3Q8R

Human DNA polymerase iota incorporating dGTP opposite 8-oxo-guanine

Summary for 3Q8R

• Entry DOI: 10.2210/pdb3q8r/pdb
• Related: 3Q8P 3Q8Q 3Q8S
• Descriptor: DNA polymerase iota, DNA (5'-D(*TP*CP*AP*(8OG)P*GP*GP*GP*TP*CP*CP*T)-3'), DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3'), ... (6 entities in total)
• Functional Keywords: dna polymerase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: Q9UNA4
• Total number of polymer chains: 3
• Total formula weight: 53071.74

Authors

Kirouac, K.N.,Ling, H. (deposition date: 2011-01-06, release date: 2011-02-23, Last modification date: 2024-02-21)

Primary citation

Kirouac, K.N.,Ling, H.
Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota.
Proc.Natl.Acad.Sci.USA, 108:3210-3215, 2011

PubMed Abstract: 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 (polι) preferentially incorporates the correct cytosine nucleotide opposite 8-oxo-G. This unique specificity may contribute to polι'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 polι in complex with DNA containing an 8-oxo-G lesion, paired with correct dCTP or incorrect dATP, dGTP, and dTTP nucleotides. An exceptionally narrow polι 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 polι 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.

PubMed: 21300901
DOI: 10.1073/pnas.1013909108

Experimental method

X-RAY DIFFRACTION (2.45 Å)