper catalysis and preventing increased incision of undamaged DNA.

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Organizational Affiliation: 

Biophysical Structural Chemistry, Leiden Institute of Chemistry, RA Leiden, The Netherlands.

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.244 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.39	α = 90
b = 113.39	β = 90
c = 89.39	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
BEST	data collection
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-18 
• Released Date: 2008-12-09 
Deposition Author(s): Meulenbroek, E.M., Paspaleva, K., Thomassen, E.A.J., Abrahams, J.P., Goosen, N., Pannu, N.S.

Revision History 

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance