1UDI | pdb_00001udi

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 (Depositor) 
  • R-Value Work: 
    0.188 (Depositor) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1038/nsb0995-752
  • Primary Citation 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 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.

    • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, University College, London, UK.

Macromolecule Content 

  • Total Structure Weight: 36.72 kDa 
  • Atom Count: 2,519 
  • Modeled Residue Count: 310 
  • Deposited Residue Count: 327 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
URACIL-DNA GLYCOSYLASEA [auth E]244Human alphaherpesvirus 1 strain 17Mutation(s): 0 
EC: 3.2.2.3 (PDB Primary Data), 3.2.2.27 (UniProt)
UniProt
Find proteins for P10186 (Human herpesvirus 1 (strain 17))
Explore P10186 
Go to UniProtKB:  P10186
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10186
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
URACIL-DNA GLYCOSYLASE INHIBITOR PROTEINB [auth I]83Takahashivirus PBS1Mutation(s): 0 
UniProt
Find proteins for P14739 (Bacillus phage PBS2)
Explore P14739 
Go to UniProtKB:  P14739
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14739
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Other