2CSB

Crystal structure of Topoisomerase V from Methanopyrus kandleri (61 kDa fragment)

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)
A	d2csba1	All alpha proteins	SAM domain-like	RuvA domain 2-like	Topoisomerase V repeat domain	Topoisomerase V	(Methanopyrus kandleri ) [TaxId: 2320 ],	SCOPe (2.08)
A	d2csba5	All alpha proteins	Topoisomerase V catalytic domain-like	Topoisomerase V catalytic domain-like	Topoisomerase V catalytic domain-like	Topoisomerase V, catalytic domain	(Methanopyrus kandleri ) [TaxId: 2320 ],	SCOPe (2.08)
B	d2csbb2	All alpha proteins	SAM domain-like	RuvA domain 2-like	Topoisomerase V repeat domain	Topoisomerase V	(Methanopyrus kandleri ) [TaxId: 2320 ],	SCOPe (2.08)
B	d2csbb1	All alpha proteins	Topoisomerase V catalytic domain-like	Topoisomerase V catalytic domain-like	Topoisomerase V catalytic domain-like	Topoisomerase V, catalytic domain	(Methanopyrus kandleri ) [TaxId: 2320 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Topoisomerase V repeat domain	8026868	4001369	SCOP2 (2022-06-29)
A	SCOP2 Family	Topoisomerase V repeat domain	8026869	4001369	SCOP2 (2022-06-29)
A	SCOP2 Family	Topoisomerase V repeat domain	8026870	4001369	SCOP2 (2022-06-29)
A	SCOP2 Family	Topoisomerase V repeat domain	8026872	4001369	SCOP2 (2022-06-29)
A	SCOP2 Family	Topoisomerase V catalytic domain-like	8026873	4001615	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8039247	3000163	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8039248	3000163	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8039249	3000163	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8039251	3000163	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Topoisomerase V catalytic domain-like	8039252	3001992	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039247	3000163	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039249	3000163	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Topoisomerase V catalytic domain-like	8039252	3001992	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039248	3000163	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039251	3000163	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	PF13404	e2csbA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF13404	ECOD (1.6)
A	F_UNCLASSIFIED	e2csbA5	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF14520	e2csbA4	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
A	PF21616	e2csbA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF21616	ECOD (1.6)
A	PF21872	e2csbA3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF21872	ECOD (1.6)
A	F_UNCLASSIFIED	e2csbA6	A: alpha bundles	X: Topoisomerase V catalytic domain-like (From Topology)	H: Topoisomerase V catalytic domain-like (From Topology)	T: Topoisomerase V catalytic domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF13404	e2csbB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF13404	ECOD (1.6)
B	F_UNCLASSIFIED	e2csbB5	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF14520	e2csbB4	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
B	PF21616	e2csbB2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF21616	ECOD (1.6)
B	PF21872	e2csbB3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF21872	ECOD (1.6)
B	F_UNCLASSIFIED	e2csbB6	A: alpha bundles	X: Topoisomerase V catalytic domain-like (From Topology)	H: Topoisomerase V catalytic domain-like (From Topology)	T: Topoisomerase V catalytic domain-like	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.250.950	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	6.10.250.950	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain	-	Domain
A, B	PF21616	Topoisomerase V, second (HhH)2 tandem domain (Topo-V_HhH_2_2nd)	Topoisomerase V, second (HhH)2 tandem domain	This domain is found in Topoisomerase V from Methanopyrus kandleri (Topo-V), is a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities. Topo-V consists of an N-terminal topoisomerase domain followed by 12 tandem (HhH)2 doma ...	This domain is found in Topoisomerase V from Methanopyrus kandleri (Topo-V), is a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities. Topo-V consists of an N-terminal topoisomerase domain followed by 12 tandem (HhH)2 domains, showing four active sites. This entry represents the second of these tandem domains [1,4,5].	Domain
A, B	PF13412	Winged helix-turn-helix DNA-binding (HTH_24)	Winged helix-turn-helix DNA-binding	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Topoisomerase V	DNA binding binding organic cyclic compound binding nucleic acid binding isomerase activity catalytic activity cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR049334	Topoisomerase V, second (HhH)2 tandem domain	Domain
A, B	IPR010994	RuvA domain 2-like	Homologous Superfamily
A, B	IPR024065	DNA topoisomerase V, catalytic domain superfamily	Homologous Superfamily
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.