6E3W image
Deposition Date 2018-07-15
Release Date 2019-04-03
Last Version Date 2023-10-11
Entry Detail
PDB ID:
6E3W
Title:
Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.02 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase beta
Gene (Uniprot):POLB
Chain IDs:A
Chain Length:335
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*TP*CP*GP*G)-3')
Chain IDs:D
Chain Length:5
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3')
Chain IDs:C (auth: P)
Chain Length:10
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*CP*GP*AP*CP*(A38) P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Chain IDs:B (auth: T)
Chain Length:16
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases.
J. Am. Chem. Soc. 141 4584 4596 (2019)
PMID: 30817143 DOI: 10.1021/jacs.8b08551

Abstact

Reactive oxygen species attack DNA to produce 7,8-dihyro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as major lesions. The structural basis for the mutagenicity of oxoG, which induces G to T mutations, is well understood. However, the structural basis for the mutagenic potential of oxoA, which induces A to C mutations, remains poorly understood. To gain insight into oxoA-induced mutagenesis, we conducted kinetic studies of human DNA polymerases β and η replicating across oxoA and structural studies of polβ incorporating dTTP/dGTP opposite oxoA. While polη readily bypassed oxoA, it incorporated dGTP opposite oxoA with a catalytic specificity comparable to that of correct insertion, underscoring the promutagenic nature of the major oxidative adenine lesion. Polη and polβ incorporated dGTP opposite oxoA ∼170-fold and ∼100-fold more efficiently than that opposite dA, respectively, indicating that the 8-oxo moiety greatly facilitated error-prone replication. Crystal structures of polβ showed that, when paired with an incoming dTTP, the templating oxoA adopted an anti conformation and formed Watson-Crick base pair. When paired with dGTP, oxoA adopted a syn conformation and formed a Hoogsteen base pair with Watson-Crick-like geometry, highlighting the dual-coding potential of oxoA. The templating oxoA was stabilized by Lys280-mediated stacking and hydrogen bonds. Overall, these results provide insight into the mutagenic potential and dual-coding nature of the major oxidative adenine lesion.

Legend

Protein

Chemical

Disease

Primary Citation of related structures