4UB4: Dna Polymerase Beta Substrate Complex With A Templating Cytosine And Incoming Dgtp, 0 S

Citation:
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 beta, 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.
PDB ID: 4UB4Download
MMDB ID: 124731
PDB Deposition Date: 2014/8/11
Updated in MMDB: 2014/12
Experimental Method:
x-ray diffraction
Resolution: 1.95  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4UB4: tetrameric; determined by author and by software (PISA)
Molecular Components in 4UB4
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase Beta(Gene symbol: POLB)
Molecule annotation
Nucleotides(3 molecules)
1
5'-d(p*gp*tp*cp*gp*g)-3'
Molecule annotation
1
5'-d(*gp*cp*tp*gp*ap*tp*gp*cp*gp*c)-3'
Molecule annotation
1
5'-d(*cp*cp*gp*ap*cp*cp*gp*cp*gp*cp*ap*tp*cp*ap*gp*c)-3'
Molecule annotation
Chemicals (3 molecules)
1
2
2
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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