4UB1

DNA polymerase beta product complex with a templating adenine and 8-oxodGMP, 90 s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.341 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/nature13886
  • Primary Citation of Related Structures:  

  • 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 vulnera ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens)
Go to Gene View: POLB
Go to UniProtKB:  P06746
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'T16synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3'P11synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(P*GP*TP*CP*GP*G)-3'D5synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
P
DNA LINKINGC10 H14 N5 O8 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.341 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.131α = 90.00
b = 80.800β = 109.58
c = 55.462γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Database references