- EMDB-24793: Structure of DNA polymerase zeta with mismatched DNA -
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Basic information
Entry
Database: EMDB / ID: EMD-24793
Title
Structure of DNA polymerase zeta with mismatched DNA
Map data
Sample
Complex: Structure of DNA complex
Protein or peptide: DNA polymerase zeta catalytic subunit
Protein or peptide: DNA polymerase zeta processivity subunit
Protein or peptide: DNA polymerase delta small subunit
Protein or peptide: DNA polymerase delta subunit 3
DNA: DNA (30-MER)
Ligand: IRON/SULFUR CLUSTER
Ligand: CALCIUM ION
Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
Ligand: water
Keywords
DNA repair / DNA replication / translesion DNA synthesis / DNA polymerase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information
delta DNA polymerase complex / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / DNA replication, removal of RNA primer / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / lagging strand elongation / double-strand break repair via break-induced replication ...delta DNA polymerase complex / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / DNA replication, removal of RNA primer / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / lagging strand elongation / double-strand break repair via break-induced replication / DNA metabolic process / DNA strand elongation involved in DNA replication / error-free translesion synthesis / leading strand elongation / error-prone translesion synthesis / nucleotide-excision repair / double-strand break repair via homologous recombination / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin / mitochondrion / DNA binding / nucleus / metal ion binding Similarity search - Function
DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase zeta catalytic subunit / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain ...DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase zeta catalytic subunit / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily Similarity search - Domain/homology
POL31 isoform 1 / DNA polymerase zeta catalytic subunit / DNA polymerase zeta processivity subunit / DNA polymerase delta subunit 3 Similarity search - Component
National Institutes of Health/National Cancer Institute (NIH/NCI)
R01-GM124047
United States
Citation
Journal: Nat Commun / Year: 2022 Title: Cryo-EM structure of translesion DNA synthesis polymerase ζ with a base pair mismatch. Authors: Radhika Malik / Robert E Johnson / Louise Prakash / Satya Prakash / Iban Ubarretxena-Belandia / Aneel K Aggarwal / Abstract: The B-family multi-subunit DNA polymerase ζ (Polζ) is important for translesion DNA synthesis (TLS) during replication, due to its ability to extend synthesis past nucleotides opposite DNA lesions ...The B-family multi-subunit DNA polymerase ζ (Polζ) is important for translesion DNA synthesis (TLS) during replication, due to its ability to extend synthesis past nucleotides opposite DNA lesions and mismatched base pairs. We present a cryo-EM structure of Saccharomyces cerevisiae Polζ with an A:C mismatch at the primer terminus. The structure shows how the Polζ active site responds to the mismatched duplex DNA distortion, including the loosening of key protein-DNA interactions and a fingers domain in an "open" conformation, while the incoming dCTP is still able to bind for the extension reaction. The structure of the mismatched DNA-Polζ ternary complex reveals insights into mechanisms that either stall or favor continued DNA synthesis in eukaryotes.
History
Deposition
Aug 31, 2021
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Header (metadata) release
Mar 9, 2022
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Map release
Mar 9, 2022
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Update
Jun 5, 2024
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Current status
Jun 5, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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