1V9P | pdb_00001v9p

Crystal Structure Of Nad+-Dependent DNA Ligase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1v9pb1	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	d1v9pb2	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	d1v9pb3	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)
A	d1v9pa1	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	d1v9pa2	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	d1v9pa3	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)
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)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8037716	3000163	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helix-hairpin-helix tandem	8037716	3000163	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8036589	3000798	SCOP2B (2022-06-29)
A	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)
B	DNA_ligase_OB	e1v9pB1	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	e1v9pB2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_2	ECOD (1.6)
B	DNA_ligase_aden	e1v9pB3	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)
A	DNA_ligase_OB	e1v9pA1	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	e1v9pA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_2	ECOD (1.6)
A	DNA_ligase_aden	e1v9pA3	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)
B	1.10.287.610	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.2.0)
B	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.2.0)
B	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.2.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.2.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.2.0)
A	1.10.287.610	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.2.0)
A	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.2.0)
A	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.2.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.2.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.2.0)

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 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 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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.