› 1rzt

X-ray diffraction
2.1Å resolution

Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule

Released:
DOI: 10.2210/pdb1rzt/pdb
PDB entry 1rzt coloured by chain, front view.
PDB entry 1rzt coloured by chain, side view.
PDB entry 1rzt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology.
Garcia-Diaz M, Bebenek K, Krahn JM, Blanco L, Kunkel TA, Pedersen LC
Mol Cell 13 561-72 (2004)
PMID: 14992725

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 domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114557 (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: 331 amino acids
Theoretical weight: 37.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGP5 (Residues: 245-575; Coverage: 58%)
Gene name: POLL
Sequence domains:
Structure domains:
5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3' Chains: B, F, J, N
Molecule details ›
Chains: B, F, J, N
Length: 11 nucleotides
Theoretical weight: 3.33 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*GP*TP*GP*CP*G)-3' Chains: C, G, K, O
Molecule details ›
Chains: C, G, K, O
Length: 5 nucleotides
Theoretical weight: 1.54 KDa
Source organism: Homo sapiens
Expression system: Not provided
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: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NA 10 x NA
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P21212
Unit cell:
a: 191.321Å b: 99.034Å c: 104.838Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.227 0.26
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Nonhomologous end joining in yeast.
Daley et al. (2005)
6 more

11 mentions without citation

The X family portrait: structural insights into biological functions of X family polymerases.
Moon et al. (2007)
10 more