1UDI

NUCLEOTIDE MIMICRY IN THE CRYSTAL STRUCTURE OF THE URACIL-DNA GLYCOSYLASE-URACIL GLYCOSYLASE INHIBITOR PROTEIN COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex.

Savva, R.Pearl, L.H.

(1995) Nat Struct Biol 2: 752-757

  • DOI: 10.1038/nsb0995-752
  • Primary Citation of Related Structures:  
    1UDI

  • PubMed Abstract: 
  • The Bacillus subtilis bacteriophages PBS-1 and PBS-2 protect their uracil-containing DNA by expressing an inhibitor protein (UGI) which inactivates the host uracil-DNA glycosylase (UDGase) base-excision repair enzyme. Also, PBS1/2 UGI efficiently ina ...

    The Bacillus subtilis bacteriophages PBS-1 and PBS-2 protect their uracil-containing DNA by expressing an inhibitor protein (UGI) which inactivates the host uracil-DNA glycosylase (UDGase) base-excision repair enzyme. Also, PBS1/2 UGI efficiently inactivates UDGases from other biological sources, including the enzyme from herpes simplex virus type-1 (HSV-1). The crystal structure of the HSV-1 UDGase-PBS1 UGI complex at 2.7 angstrum reveals an alpha-beta-alpha sandwich structure for UGI which interacts with conserved regions of UDGase involved in DNA binding, and directly mimics protein-DNA interactions observed in the UDGase-oligonucleotide complex. The inhibitor completely blocks access to the active site of UDGase, but makes no direct contact with the uracil-binding pocket itself.


    Related Citations: 
    • Cloning and Expression of the Uracil-DNA Glycosylase Inhibitor from Bacteriophage Pbs1, and Crystallisation of a Uracil-DNA Glycosylase Uracil-DNA Glycosylase Inhibitor Complex
      Savva, R., Pearl, L.H.
      (1995) Proteins 22: 287
    • The Structural Basis of Specific Base Excision Repair by Uracil-DNA Glycosylase
      Savva, R., Mcauley-Hecht, K., Brown, T., Pearl, L.H.
      (1995) Nature 373: 487
    • Crystallization and Preliminary X-Ray Analysis of the Uracil-DNA Glycosylase DNA Repair Enzyme from Herpes Simplex Virus Type 1
      Savva, R., Pearl, L.H.
      (1993) J Mol Biol 234: 910

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University College, London, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
URACIL-DNA GLYCOSYLASEE244Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: UL2
EC: 3.2.2.3 (PDB Primary Data), 3.2.2.27 (UniProt)
Find proteins for P10186 (Human herpesvirus 1 (strain 17))
Explore P10186 
Go to UniProtKB:  P10186
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
URACIL-DNA GLYCOSYLASE INHIBITOR PROTEINI83Bacillus virus PBS1Mutation(s): 0 
Find proteins for P14739 (Bacillus phage PBS2)
Explore P14739 
Go to UniProtKB:  P14739
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.12α = 90
b = 144.12β = 90
c = 40.95γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1995-10-30 
  • Released Date: 1996-03-08 
  • Deposition Author(s): Pearl, L.H., Savva, R.

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance