Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.79 kDa 
• Atom Count: 3661 
• Modelled Residue Count: 357 
• Deposited Residue Count: 367 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

4UAZ

DNA polymerase beta reactant complex with a templating adenine and incoming 8-oxodGTP, 20 s

• PDB DOI: 10.2210/pdb4UAZ/pdb
• NDB: 4UAZ

• Classification: TRANSFERASE, LYASE/DNA
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-11 Released: 2014-11-12 
• Deposition Author(s): Freudenthal, B.D., Wilson, S.H., Beard, W.A.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.220 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.

Freudenthal, B.D., Beard, W.A., Perera, L., Shock, D.D., Kim, T., Schlick, T., Wilson, S.H.

(2015) Nature 517: 635-639

• PubMed: 25409153 
• DOI: 10.1038/nature13886
• Primary Citation of Related Structures:  
  4UAW, 4UAY, 4UAZ, 4UB1, 4UB2, 4UB3, 4UB4, 4UB5, 4UBB, 4UBC


• PubMed Abstract: 
  

Oxidative stress promotes genomic instability and human diseases. A common oxidized nucleoside is 8-oxo-7,8-dihydro-2'-deoxyguanosine, which is found both in DNA (8-oxo-G) and as a free nucleotide (8-oxo-dGTP). Nucleotide pools are especially vulnerable to oxidative damage. Therefore cells encode an enzyme (MutT/MTH1) that removes free oxidized nucleotides. This cleansing function is required for cancer cell survival and to modulate Escherichia coli antibiotic sensitivity in a DNA polymerase (pol)-dependent manner. How polymerases discriminate between damaged and non-damaged nucleotides is not well understood. This analysis is essential given the role of oxidized nucleotides in mutagenesis, cancer therapeutics, and bacterial antibiotics. Even with cellular sanitizing activities, nucleotide pools contain enough 8-oxo-dGTP to promote mutagenesis. This arises from the dual coding potential where 8-oxo-dGTP(anti) base pairs with cytosine and 8-oxo-dGTP(syn) uses its Hoogsteen edge to base pair with adenine. Here we use time-lapse crystallography to follow 8-oxo-dGTP insertion opposite adenine or cytosine with human pol β, to reveal that insertion is accommodated in either the syn- or anti-conformation, respectively. For 8-oxo-dGTP(anti) insertion, a novel divalent metal relieves repulsive interactions between the adducted guanine base and the triphosphate of the oxidized nucleotide. With either templating base, hydrogen-bonding interactions between the bases are lost as the enzyme reopens after catalysis, leading to a cytotoxic nicked DNA repair intermediate. Combining structural snapshots with kinetic and computational analysis reveals how 8-oxo-dGTP uses charge modulation during insertion that can lead to a blocked DNA repair intermediate.

---

Organizational Affiliation: 

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, North Carolina 27709-2233, USA.

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	D [auth A]	335	Homo sapiens	Mutation(s): 0  Gene Names: POLB EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens) Explore P06746  Go to UniProtKB:  P06746
PHAROS:  P06746

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'	A [auth T]	16	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3'	B [auth P]	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*TP*CP*GP*G)-3'	C [auth D]	5	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8DG	G [auth A]	8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 BUZOGVVQWCXXDP-VPENINKCSA-N
PPV	H [auth A]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.220 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.835	α = 90
b = 79.921	β = 107.64
c = 55.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-08-11 
• Released Date: 2014-11-12 
Deposition Author(s): Freudenthal, B.D., Wilson, S.H., Beard, W.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES050158
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES050161
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES043010

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2014-12-03
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Database references
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy