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 PISA (software)

Macromolecule Content

• Total Structure Weight: 25.51 kDa 
• Atom Count: 2122 
• Modelled Residue Count: 223 
• Deposited Residue Count: 226 
• Unique protein chains: 1

2JHQ

Crystal structure of Uracil DNA-glycosylase from Vibrio cholerae

• PDB DOI: 10.2210/pdb2JHQ/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-02-23 Released: 2008-06-03 
• Deposition Author(s): Raeder, I.L.U., Moe, E., Willassen, N.P., Smalas, A.O., Leiros, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.210 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Structure of Uracil-DNA N-Glycosylase (Ung) from Vibrio Cholerae. Mapping Temperature Adaptation Through Structural and Mutational Analysis.

Raeder, I.L.U., Moe, E., Willassen, N.P., Smalas, A.O., Leiros, I.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 130

• PubMed: 20124707 
• DOI: 10.1107/S1744309109052063
• Primary Citation of Related Structures:  
  2JHQ


• PubMed Abstract: 
  

The crystal structure of Vibrio cholerae uracil-DNA N-glycosylase (vcUNG) has been determined to 1.5 A resolution. Based on this structure, a homology model of Aliivibrio salmonicida uracil-DNA N-glycosylase (asUNG) was built. A previous study demonstrated that asUNG possesses typical cold-adapted features compared with vcUNG, such as a higher catalytic efficiency owing to increased substrate affinity. Specific amino-acid substitutions in asUNG were suggested to be responsible for the increased substrate affinity and the elevated catalytic efficiency by increasing the positive surface charge in the DNA-binding region. The temperature adaptation of these enzymes has been investigated using structural and mutational analyses, in which mutations of vcUNG demonstrated an increased substrate affinity that more resembled that of asUNG. Visualization of surface potentials revealed a more positive potential for asUNG compared with vcUNG; a modelled double mutant of vcUNG had a potential around the substrate-binding region that was more like that of asUNG, thus rationalizing the results obtained from the kinetic studies.

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Organizational Affiliation: 

Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URACIL DNA-GLYCOSYLASE	A	226	Vibrio cholerae	Mutation(s): 0  EC: 3.2.2.3 (PDB Primary Data), 3.2.2.27 (UniProt)
UniProt
Find proteins for Q9KPK8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KPK8  Go to UniProtKB:  Q9KPK8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.210 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.14	α = 90
b = 60.44	β = 90
c = 61.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-23 
• Released Date: 2008-06-03 
Deposition Author(s): Raeder, I.L.U., Moe, E., Willassen, N.P., Smalas, A.O., Leiros, I.

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance