Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.32 kDa 
• Atom Count: 2,299 
• Modelled Residue Count: 242 
• Deposited Residue Count: 242 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 2OXM

Crystal structure of a UNG2/modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping

• PDB DOI:  https://doi.org/10.2210/pdb2OXM/pdb
• NDB: PD0973

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


• Deposited: 2007-02-20 Released: 2007-10-30 
• Deposition Author(s): Bianchet, M.A., Krosky, D.J., Stivers, J.T., Amzel, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.328 
• R-Value Work: 0.254 
• R-Value Observed: 0.257 

Literature

Enzymatic capture of an extrahelical thymine in the search for uracil in DNA.

Parker, J.B., Bianchet, M.A., Krosky, D.J., Friedman, J.I., Amzel, L.M., Stivers, J.T.

(2007) Nature 449: 433-437

• PubMed: 17704764 
• DOI: https://doi.org/10.1038/nature06131
• Primary Citation of Related Structures:  
  2OXM, 2OYT


• PubMed Abstract: 
  

The enzyme uracil DNA glycosylase (UNG) excises unwanted uracil bases in the genome using an extrahelical base recognition mechanism. Efficient removal of uracil is essential for prevention of C-to-T transition mutations arising from cytosine deamination, cytotoxic U*A pairs arising from incorporation of dUTP in DNA, and for increasing immunoglobulin gene diversity during the acquired immune response. A central event in all of these UNG-mediated processes is the singling out of rare U*A or U*G base pairs in a background of approximately 10(9) T*A or C*G base pairs in the human genome. Here we establish for the human and Escherichia coli enzymes that discrimination of thymine and uracil is initiated by thermally induced opening of T*A and U*A base pairs and not by active participation of the enzyme. Thus, base-pair dynamics has a critical role in the genome-wide search for uracil, and may be involved in initial damage recognition by other DNA repair glycosylases.

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Organizational Affiliation: 

Department of Pharmacology and Molecular Sciences, Johns Hopkins Medical School, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.

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, DGU, UNG1, UNG15 EC: 3.2.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P13051 (Homo sapiens) Explore P13051  Go to UniProtKB:  P13051
PHAROS:  P13051

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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*GP*AP*TP*(4MF)P*AP*CP*A)-3')	B [auth C]	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.328 
• R-Value Work: 0.254 
• R-Value Observed: 0.257 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.467	α = 90
b = 65.567	β = 90
c = 98.472	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Bianchet, M.A., Krosky, D.J., Stivers, J.T., Amzel, L.M.

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary