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Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV

Source organism: Homo sapiens
Biochemical function: ATP binding
Biological process: DNA ligation involved in DNA repair
Cellular component: not assigned

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EC 6.5.1.1: DNA ligase (ATP)

Reaction catalysed:
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Systematic name:
Poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP)
Alternative Name(s):
  • DNA joinase
  • DNA ligase
  • DNA repair enzyme
  • DNA-joining enzyme
  • Deoxyribonucleate ligase
  • Deoxyribonucleic acid joinase
  • Deoxyribonucleic acid ligase
  • Deoxyribonucleic acid repair enzyme
  • Deoxyribonucleic acid-joining enzyme
  • Deoxyribonucleic joinase
  • Deoxyribonucleic ligase
  • Deoxyribonucleic repair enzyme
  • Deoxyribonucleic-joining enzyme
  • Poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming)
  • Polydeoxyribonucleotide synthase (ATP)
  • Polynucleotide ligase
  • Polynucleotide ligase (ATP)
  • Sealase

GO terms

Sequence family

Pfam Protein family (Pfam)
PF01068
Domain description: ATP dependent DNA ligase domain
Occurring in:
  1. DNA ligase 4
The deposited structure of PDB entry 3vnn contains 1 copy of Pfam domain PF01068 (ATP dependent DNA ligase domain) in DNA ligase 4. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR012310
Domain description: DNA ligase, ATP-dependent, central
Occurring in:
  1. DNA ligase 4
IPR016059
Domain description: DNA ligase, ATP-dependent, conserved site
Occurring in:
  1. DNA ligase 4
IPR044125
Domain description: DNA Ligase 4, adenylation domain
Occurring in:
  1. DNA ligase 4
IPR029710
Domain description: DNA ligase 4
Occurring in:
  1. DNA ligase 4

Structure domain

CATH CATH domain
3.30.470.30
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: D-amino Acid Aminotransferase; Chain A, domain 1
Homology: DNA ligase/mRNA capping enzyme
Occurring in:
  1. DNA ligase 4
The deposited structure of PDB entry 3vnn contains 1 copy of CATH domain 3.30.470.30 (D-amino Acid Aminotransferase; Chain A, domain 1) in DNA ligase 4. Showing 1 copy in chain A.

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