2Q2U

Structure of Chlorella virus DNA ligase-product DNA complex

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
I [auth A]	d2q2ua1	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	ATP-dependent DNA ligase	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
I [auth A]	d2q2ua2	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	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
J [auth B]	d2q2ub1	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	ATP-dependent DNA ligase	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
J [auth B]	d2q2ub2	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	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
K [auth C]	d2q2uc1	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	ATP-dependent DNA ligase	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
K [auth C]	d2q2uc2	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	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
L [auth D]	d2q2ud1	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	ATP-dependent DNA ligase	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
L [auth D]	d2q2ud2	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	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth A]	SCOP2B Superfamily	Nucleic acid-binding proteins	8035164	3000135	SCOP2B (2022-06-29)
I [auth A]	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8035166	3000798	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8035166	3000798	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	Nucleic acid-binding proteins	8035164	3000135	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8035166	3000798	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	Nucleic acid-binding proteins	8035164	3000135	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	Nucleic acid-binding proteins	8035164	3000135	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8035166	3000798	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)
I [auth A]	DNA_ligase_OB_2	e2q2uA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_ligase_OB_2	ECOD (1.6)
I [auth A]	DNA_ligase_A_M	e2q2uA3	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)
J [auth B]	DNA_ligase_OB_2	e2q2uB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_ligase_OB_2	ECOD (1.6)
J [auth B]	DNA_ligase_A_M	e2q2uB3	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)
K [auth C]	DNA_ligase_OB_2	e2q2uC1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_ligase_OB_2	ECOD (1.6)
K [auth C]	DNA_ligase_A_M	e2q2uC3	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)
L [auth D]	DNA_ligase_OB_2	e2q2uD1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_ligase_OB_2	ECOD (1.6)
L [auth D]	DNA_ligase_A_M	e2q2uD3	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)
I [auth A]	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
I [auth A]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
I [auth A]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
J [auth B]	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
J [auth B]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
J [auth B]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
K [auth C]	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
K [auth C]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
K [auth C]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
L [auth D]	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
L [auth D]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
L [auth D]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth A], J [auth B], K [auth C], L [auth D]	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
I [auth A], J [auth B], K [auth C], L [auth D]	PF14743	DNA ligase OB-like domain (DNA_ligase_OB_2)	DNA ligase OB-like domain	This domain has an OB-like fold, but does not appear to be related to Pfam:PF03120. It is found at the C-terminus of the ATP dependent DNA ligase domain Pfam:PF01068 [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], C [auth G], E [auth I], G [auth K]	5'-D(TPTPCPCPGPAPTPAPGPTPGPGPGPGPTPCPGPCPAPAP*T)-3'	-	-	-
B [auth F], D [auth H], F [auth J], H [auth L]	5'-D(APTPTPGPCPGPAPCP(OMC)PCPCPAPCPTPAPTPCPGPGPAP*A)-3'	-	-	-
I [auth A], J [auth B], K [auth C], L [auth D]	Chlorella virus 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 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	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
I [auth A], J [auth B], K [auth C], L [auth D]	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
I [auth A], J [auth B], K [auth C], L [auth D]	IPR012310	DNA ligase, ATP-dependent, central	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR050326	NAD-dependent DNA ligase B	Family
I [auth A], J [auth B], K [auth C], L [auth D]	IPR029319	DNA ligase, OB-like domain	Domain

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.