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CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS

Source organism: Thermus filiformis
Biochemical function: DNA ligase (NAD+) activity
Biological process: DNA repair
Cellular component: not assigned

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EC 6.5.1.2: DNA ligase (NAD(+))

Reaction catalysed:
(1a) NAD(+) + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + beta-nicotinamide D-nucleotide
Systematic name:
Poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (NAD(+))
Alternative Name(s):
  • DNA joinase
  • DNA ligase
  • DNA repair enzyme
  • DNA-joining enzyme
  • Deoxyribonucleate ligase
  • Deoxyribonucleic acid joinase
  • Deoxyribonucleic acid ligase
  • Deoxyribonucleic joinase
  • Deoxyribonucleic ligase
  • Deoxyribonucleic repair enzyme
  • Deoxyribonucleic-joining enzyme
  • Poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming)
  • Polydeoxyribonucleotide synthase (NAD(+))
  • Polydeoxyribonucleotide synthase (NAD+)
  • Polynucleotide ligase
  • Polynucleotide ligase (NAD(+))
  • Polynucleotide ligase (NAD+)
  • Polynucleotide ligase (nicotinamide adenine dinucleotide)
  • Polynucleotide synthetase
  • Polynucleotide synthetase (nicotinamide adenine dinucleotide)

GO terms

Biochemical function:
Biological process:
Cellular component:
  • not assigned

Sequence families

Pfam Protein families (Pfam)
PF00533
Domain description: BRCA1 C Terminus (BRCT) domain
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of Pfam domain PF00533 (BRCA1 C Terminus (BRCT) domain) in DNA ligase. Showing 1 copy in chain A (this domain is out of the observed residue ranges!).

PF12826
Domain description: Helix-hairpin-helix motif
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of Pfam domain PF12826 (Helix-hairpin-helix motif) in DNA ligase. Showing 1 copy in chain A.

PF14520
Domain description: Helix-hairpin-helix domain
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of Pfam domain PF14520 (Helix-hairpin-helix domain) in DNA ligase. Showing 1 copy in chain A.

PF03119
Domain description: NAD-dependent DNA ligase C4 zinc finger domain
Occurring in:
  1. DNA ligase

PF03120
Domain description: NAD-dependent DNA ligase OB-fold domain
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of Pfam domain PF03120 (NAD-dependent DNA ligase OB-fold domain) in DNA ligase. Showing 1 copy in chain A.

PF01653
Domain description: NAD-dependent DNA ligase adenylation domain
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of Pfam domain PF01653 (NAD-dependent DNA ligase adenylation domain) in DNA ligase. Showing 1 copy in chain A.

PF22745
Domain description: DNA ligase-like, N-terminal NAD+-binding domain
Occurring in:
  1. DNA ligase

InterPro InterPro annotations
IPR003583
Domain description: Helix-hairpin-helix DNA-binding motif, class 1
Occurring in:
  1. DNA ligase
IPR001357
Domain description: BRCT domain
Occurring in:
  1. DNA ligase
IPR001679
Domain description: NAD-dependent DNA ligase
Occurring in:
  1. DNA ligase
IPR036420
Domain description: BRCT domain superfamily
Occurring in:
  1. DNA ligase
IPR012340
Domain description: Nucleic acid-binding, OB-fold
Occurring in:
  1. DNA ligase
IPR013839
Domain description: NAD-dependent DNA ligase, adenylation
Occurring in:
  1. DNA ligase
IPR041663
Domain description: DisA/LigA, helix-hairpin-helix motif
Occurring in:
  1. DNA ligase
IPR010994
Domain description: RuvA domain 2-like
Occurring in:
  1. DNA ligase
IPR033136
Domain description: NAD-dependent DNA ligase, conserved site
Occurring in:
  1. DNA ligase
IPR004150
Domain description: NAD-dependent DNA ligase, OB-fold
Occurring in:
  1. DNA ligase
IPR013840
Domain description: NAD-dependent DNA ligase, N-terminal
Occurring in:
  1. DNA ligase

Structure domains

CATH CATH domains
1.10.150.20
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: DNA polymerase; domain 1
Homology: 5' to 3' exonuclease, C-terminal subdomain
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 4 copies of CATH domain 1.10.150.20 (DNA polymerase; domain 1) in DNA ligase. Showing 2 copies in chain A.
3.30.1490.70
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Dna Ligase; domain 1
Homology: Dna Ligase; domain 1
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of CATH domain 3.30.1490.70 (Dna Ligase; domain 1) in DNA ligase. Showing 1 copy in chain A.
2.40.50.140
Class: Mainly Beta
Architecture: Beta Barrel
Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homology: Nucleic acid-binding proteins
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of CATH domain 2.40.50.140 (OB fold (Dihydrolipoamide Acetyltransferase, E2P)) in DNA ligase. Showing 1 copy in chain A.
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
The deposited structure of PDB entry 1dgs contains 2 copies of CATH domain 3.30.470.30 (D-amino Acid Aminotransferase; Chain A, domain 1) in DNA ligase. Showing 1 copy in chain A.
1.10.287.610
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Helix Hairpins
Homology: Helix hairpin bin
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of CATH domain 1.10.287.610 (Helix Hairpins) in DNA ligase. Showing 1 copy in chain A.
SCOP SCOP annotations
47786
Class: All alpha proteins
Fold: SAM domain-like
Superfamily: RuvA domain 2-like
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of SCOP domain 47786 (NAD+-dependent DNA ligase, domain 3) in DNA ligase. Showing 1 copy in chain A.
50307
Class: All beta proteins
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of SCOP domain 50307 (DNA ligase/mRNA capping enzyme postcatalytic domain) in DNA ligase. Showing 1 copy in chain A.
56096
Class: Alpha and beta proteins (a+b)
Fold: ATP-grasp
Superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
Occurring in:
  1. DNA ligase
The deposited structure of PDB entry 1dgs contains 2 copies of SCOP domain 56096 (Adenylation domain of NAD+-dependent DNA ligase) in DNA ligase. Showing 1 copy in chain A.

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