› 5dkw

X-ray diffraction
2.69Å resolution

Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus with Ca2+ in the active

Released:
DOI: 10.2210/pdb5dkw/pdb
PDB entry 5dkw coloured by chain, front view.
PDB entry 5dkw coloured by chain, side view.
PDB entry 5dkw coloured by chain, top view.
Source organisms:
Primary publication:
Structural Mechanism for the Fidelity Modulation of DNA Polymerase λ.
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD
J Am Chem Soc 138 2389-98 (2016)
PMID: 26836966

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-118572 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chains: A, B
Molecule details ›
Chains: A, B
Length: 327 amino acids
Theoretical weight: 36.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGP5 (Residues: 249-575; Coverage: 57%)
Gene name: POLL
Sequence domains:
Structure domains:
DNA (5'-D(P*GP*CP*CP*G)-3') Chains: C, D
Molecule details ›
Chains: C, 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') Chains: E, P
Molecule details ›
Chains: E, P
Length: 6 nucleotides
Theoretical weight: 1.79 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3') Chains: F, T
Molecule details ›
Chains: F, T
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 2 x DTP
Ligand CA 5 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21212
Unit cell:
a: 99.466Å b: 151.31Å c: 83.606Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.233
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Nonhomologous DNA end-joining for repair of DNA double-strand breaks.
Pannunzio et al. (2018)
1 more