2ZBK

Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8003724	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8003724	3000100	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8003724	3000100	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8003724	3000100	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	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	PRK04342_1st	e2zbkA2	A: beta barrels	X: all-beta domain in DNA topoisomerase IV alpha subunit (From Topology)	H: all-beta domain in DNA topoisomerase IV alpha subunit (From Topology)	T: all-beta domain in DNA topoisomerase IV alpha subunit	F: PRK04342_1st	ECOD (1.6)
A	TP6A_N	e2zbkA1	A: alpha arrays	X: HTH	H: HTH domain in DNA topoisomerase IV alpha subunit (From Topology)	T: HTH domain in DNA topoisomerase IV alpha subunit	F: TP6A_N	ECOD (1.6)
A	PRK04342_2nd	e2zbkA3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PRK04342_2nd	ECOD (1.6)
C	TP6A_N	e2zbkC2	A: alpha arrays	X: HTH	H: HTH domain in DNA topoisomerase IV alpha subunit (From Topology)	T: HTH domain in DNA topoisomerase IV alpha subunit	F: TP6A_N	ECOD (1.6)
C	PRK04342_2nd,PRK04342_1st	e2zbkC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PRK04342_2nd,PRK04342_1st	ECOD (1.6)
E	TP6A_N	e2zbkE2	A: alpha arrays	X: HTH	H: HTH domain in DNA topoisomerase IV alpha subunit (From Topology)	T: HTH domain in DNA topoisomerase IV alpha subunit	F: TP6A_N	ECOD (1.6)
E	PRK04342_2nd,PRK04342_1st	e2zbkE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PRK04342_2nd,PRK04342_1st	ECOD (1.6)
G	TP6A_N	e2zbkG2	A: alpha arrays	X: HTH	H: HTH domain in DNA topoisomerase IV alpha subunit (From Topology)	T: HTH domain in DNA topoisomerase IV alpha subunit	F: TP6A_N	ECOD (1.6)
G	PRK04342_2nd,PRK04342_1st	e2zbkG1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PRK04342_2nd,PRK04342_1st	ECOD (1.6)
B	FbpA_2nd_1	e2zbkB2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
B	Topo-VIb_trans	e2zbkB1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: Topo-VIb_trans	ECOD (1.6)
B	HATPase_c_3	e2zbkB3	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_3	ECOD (1.6)
D	FbpA_2nd_1	e2zbkD3	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
D	Topo-VIb_trans	e2zbkD2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: Topo-VIb_trans	ECOD (1.6)
D	HATPase_c_3	e2zbkD1	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_3	ECOD (1.6)
F	FbpA_2nd_1	e2zbkF1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
F	Topo-VIb_trans	e2zbkF3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: Topo-VIb_trans	ECOD (1.6)
F	HATPase_c_3	e2zbkF2	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_3	ECOD (1.6)
H	FbpA_2nd_1	e2zbkH1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
H	Topo-VIb_trans	e2zbkH3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: Topo-VIb_trans	ECOD (1.6)
H	HATPase_c_3	e2zbkH2	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
E	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
G	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
G	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
B	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
B	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
D	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
D	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
F	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
F	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
F	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
H	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
H	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
H	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF04406	Type IIB DNA topoisomerase (TP6A_N)	Type IIB DNA topoisomerase	Type II DNA topoisomerases are ubiquitous enzymes that catalyse the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break. Type II DNA topoisomerases are now subdivided into two sub-families, type ...	Type II DNA topoisomerases are ubiquitous enzymes that catalyse the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break. Type II DNA topoisomerases are now subdivided into two sub-families, type IIA and IIB DNA topoisomerases. TP6A_N is present in type IIB topoisomerase and is thought to be involved in DNA binding owing to its sequence similarity to E. coli catabolite activator protein (CAP) [1].	Domain
A, C, E, G	PF21180	Topoisomerase 6 subunit A/Spo11, Toprim domain (TOP6A-Spo11_Toprim)	Topoisomerase 6 subunit A/Spo11, Toprim domain	This topoisomerase-primase (Toprim) nucleotidyl transferase/hydrolase domain is found in the type II topoisomerase VIA and Spo11, which structurally related. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination ...	This topoisomerase-primase (Toprim) nucleotidyl transferase/hydrolase domain is found in the type II topoisomerase VIA and Spo11, which structurally related. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Topoisomerase VI is a type IIB enzyme that breaks double-stranded DNA and assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis [1-3].	Domain
A, C, E, G	PF20768	All-beta domain in DNA topoisomerase VI alpha subunit (Topo_VI_alpha)	All-beta domain in DNA topoisomerase VI alpha subunit	In all organisms, type II DNA topoisomerases are essential for untangling chromosomal DNA. The archaeal type II protein is termed DNA topoisomerase VI. This entry represents an all beta domain found in these proteins.	Domain
B, D, F, H	PF02518	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (HATPase_c)	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.	Domain
B, D, F, H	PF09239	Topoisomerase VI B subunit, transducer (Topo-VIb_trans)	Topoisomerase VI B subunit, transducer	Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to ...	Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Type II DNA topoisomerase VI subunit A	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding DNA binding nucleic acid binding ATP-dependent activity, acting on DNA isomerase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA topoisomerase activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity catalytic activity ATP-dependent activity	chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process DNA duplex unwinding chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process DNA duplex unwinding DNA-templated DNA replication DNA geometric change DNA unwinding involved in DNA replication DNA replication	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex
B, D, F, H	Type 2 DNA topoisomerase 6 subunit B	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding ATP-dependent activity, acting on DNA isomerase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA topoisomerase activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity catalytic activity ATP-dependent activity identical protein binding protein binding	chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process DNA duplex unwinding chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process DNA duplex unwinding DNA-templated DNA replication DNA geometric change DNA unwinding involved in DNA replication DNA replication	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR034136	Topoisomerase 6 subunit A/Spo11, TOPRIM domain	Domain
A, C, E, G	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, C, E, G	IPR002815	Spo11/DNA topoisomerase VI subunit A	Family
A, C, E, G	IPR049333	Type II DNA topoisomerase VI subunit A, all-beta domain	Domain
A, C, E, G	IPR036078	Spo11/DNA topoisomerase VI subunit A superfamily	Homologous Superfamily
A, C, E, G	IPR013049	Spo11/DNA topoisomerase VI, subunit A, N-terminal	Domain
A, C, E, G	IPR004085	DNA topoisomerase VI, subunit A	Family
B, D, F, H	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
B, D, F, H	IPR050761	TOP6B	Unknown
B, D, F, H	IPR005734	DNA topoisomerase VI, subunit B	Family
B, D, F, H	IPR015320	DNA topoisomerase VI, subunit B, transducer	Domain