› 5iio

X-ray diffraction
2.08Å resolution

Crystal structure of the DNA polymerase lambda binary complex

Released:
DOI: 10.2210/pdb5iio/pdb
PDB entry 5iio coloured by chain, front view.
PDB entry 5iio coloured by chain, side view.
PDB entry 5iio 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-118790 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chains: A, E, I, M
Molecule details ›
Chains: A, E, I, M
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(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3') Chains: B, F, J, N
Molecule details ›
Chains: B, F, J, N
Length: 11 nucleotides
Theoretical weight: 3.41 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') Chains: C, G, K, O
Molecule details ›
Chains: C, G, K, O
Length: 6 nucleotides
Theoretical weight: 1.79 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*CP*CP*G)-3') Chains: D, H, L, P
Molecule details ›
Chains: D, H, L, P
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 6 x NA
1 modified residue:
Ligand 8OG 4 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21212
Unit cell:
a: 191.423Å b: 98.98Å c: 105.034Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.191 0.235
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

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

3 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)
2 more