› 3l2p

X-ray diffraction
3Å resolution

Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States

Released:
DOI: 10.2210/pdb3l2p/pdb
PDB entry 3l2p coloured by chain, front view.
PDB entry 3l2p coloured by chain, side view.
PDB entry 3l2p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states.
Cotner-Gohara E, Kim IK, Hammel M, Tainer JA, Tomkinson AE, Ellenberger T
Biochemistry 49 6165-76 (2010)
PMID: 20518483

Function and Biology Details

Reaction catalysed: 
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
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-116515 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA ligase 3 Chain: A
Molecule details ›
Chain: A
Length: 579 amino acids
Theoretical weight: 65.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49916 (Residues: 257-833; Coverage: 57%)
Gene name: LIG3
Sequence domains:
Structure domains:
5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.77 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 22 nucleotides
Theoretical weight: 6.68 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand AMP 1 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P41212
Unit cell:
a: 130.149Å b: 130.149Å c: 150.431Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.233 0.271
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

14 review citations

Alternative end-joining pathway(s): bricolage at DNA breaks.
Frit et al. (2014)
13 more

26 mentions without citation

Recognition and repair of chemically heterogeneous structures at DNA ends.
Andres et al. (2015)
25 more