8DF9 | pdb_00008df9

Structure of M. kandleri topoisomerase V in complex with DNA. 38 base pair asymmetric DNA complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Topoisomerase V catalytic domain-like	8039252	3001992	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039248	3000163	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039249	3000163	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039251	3000163	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039247	3000163	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039247	3000163	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8039248	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	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	HTH_AsnC-type_2	e8df9A1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_AsnC-type_2	ECOD (1.6)
A	HHH_2_1	e8df9A5	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_2_1	ECOD (1.6)
A	EUF07927	e8df9A6	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EUF07927	ECOD (1.6)
A	EUF07924,EUF07925	e8df9A9	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EUF07924,EUF07925	ECOD (1.6)
A	EUF08090	e8df9A8	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: EUF08090	ECOD (1.6)
B	HTH_AsnC-type_2	e8df9B3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HTH_AsnC-type_2	ECOD (1.6)
B	HHH_5	e8df9B10	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_5	ECOD (1.6)
B	HHH_2_1	e8df9B7	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_2_1	ECOD (1.6)
B	EUF07927	e8df9B8	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EUF07927	ECOD (1.6)
B	EUF07924,EUF07925	e8df9B2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EUF07924,EUF07925	ECOD (1.6)
B	EUF08090	e8df9B1	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: EUF08090	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21872	SAM domain-like (SAM_5)	SAM domain-like	This entry corresponds to the most N-terminal SAM domain of several that is found topoisomerase V protein.	Domain
A, B	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain		Domain
A, B	PF22409	Topoisomerase V, HHH domain (TopoV_HHH)	Topoisomerase V, HHH domain	This entry represents a helix-hairpin-helix (HHH) domain of topoisomerase V (Topo-V), the only member of a novel topoisomerase subtype. Topo-V is unique as it is a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities within ...	This entry represents a helix-hairpin-helix (HHH) domain of topoisomerase V (Topo-V), the only member of a novel topoisomerase subtype. Topo-V is unique as it is a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities within the same protein [1,2]. This prptein contains a topoisomerase domain at the N-terminal, followed byt twelve tandem helix-hairpin-helix (HhH)2 domains.	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 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 cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	-
C [auth S]	DNA (33-MER)	-	-	-
D [auth T]	DNA (33-MER)	-	-	-
E [auth U]	DNA (5'-D(PGPCPCPTPGPCPAPCPGPAPAPGPTPAPAPGP*C)-3')	-	-	-
F [auth V], H [auth X]	DNA (5'-D(PTPGPCPTPTPAPCPTPTPCPGPTPGPCPAPGPGPCPCPA)-3')	-	-	-
G [auth W]	DNA (5'-D(PGPCPCPTPGPCPAPCPGPAPAPGPTPAPAPGPCPA)-3')	-	-	-

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	IPR055246	Topoisomerase V, HHH domain	Domain
A, B	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
A, B	IPR054066	SAM domain-like	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.