1DGS

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

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1dgsa1	All alpha proteins	SAM domain-like	RuvA domain 2-like	NAD+-dependent DNA ligase, domain 3	NAD+-dependent DNA ligase, domain 3	(Thermus filiformis ) [TaxId: 276 ],	SCOPe (2.08)
A	d1dgsa2	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	NAD+-dependent DNA ligase	(Thermus filiformis ) [TaxId: 276 ],	SCOPe (2.08)
A	d1dgsa3	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	Adenylation domain of NAD+-dependent DNA ligase	Adenylation domain of NAD+-dependent DNA ligase	(Thermus filiformis ) [TaxId: 276 ],	SCOPe (2.08)
B	d1dgsb1	All alpha proteins	SAM domain-like	RuvA domain 2-like	NAD+-dependent DNA ligase, domain 3	NAD+-dependent DNA ligase, domain 3	(Thermus filiformis ) [TaxId: 276 ],	SCOPe (2.08)
B	d1dgsb2	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	NAD+-dependent DNA ligase	(Thermus filiformis ) [TaxId: 276 ],	SCOPe (2.08)
B	d1dgsb3	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	Adenylation domain of NAD+-dependent DNA ligase	Adenylation domain of NAD+-dependent DNA ligase	(Thermus filiformis ) [TaxId: 276 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Adenylation domain of NAD+-dependent DNA ligase	8024210	4002085	SCOP2 (2022-06-29)
A	SCOP2 Family	NAD+-dependent DNA ligase, domain 3	8025337	4001027	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA ligase/mRNA capping enzyme postcatalytic domain-like	8029581	4001931	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8036589	3000798	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8037716	3000163	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8041960	3000135	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	DNA_ligase_OB	e1dgsA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_ligase_OB	ECOD (1.6)
A	HHH_2	e1dgsA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_2	ECOD (1.6)
A	DNA_ligase_aden	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: DNA_ligase_aden	ECOD (1.6)
B	DNA_ligase_OB	e1dgsB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_ligase_OB	ECOD (1.6)
B	HHH_2	e1dgsB2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_2	ECOD (1.6)
B	DNA_ligase_aden	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: DNA_ligase_aden	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.287.610	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
A	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	1.10.287.610	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
B	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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] ...	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]. IT is found only in NAD dependent DNA ligases [1].	Domain
A, B	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 ...	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:PF01653 in NAD dependent ligases [1]. OB-fold domains generally are involved in nucleic acid binding.	Domain
A, B	PF12826	Helix-hairpin-helix motif (HHH_2)	Helix-hairpin-helix motif	-	Motif
A, B	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain	-	Domain
A, B	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 ...	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 covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism [1].	Domain
A, B	PF22745	DNA ligase-like, N-terminal NAD+-binding domain (Nlig-Ia)	DNA ligase-like, N-terminal NAD+-binding domain	The alpha-helical Nlig-Ia domain is found at the N-terminal of DNA ligases and it has been proposed to either swivel the NAD+ close to the ligase active site lysine on the RAGNYA domain or function as an allosteric NAD+ binding site. The Nlig-Ia doma ...	The alpha-helical Nlig-Ia domain is found at the N-terminal of DNA ligases and it has been proposed to either swivel the NAD+ close to the ligase active site lysine on the RAGNYA domain or function as an allosteric NAD+ binding site. The Nlig-Ia domain is also observed as a solo protein in phages that do not encode a separate NAD+-dependent ligase catalytic module, suggesting the domain can function independently of a DNA ligase. It has been proposed that these domains likely function as NAD+ sensors which might help indicate to the phage the development of NADase host effectors or shield NAD+ from the action of such effectors [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA LIGASE	ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase (NAD+) activity DNA ligase activity ligase activity DNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase (NAD+) activity DNA ligase activity ligase activity DNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus response to stimulus base-excision repair, DNA ligation DNA ligation involved in DNA repair DNA ligation base-excision repair nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus response to stimulus base-excision repair, DNA ligation DNA ligation involved in DNA repair DNA ligation base-excision repair cellular response to stress DNA damage response response to stress DNA repair	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR041663	DisA/LigA, helix-hairpin-helix motif	Domain
A, B	IPR004149	Zinc-finger, NAD-dependent DNA ligase C4-type	Domain
A, B	IPR001679	NAD-dependent DNA ligase	Family
A, B	IPR010994	RuvA domain 2-like	Homologous Superfamily
A, B	IPR001357	BRCT domain	Domain
A, B	IPR018239	NAD-dependent DNA ligase, active site	Active Site
A, B	IPR013840	NAD-dependent DNA ligase, N-terminal	Domain
A, B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B	IPR013839	NAD-dependent DNA ligase, adenylation	Domain
A, B	IPR004150	NAD-dependent DNA ligase, OB-fold	Domain
A, B	IPR033136	NAD-dependent DNA ligase, conserved site	Conserved Site
A, B	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
A, B	IPR036420	BRCT domain superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	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 \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 6.5.1.2 (PDB Primary Data)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.