› 4xa5

X-ray diffraction
1.9Å resolution

Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating A and an incoming 8-oxo-dGTP

Released:
DOI: 10.2210/pdb4xa5/pdb
PDB entry 4xa5 coloured by chain, front view.
PDB entry 4xa5 coloured by chain, side view.
PDB entry 4xa5 coloured by chain, top view.
Source organisms:
Primary publication:
Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda.
Burak MJ, Guja KE, Garcia-Diaz M
Nucleic Acids Res 43 8089-99 (2015)
PMID: 26220180

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-118260 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chain: A
Molecule details ›
Chain: A
Length: 325 amino acids
Theoretical weight: 36.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UGP5 (Residues: 251-575; Coverage: 57%)
Gene name: POLL
Sequence domains:
Structure domains:
DOWNSTREAM PRIMER 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
PRIMER DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3') Chain: P
Molecule details ›
Chain: P
Length: 6 nucleotides
Theoretical weight: 1.78 KDa
Source organism: synthetic construct
Expression system: Not provided
TEMPLATE DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand 8DG 1 x 8DG
Ligand MG 2 x MG
Ligand ACT 3 x ACT
Ligand GOL 2 x GOL
2 modified residues:
Ligand CAS 1 x CAS
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 55.967Å b: 62.34Å c: 141.613Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.199 0.227
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

Towards a comprehensive view of 8-oxo-7,8-dihydro-2'-deoxyguanosine: Highlighting the intertwined roles of DNA damage and epigenetics in genomic instability.
Gorini et al. (2021)
3 more

1 mention without citation

Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda.
Burak et al. (2015)