› 5iin

X-ray diffraction
2.15Å resolution

Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dG:dC base-pair

Released:
DOI: 10.2210/pdb5iin/pdb
PDB entry 5iin coloured by chain, front view.
PDB entry 5iin coloured by chain, side view.
PDB entry 5iin coloured by chain, top view.
Source organisms:
Primary publication:
A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG.
Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M
EMBO J 35 2045-59 (2016)
PMID: 27481934

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118789 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chain: A
Molecule details ›
Chain: A
Length: 334 amino acids
Theoretical weight: 37.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UGP5 (Residues: 242-575; Coverage: 58%)
Gene name: POLL
Sequence domains:
Structure domains:
DNA (5'-D(P*GP*CP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 6 nucleotides
Theoretical weight: 1.79 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*GP*GP*CP*AP*(8OG)P*TP*AP*CP*TP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DUP 1 x DUP
Ligand NA 1 x NA
Ligand MG 1 x MG
1 modified residue:
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 56.471Å b: 62.718Å c: 140.006Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.187 0.231
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

Sunlight damage to cellular DNA: Focus on oxidatively generated lesions.
Schuch et al. (2017)
3 more

2 mentions without citation

Structural Insights into the Specificity of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Family X DNA Polymerases.
Kaminski et al. (2021)
1 more