› 7jkp

X-ray diffraction
2.59Å resolution

Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion

Released:
DOI: 10.2210/pdb7jkp/pdb
PDB entry 7jkp coloured by chain, front view.
PDB entry 7jkp coloured by chain, side view.
PDB entry 7jkp coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase.
Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK
OpenAccess logo Nat Commun 12 4020 (2021)
PMID: 34188055

Function and Biology Details

Reactions catalysed: 
SsDNA + n NTP = ssDNA/pppN(pN)(n-1) hybrid + (n-1) diphosphate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121354 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-directed primase/polymerase protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 354 amino acids
Theoretical weight: 41.04 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q96LW4 (Residues: 1-354; Coverage: 63%)
Gene names: CCDC111, PRIMPOL
Sequence domains: DNA primase small subunit
DNA (5'-D(P*AP*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3') Chains: C, G
Molecule details ›
Chains: C, G
Length: 17 nucleotides
Theoretical weight: 5.08 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*G)-3') Chains: D, H
Molecule details ›
Chains: D, H
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DTP 2 x DTP
Ligand CA 3 x CA
Ligand GOL 1 x GOL
1 modified residue:
Ligand 8OG 2 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P1
Unit cell:
a: 52.225Å b: 65.656Å c: 74.482Å
α: 69.3° β: 82.87° γ: 88.06°
R-values:
R R work R free
0.25 0.248 0.307
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

3 review citations

Roles for the 8-Oxoguanine DNA Repair System in Protecting Telomeres From Oxidative Stress.
De Rosa et al. (2021)
2 more

3 mentions without citation

PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy.
Díaz-Talavera et al. (2022)
2 more