1UDI

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

• PDB DOI:  https://doi.org/10.2210/pdb1UDI/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Human alphaherpesvirus 1 strain 17, Takahashivirus PBS1
• Mutation(s): No 


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

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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 

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

• PubMed: 7552746 
• DOI: https://doi.org/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 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URACIL-DNA GLYCOSYLASE	A [auth E]	244	Human alphaherpesvirus 1 strain 17	Mutation(s): 0  Gene Names: UL2 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN	B [auth I]	83	Takahashivirus PBS1	Mutation(s): 0
UniProt
Find proteins for P14739 (Bacillus phage PBS2) Explore P14739  Go to UniProtKB:  P14739

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 = 144.12	α = 90
b = 144.12	β = 90
c = 40.95	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• 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