Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 25511.32 
• Atom Count: 1795 
• Residue Count: 226 
• Unique protein chains: 1

2JHQ

Crystal structure of Uracil DNA-glycosylase from Vibrio cholerae

• DOI: 10.2210/pdb2JHQ/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
• Expression System: Escherichia coli BL21


• 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: 1.5 Å
• R-Value Free: 0.210 
• R-Value Work: 0.175 

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 66: 130

• PubMed: 20124707 
• DOI: 10.1107/S1744309109052063


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
URACIL DNA-GLYCOSYLASE	A	226	Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)	Mutation(s): 0  Gene Names: ung EC: 3.2.2.27
Find proteins for Q9KPK8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Go to UniProtKB:  Q9KPK8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.210 
• R-Value Work: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 60.140	α = 90.00
b = 60.440	β = 90.00
c = 61.330	γ = 90.00

Software Package:

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

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
  Type: Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance