1A0I | pdb_00001a0i

ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7 COMPLEX WITH ATP

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	d1a0ia1	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	ATP-dependent DNA ligase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
A	d1a0ia2	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	ATP-dependent DNA ligase catalytic domain	ATP-dependent DNA ligase, N-terminal domain	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	ATP-dependent DNA ligase catalytic domain	8024205	4002079	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA ligase/mRNA capping enzyme postcatalytic domain-like	8029580	4001931	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8036584	3000798	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8041959	3000135	SCOP2 (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_A_C_1	e1a0iA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_ligase_A_C_1	ECOD (1.6)
A	DNA_ligase_A_M	e1a0iA2	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_A_M	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	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	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01068	ATP dependent DNA ligase domain (DNA_ligase_A_M)	ATP dependent DNA ligase domain	This domain belongs to a more diverse superfamily, including Pfam:PF01331 and Pfam:PF01653 [3].	Domain
A	PF17879	DNA ligase C-terminal domain (DNA_ligase_C)	DNA ligase C-terminal domain	This is the C-terminal domain found in ATP-Dependent DNA Ligase from Bacteriophage T7. This domain has no ligase activity, however together with the N-terminal domain they bind to double-stranded DNA consistent with the idea that the DNA-binding site ...	This is the C-terminal domain found in ATP-Dependent DNA Ligase from Bacteriophage T7. This domain has no ligase activity, however together with the N-terminal domain they bind to double-stranded DNA consistent with the idea that the DNA-binding site is between the domains in the intact protein. Furthermore, although the fold of domain 2 is very similar to a number of other proteins that bind single-stranded DNA, this domain does not bind to single-stranded DNA but instead has a high affinity for double-stranded DNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA LIGASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding double-stranded DNA binding nucleic acid binding ligase activity, forming phosphoric ester bonds DNA ligase (ATP) activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity cation binding metal ion 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 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 DNA recombination	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
A	IPR016306	DNA ligase, bacteriophage T7-type	Family
A	IPR012310	DNA ligase, ATP-dependent, central	Domain
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR041559	DNA ligase, ATP-dependent, bacteriophage T7-type, C-terminal	Domain
A	IPR050326	NAD-dependent DNA ligase B	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	DNA ligase (ATP) M-CSA #202	DNA ligase is an essential enzyme required for the repair, replication and recombination of DNA. In all organisms except the prokaryotes it is dependent on the hydrolysis of ATP to AMP and pyrophosphate.	Defined by 3 residues: LYS:A-33 [auth A-34]LYS:A-237 [auth A-238]LYS:A-239 [auth A-240] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.5.1.1 (PDB Primary Data) Search M-CSA Motif + EC 6.5.1.1

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.