› 3upq

X-ray diffraction
1.95Å resolution

Crystal structure of the pre-catalytic ternary complex of polymerase lambda with an rATP analog opposite a templating T.

Released:
DOI: 10.2210/pdb3upq/pdb
PDB entry 3upq coloured by chain, front view.
PDB entry 3upq coloured by chain, side view.
PDB entry 3upq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The catalytic cycle for ribonucleotide incorporation by human DNA Pol λ.
Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek K
Nucleic Acids Res 40 7518-27 (2012)
PMID: 22584622

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-117001 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chain: A
Molecule details ›
Chain: A
Length: 329 amino acids
Theoretical weight: 36.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGP5 (Residues: 242-575; Coverage: 57%)
Gene name: POLL
Sequence domains:
Structure domains:
5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3' Chain: T
Molecule details ›
Chain: T
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: Homo sapiens
Expression system: Not provided
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: Homo sapiens
Expression system: Not provided
5'-D(P*GP*CP*CP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZAN 1 x ZAN
Ligand MN 3 x MN
Ligand NA 1 x NA
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 55.975Å b: 63.66Å c: 139.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.208 0.244
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Ribonucleotides in DNA: origins, repair and consequences.
Williams et al. (2014)
7 more

6 mentions without citation

Structure-function studies of DNA polymerase λ.
Bebenek et al. (2014)
5 more