1Q3F

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

• PDB DOI: https://doi.org/10.2210/pdb1Q3F/pdb
• NAKB: 1Q3F

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-07-29 Released: 2004-03-23 
• Deposition Author(s): Bianchet, M.A., Seiple, L.A., Jiang, Y.L., Ichikawa, Y., Amzel, L.M., Stivers, J.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Starting Model: experimental

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

• PubMed: 14580190 
• DOI: https://doi.org/10.1021/bi035372+
• Primary Citation of Related Structures:  
  1Q3F


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.41 kDa 
• Atom Count: 2,471 
• Modelled Residue Count: 242 
• Deposited Residue Count: 242 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	C [auth A]	223	Homo sapiens	Mutation(s): 0  Gene Names: UNG OR DGU OR UNG15 EC: 3.2.2 (PDB Primary Data), 3.2.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P13051 (Homo sapiens) Explore P13051  Go to UniProtKB:  P13051
PHAROS:  P13051 GTEx:  ENSG00000076248

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*TP*(NRI)P*AP*TP*CP*TP*T)-3'	A [auth B]	9	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3'	B [auth C]	10	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URA	D [auth B]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.64	α = 90
b = 65.89	β = 90
c = 99.41	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-23 
Deposition Author(s): Bianchet, M.A., Seiple, L.A., Jiang, Y.L., Ichikawa, Y., Amzel, L.M., Stivers, J.T.

Revision History  

• Version 1.0: 2004-03-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2015-10-07
  Changes: Structure summary
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description