2ZBK | pdb_00002zbk

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
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)
B	GFP	e2zbkB1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: GFP	ECOD (v294.1)
D	GFP	e2zbkD1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: GFP	ECOD (v294.1)
F	HGTP_anticodon	e2zbkF1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: HGTP_anticodon	ECOD (v294.1)
H	GFP	e2zbkH1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: GFP	ECOD (v294.1)
A	zf-CXXC	e2zbkA1	A: a/b three-layered sandwiches	X: CXXC domain-like	H: CXXC domain	T: CXXC domain	F: zf-CXXC	ECOD (v294.1)
C	Amidohydro_1	e2zbkC2	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Amidohydro_1	ECOD (v294.1)
C	peroxidase	e2zbkC1	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: peroxidase	ECOD (v294.1)
E	TetR_N	e2zbkE1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: TetR_N	ECOD (v294.1)
E	AMP-dom_DIP2-like	e2zbkE2	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: AMP-dom_DIP2-like	ECOD (v294.1)
G	TetR_N	e2zbkG1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: TetR_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 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 nucleic acid binding ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity 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 macromolecular conformation isomerase activity ATP-dependent activity identical protein binding protein 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 chromosome organization DNA conformation change cellular component organization DNA topological change organelle organization cellular component organization or biogenesis	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex
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 anion binding adenyl nucleotide 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 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 nucleic acid conformation isomerase activity 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 macromolecular conformation isomerase activity ATP-dependent 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 chromosome organization DNA conformation change cellular component organization DNA topological change organelle organization cellular component organization or biogenesis	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
B, D, F, H	IPR005734	DNA topoisomerase VI, subunit B	Family
B, D, F, H	IPR015320	DNA topoisomerase VI, subunit B, transducer	Domain
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