3Q8R: Human Dna Polymerase Iota Incorporating Dgtp Opposite 8-Oxo-Guanine

The 8-oxo-guanine (8-oxo-G) lesion is the most abundant and mutagenic oxidative DNA damage existing in the genome. Due to its dual coding nature, 8-oxo-G causes most DNA polymerases to misincorporate adenine. Human Y-family DNA polymerase iota (poliota) preferentially incorporates the correct cytosine nucleotide opposite 8-oxo-G. This unique specificity may contribute to poliota's biological role in cellular protection against oxidative stress. However, the structural basis of this preferential cytosine incorporation is currently unknown. Here we present four crystal structures of poliota in complex with DNA containing an 8-oxo-G lesion, paired with correct dCTP or incorrect dATP, dGTP, and dTTP nucleotides. An exceptionally narrow poliota active site restricts the purine bases in a syn conformation, which prevents the dual coding properties of 8-oxo-G by inhibiting syn/anti conformational equilibrium. More importantly, the 8-oxo-G base in a syn conformation is not mutagenic in poliota because its Hoogsteen edge does not form a stable base pair with dATP in the narrow active site. Instead, the syn 8-oxo-G template base forms the most stable replicating base pair with correct dCTP due to its small pyrimidine base size and enhanced hydrogen bonding with the Hoogsteen edge of 8-oxo-G. In combination with site directed mutagenesis, we show that Gln59 in the finger domain specifically interacts with the additional O(8) atom of the lesion base, which influences nucleotide selection, enzymatic efficiency, and replication stalling at the lesion site. Our work provides the structural mechanism of high-fidelity 8-oxo-G replication by a human DNA polymerase.
PDB ID: 3Q8RDownload
MMDB ID: 88871
PDB Deposition Date: 2011/1/6
Updated in MMDB: 2011/05
Experimental Method:
x-ray diffraction
Resolution: 2.45  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 3Q8R: trimeric; determined by author and by software (PISA)
Molecular Components in 3Q8R
Label Count Molecule
Protein (1 molecule)
DNA Polymerase Iota(Gene symbol: POLI)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*tp*cp*ap*(8og)p*gp*gp*gp*tp*cp*cp*t)-3')
Molecule annotation
DNA (5'-d(p*ap*gp*gp*ap*cp*cp*c)-3')
Molecule annotation
Chemicals (3 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB