1Q3F

Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase.

Bianchet, M.A.Seiple, L.A.Jiang, Y.L.Ichikawa, Y.Amzel, L.M.Stivers, J.T.

(2003) Biochemistry 42: 12455-12460

  • DOI: 10.1021/bi035372+

  • PubMed Abstract: 
  • The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarb ...

    The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbenium ion-uracil anion reaction intermediate. Comparison with substrate and product structures, and the previous structure of the intermediate determined by kinetic isotope effects, reveals an exquisite example of geometric strain, least atomic motion, and electrophile migration in biological catalysis. This structure provides a rare opportunity to reconstruct the detailed structural transformations that occur along an enzymatic reaction coordinate.


    Organizational Affiliation

    Departments of Biophysics, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
A
223Homo sapiensMutation(s): 0 
Gene Names: UNG (DGU, UNG1, UNG15)
EC: 3.2.2.27
Find proteins for P13051 (Homo sapiens)
Go to Gene View: UNG
Go to UniProtKB:  P13051
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*GP*TP*(NRI)P*AP*TP*CP*TP*T)-3'B9N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3'C10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
URA
Query on URA

Download SDF File 
Download CCD File 
B
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NRI
Query on NRI
B
DNA LINKINGC5 H12 N O5 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.640α = 90.00
b = 65.890β = 90.00
c = 99.410γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2015-10-07
    Type: Structure summary