Annotations: 2Q2E

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PRK04342_1st_2	e2q2eA2	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_2	ECOD (1.6)
A	TP6A_N	e2q2eA3	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	e2q2eA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PRK04342_2nd	ECOD (1.6)
B	PRK14868	e2q2eB4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PRK14868	ECOD (1.6)
B	FbpA_2nd_1	e2q2eB2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
B	Topo-VIb_trans	e2q2eB3	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	e2q2eB1	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)
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)
B	6.10.20.80	Special	Helix non-globular	Arc Repressor Mutant, subunit A		CATH (4.3.0)
B	2.60.40.2960	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	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	PF18000	Type 2 DNA topoisomerase 6 subunit B C-terminal domain (Top6b_C)	Type 2 DNA topoisomerase 6 subunit B C-terminal domain	This is the C-terminal domain found in archaeal type 2 DNA topoisomerase 6 subunit B (EC:5.99.1.3). This region is a small helix-two turns-helix (H2TH) domain inserted between the GHKL and transducer domains which adopts an immunoglobulin-like fold. ...	This is the C-terminal domain found in archaeal type 2 DNA topoisomerase 6 subunit B (EC:5.99.1.3). This region is a small helix-two turns-helix (H2TH) domain inserted between the GHKL and transducer domains which adopts an immunoglobulin-like fold. Mutation analysis of this C-terminal domain showed that the overall activity of the mutant mesophilic methanogen M. mazei Top6B (MmT6) is modestly reduced but its relative activity on different substrates is not affected. Due to the similarity of the B subunit's CTD to known protein- and carbohydrate-binding modules, it has been suggested that it could regulate topo VI spatially, perhaps by localizing the enzyme to a specific subcellular region or functional partner [1].	Domain
B	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	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	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 organic cyclic compound metabolic process organelle organization organic substance metabolic process cellular process metabolic process cellular component organization or biogenesis 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 organic cyclic compound metabolic process organelle organization organic substance metabolic process 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 intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle
B	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	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 organic cyclic compound metabolic process organelle organization organic substance metabolic process cellular process metabolic process cellular component organization or biogenesis 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 organic cyclic compound metabolic process organelle organization organic substance metabolic process 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR034136	Topoisomerase 6 subunit A/Spo11, TOPRIM domain	Domain
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR002815	Spo11/DNA topoisomerase VI subunit A	Family
A	IPR049333	Type II DNA topoisomerase VI subunit A, all-beta domain	Domain
A	IPR036078	Spo11/DNA topoisomerase VI subunit A superfamily	Homologous Superfamily
A	IPR013049	Spo11/DNA topoisomerase VI, subunit A, N-terminal	Domain
A	IPR004085	DNA topoisomerase VI, subunit A	Family
B	IPR003594	Histidine kinase/HSP90-like ATPase	Domain
B	IPR005734	DNA topoisomerase VI, subunit B	Family
B	IPR015320	DNA topoisomerase VI, subunit B, transducer	Domain
B	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
B	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
B	IPR040494	DNA topoisomerase VI, subunit B, C-terminal	Domain
B	IPR010979	Small ribosomal subunit protein uS13-like, H2TH	Homologous Superfamily
B	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily

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.