1DGS
CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | DNA ligase/mRNA capping enzyme postcatalytic domain-like | 8029581 | 4001931 | SCOP2 (2022-06-29) |
A | SCOP2 Family | NAD+-dependent DNA ligase domain 3 | 8025337 | 4001027 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Adenylation domain of NAD+-dependent DNA ligase | 8024210 | 4002085 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Nucleic acid-binding proteins | 8041960 | 3000135 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Helix-hairpin-helix tandem | 8037716 | 3000163 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | DNA ligase/mRNA capping enzyme catalytic domain | 8036589 | 3000798 | SCOP2 (2022-06-29) |
B | SCOP2B Superfamily | Helix-hairpin-helix tandem | 8037716 | 3000163 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | DNA ligase/mRNA capping enzyme catalytic domain | 8036589 | 3000798 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Nucleic acid-binding proteins | 8041960 | 3000135 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | PF03120 | e1dgsA1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF03120 | ECOD (1.6) |
A | PF12826 | e1dgsA2 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: PF12826 | ECOD (1.6) |
A | PF01653,PF22745 | e1dgsA3 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: PF01653,PF22745 | ECOD (1.6) |
B | PF03120 | e1dgsB1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF03120 | ECOD (1.6) |
B | PF12826 | e1dgsB2 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: PF12826 | ECOD (1.6) |
B | PF01653,PF22745 | e1dgsB3 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: ATP-grasp | F: PF01653,PF22745 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF03119 | NAD-dependent DNA ligase C4 zinc finger domain (DNA_ligase_ZBD) | NAD-dependent DNA ligase C4 zinc finger domain | DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This family is a small zinc binding motif that is presumably DNA binding [1] ... | Domain | |
PF03120 | NAD-dependent DNA ligase OB-fold domain (DNA_ligase_OB) | NAD-dependent DNA ligase OB-fold domain | DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This family is a small domain found after the adenylation domain Pfam:PF0165 ... | Domain | |
PF12826 | Helix-hairpin-helix motif (HHH_2) | Helix-hairpin-helix motif | - | Motif | |
PF14520 | Helix-hairpin-helix domain (HHH_5) | Helix-hairpin-helix domain | - | Domain | |
PF01653 | NAD-dependent DNA ligase adenylation domain (DNA_ligase_aden) | NAD-dependent DNA ligase adenylation domain | DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This domain is the catalytic adenylation domain. The NAD+ group is covalent ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR041663 | DisA/LigA, helix-hairpin-helix motif | Domain | |
IPR004149 | Zinc-finger, NAD-dependent DNA ligase C4-type | Domain | |
IPR001679 | NAD-dependent DNA ligase | Family | |
IPR010994 | RuvA domain 2-like | Homologous Superfamily | |
IPR001357 | BRCT domain | Domain | |
IPR018239 | NAD-dependent DNA ligase, active site | Active Site | |
IPR013840 | NAD-dependent DNA ligase, N-terminal | Domain | |
IPR012340 | Nucleic acid-binding, OB-fold | Homologous Superfamily | |
IPR013839 | NAD-dependent DNA ligase, adenylation | Domain | |
IPR004150 | NAD-dependent DNA ligase, OB-fold | Domain | |
IPR033136 | NAD-dependent DNA ligase, conserved site | Conserved Site | |
IPR003583 | Helix-hairpin-helix DNA-binding motif, class 1 | Domain | |
IPR036420 | BRCT domain superfamily | Homologous Superfamily |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
DNA ligase (NAD+) M-CSA #450 | DNA ligases catalyse the formation of phosphodiester bonds at single-strand breaks in double stranded DNA and are required in DNA replication, repair and recombination. DNA ligases are also used extensively for in vitro DNA manipulation and cloning techniques. Eukaryotic, viral and achaebacteria encoded enzyme al require ATP, where as NAD+ requiring DNA ligases are found exclusively in eubacteria. | Defined by 9 residues: GLU:A-114LYS:A-116ASP:A-118TYR:A-221LYS:A-312CYS:A-406CYS:A-409CYS:A-422CYS:A-427 | EC: 6.5.1.2 (PDB Primary Data) |