6VF7

DNA Polymerase Mu, 8-oxodGTP:At Ground State Ternary Complex, 50 mM Mn2+ (15 min)

Summary for 6VF7

• Entry DOI: 10.2210/pdb6vf7/pdb
• Related: 6VEZ
• Descriptor: DNA-directed DNA/RNA polymerase mu, 1,2-ETHANEDIOL, DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3'), ... (11 entities in total)
• Functional Keywords: time-lapse crystallography, oxidized ribonucleotide insertion, dna polymerase mu, double strand break repair, replication
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 46742.33

Authors

Jamsen, J.A.,Wilson, S.H. (deposition date: 2020-01-03, release date: 2021-09-01, Last modification date: 2025-09-03)

Primary citation

Jamsen, J.A.,Sassa, A.,Perera, L.,Shock, D.D.,Beard, W.A.,Wilson, S.H.
Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair.
Nat Commun, 12:5055-5055, 2021

PubMed Abstract: Reactive oxygen species (ROS) oxidize cellular nucleotide pools and cause double strand breaks (DSBs). Non-homologous end-joining (NHEJ) attaches broken chromosomal ends together in mammalian cells. Ribonucleotide insertion by DNA polymerase (pol) μ prepares breaks for end-joining and this is required for successful NHEJ in vivo. We previously showed that pol μ lacks discrimination against oxidized dGTP (8-oxo-dGTP), that can lead to mutagenesis, cancer, aging and human disease. Here we reveal the structural basis for proficient oxidized ribonucleotide (8-oxo-rGTP) incorporation during DSB repair by pol μ. Time-lapse crystallography snapshots of structural intermediates during nucleotide insertion along with computational simulations reveal substrate, metal and side chain dynamics, that allow oxidized ribonucleotides to escape polymerase discrimination checkpoints. Abundant nucleotide pools, combined with inefficient sanitization and repair, implicate pol μ mediated oxidized ribonucleotide insertion as an emerging source of widespread persistent mutagenesis and genomic instability.

PubMed: 34417448
DOI: 10.1038/s41467-021-24486-x

Experimental method

X-RAY DIFFRACTION (1.871 Å)