1UDG

THE STRUCTURAL BASIS OF SPECIFIC BASE EXCISION REPAIR BY URACIL-DNA GLYCOSYLASE

• PDB DOI: https://doi.org/10.2210/pdb1UDG/pdb

• Classification: HYDROLASE
• Organism(s): Human alphaherpesvirus 1 strain 17
• Mutation(s): No 


• Deposited: 1995-06-23 Released: 1996-01-29 
• Deposition Author(s): Pearl, L.H., Savva, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

The structural basis of specific base-excision repair by uracil-DNA glycosylase.

Savva, R., McAuley-Hecht, K., Brown, T., Pearl, L.

(1995) Nature 373: 487-493

• PubMed: 7845459 
• DOI: https://doi.org/10.1038/373487a0
• Primary Citation of Related Structures:  
  1LAU, 1UDG, 1UDH


• PubMed Abstract: 
  

  The 1.75-A crystal structure of the uracil-DNA glycosylase from herpes simplex virus type-1 reveals a new fold, distantly related to dinucleotide-binding proteins. Complexes with a trideoxynucleotide, and with uracil, define the DNA-binding site and allow a detailed understanding of the exquisitely specific recognition of uracil in DNA. The overall structure suggests binding models for elongated single- and double-stranded DNA substrates. Conserved residues close to the uracil-binding site suggest a catalytic mechanism for hydrolytic base excision.

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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: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.56 kDa 
• Atom Count: 1,957 
• Modelled Residue Count: 228 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URACIL-DNA GLYCOSYLASE	A	244	Human alphaherpesvirus 1 strain 17	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.14	α = 90
b = 65.14	β = 90
c = 49.16	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: 1996-01-29 
Deposition Author(s): Pearl, L.H., Savva, R.

Revision History  

• Version 1.0: 1996-01-29
  Type: Initial release
  
• Version 1.1: 2008-03-03
  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, Derived calculations, Other