Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.71 kDa 
• Atom Count: 2090 
• Modelled Residue Count: 225 
• Deposited Residue Count: 229 
• Unique protein chains: 1

1EUG

CRYSTAL STRUCTURE OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE AND ITS COMPLEXES WITH URACIL AND GLYCEROL: STRUCTURE AND GLYCOSYLASE MECHANISM REVISITED

• PDB DOI: 10.2210/pdb1EUG/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli B
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-10-12 Released: 1999-10-12 
• Deposition Author(s): Xiao, G., Tordova, M., Jagadeesh, J., Drohat, A.C., Stivers, J.T., Gilliland, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.250 
• R-Value Observed: 0.202 

Literature

Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited.

Xiao, G., Tordova, M., Jagadeesh, J., Drohat, A.C., Stivers, J.T., Gilliland, G.L.

(1999) Proteins 35: 13-24

• PubMed: 10090282 
• Primary Citation of Related Structures:  
  1EUG, 2EUG, 3EUG, 5EUG


• PubMed Abstract: 
  

The DNA repair enzyme uracil DNA glycosylase (UDG) catalyzes the hydrolysis of premutagenic uracil residues from single-stranded or duplex DNA, producing free uracil and abasic DNA. Here we report the high-resolution crystal structures of free UDG from Escherichia coli strain B (1.60 A), its complex with uracil (1.50 A), and a second active-site complex with glycerol (1.43 A). These represent the first high-resolution structures of a prokaryotic UDG to be reported. The overall structure of the E. coli enzyme is more similar to the human UDG than the herpes virus enzyme. Significant differences between the bacterial and viral structures are seen in the side-chain positions of the putative general-acid (His187) and base (Asp64), similar to differences previously observed between the viral and human enzymes. In general, the active-site loop that contains His187 appears preorganized in comparison with the viral and human enzymes, requiring smaller substrate-induced conformational changes to bring active-site groups into catalytic position. These structural differences may be related to the large differences in the mechanism of uracil recognition used by the E. coli and viral enzymes. The pH dependence of k(cat) for wild-type UDG and the D64N and H187Q mutant enzymes is consistent with general-base catalysis by Asp64, but provides no evidence for a general-acid catalyst. The catalytic mechanism of UDG is critically discussed with respect to these results.

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Organizational Affiliation: 

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute for Standards and Technology, Rockville, 20850, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GLYCOSYLASE)	A	229	Escherichia coli B	Mutation(s): 1  Gene Names: ung EC: 3.2.2.3 (PDB Primary Data), 3.2.2.27 (UniProt)
UniProt
Find proteins for P12295 (Escherichia coli (strain K12)) Explore P12295  Go to UniProtKB:  P12295

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.250 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.13	α = 90
b = 61.32	β = 90
c = 64.4	γ = 90

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-10-12 
• Released Date: 1999-10-12 
Deposition Author(s): Xiao, G., Tordova, M., Jagadeesh, J., Drohat, A.C., Stivers, J.T., Gilliland, G.L.

Revision History  

• Version 1.0: 1999-10-12
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-03-14
  Changes: Database references