8YON | pdb_00008yon

structure of phage T6 full-length topoisomerase II bound with DNA

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	WD40	e8yonD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
C	WD40	e8yonC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
B	WD40	e8yonB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
A	WD40	e8yonA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF00204	DNA gyrase B (DNA_gyraseB)	DNA gyrase B	This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.	Domain
C, D	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
A, B	PF00521	DNA gyrase/topoisomerase IV, subunit A (DNA_topoisoIV)	DNA gyrase/topoisomerase IV, subunit A	This entry represents a domain found in type IIA topoisomerases, such as bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA), and mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that r ...	This entry represents a domain found in type IIA topoisomerases, such as bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA), and mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F	DNA (50-MER)	-	-	-
E	DNA (50-MER)	-	-	-
C, D	DNA topoisomerase (ATP-hydrolyzing)	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 cation binding metal ion binding	cellular component organization organelle organization nuclear chromosome segregation chromosome organization sister chromatid segregation cellular process cellular component organization or biogenesis cell cycle chromosome segregation cell cycle process primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization organelle organization nuclear chromosome segregation chromosome organization sister chromatid segregation cellular process cellular component organization or biogenesis cell cycle chromosome segregation cell cycle process primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA topological change metabolic process macromolecule metabolic process	-
A, B	DNA topoisomerase medium subunit	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	cellular component organization organelle organization nuclear chromosome segregation chromosome organization sister chromatid segregation cellular process cellular component organization or biogenesis cell cycle chromosome segregation cell cycle process primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization organelle organization nuclear chromosome segregation chromosome organization sister chromatid segregation cellular process cellular component organization or biogenesis cell cycle chromosome segregation cell cycle process primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA topological change metabolic process macromolecule metabolic process	protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR018522	DNA topoisomerase, type IIA, conserved site	Conserved Site
C, D	IPR013506	DNA topoisomerase, type IIA, subunit B, domain 2	Domain
C, D	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
C, D	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
C, D	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
C, D	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
C, D	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
C, D	IPR001241	DNA topoisomerase, type IIA	Family
C, D	IPR050634	DNA Topoisomerase II	Family
C, D	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
A, B	IPR001154	DNA topoisomerase II, eukaryotic-type	Family
A, B	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A, B	IPR050634	DNA Topoisomerase II	Family
A, B	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A, B	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A, B	IPR002205	DNA topoisomerase, type IIA, domain A	Domain

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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.