Annotations: 1D3Y

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1d3yb_	Multi-domain proteins (alpha and beta)	DNA topoisomerase IV, alpha subunit	DNA topoisomerase IV, alpha subunit	DNA topoisomerase IV, alpha subunit	DNA topoisomerase IV, alpha subunit	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A	d1d3ya_	Multi-domain proteins (alpha and beta)	DNA topoisomerase IV, alpha subunit	DNA topoisomerase IV, alpha subunit	DNA topoisomerase IV, alpha subunit	DNA topoisomerase IV, alpha subunit	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Toprim domain-like	8055737	3000737	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8037557	3000034	SCOP2B (2022-06-29)
A	SCOP2 Family	Top6A N-terminal domain-like	8025178	4002838	SCOP2 (2022-06-29)
A	SCOP2 Family	Top6A C-terminal domain-like	8055736	4007651	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8037557	3000034	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Toprim domain-like	8055737	3000737	SCOP2 (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		e1d3yB1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: dUTPase	F:	ECOD (20:10:01)
B		e1d3yB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: IMS_HHH	F:	ECOD (20:10:01)
B		e1d3yB3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: SNO, Peptidase_S51	F:	ECOD (20:10:01)
A		e1d3yA1	A: all-beta domain in DNA topoisomerase IV alpha subunit	X: all-beta domain in DNA topoisomerase IV alpha subunit	H: all-beta domain in DNA topoisomerase IV alpha subunit	T: Topo_VI_alpha	F:	ECOD (20:10:01)
A		e1d3yA2	A: HTH	X: HTH domain in DNA topoisomerase IV alpha subunit	H: HTH domain in DNA topoisomerase IV alpha subunit	T: TP6A_N	F:	ECOD (20:10:01)
A		e1d3yA3	A: Flavodoxin-like	X: HAD domain-related	H: Toprim domain	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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)
B	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, 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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	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
A, B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA TOPOISOMERASE VI A SUBUNIT	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR034136	Topoisomerase 6 subunit A/Spo11, TOPRIM domain	Domain
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR002815	Spo11/DNA topoisomerase VI subunit A	Family
A, B	IPR049333	Type II DNA topoisomerase VI subunit A, all-beta domain	Domain
A, B	IPR036078	Spo11/DNA topoisomerase VI subunit A superfamily	Homologous Superfamily
A, B	IPR013049	Spo11/DNA topoisomerase VI, subunit A, N-terminal	Domain
A, B	IPR004085	DNA topoisomerase VI, subunit A	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.