3ZOR

Structure of BsUDG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure and Functional Insights Into Uracil-DNA Glycosylase Inhibition by Phage Phi29 DNA Mimic Protein P56

Banos-Sanz, J.I.Mojardin, L.Sanz-Aparicio, J.Lazaro, J.M.Villar, L.Serrano-Heras, G.Gonzalez, B.Salas, M.

(2013) Nucleic Acids Res. 41: 6761

  • DOI: 10.1093/nar/gkt395
  • Primary Citation of Related Structures:  3ZOQ

  • PubMed Abstract: 
  • Uracil-DNA glycosylase (UDG) is a key repair enzyme responsible for removing uracil residues from DNA. Interestingly, UDG is the only enzyme known to be inhibited by two different DNA mimic proteins: p56 encoded by the Bacillus subtilis phage 29 and ...

    Uracil-DNA glycosylase (UDG) is a key repair enzyme responsible for removing uracil residues from DNA. Interestingly, UDG is the only enzyme known to be inhibited by two different DNA mimic proteins: p56 encoded by the Bacillus subtilis phage 29 and the well-characterized protein Ugi encoded by the B. subtilis phage PBS1/PBS2. Atomic-resolution crystal structures of the B. subtilis UDG both free and in complex with p56, combined with site-directed mutagenesis analysis, allowed us to identify the key amino acid residues required for enzyme activity, DNA binding and complex formation. An important requirement for complex formation is the recognition carried out by p56 of the protruding Phe191 residue from B. subtilis UDG, whose side-chain is inserted into the DNA minor groove to replace the flipped-out uracil. A comparative analysis of both p56 and Ugi inhibitors enabled us to identify their common and distinctive features. Thereby, our results provide an insight into how two DNA mimic proteins with different structural and biochemical properties are able to specifically block the DNA-binding domain of the same enzyme.


    Organizational Affiliation

    Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física 'Rocasolano' (CSIC), Serrano 119, 28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
URACIL-DNA GLYCOSYLASE
A
225Bacillus subtilis (strain 168)Gene Names: ung (ywdG)
EC: 3.2.2.27
Find proteins for P39615 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39615
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.238 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 65.305α = 90.00
b = 79.795β = 90.00
c = 97.362γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-05-29
    Type: Database references
  • Version 1.2: 2013-07-31
    Type: Database references