5J5Q | pdb_00005j5q

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	DNA_gyraseB	e5j5qD2	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: DNA_gyraseB	ECOD (1.6)
D	HATPase_c_1	e5j5qD1	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_1	ECOD (1.6)
C	DNA_gyraseB	e5j5qC1	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: DNA_gyraseB	ECOD (1.6)
C	HATPase_c_1	e5j5qC2	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_1	ECOD (1.6)
B	DNA_gyraseB	e5j5qB2	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: DNA_gyraseB	ECOD (1.6)
B	HATPase_c_1	e5j5qB1	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_1	ECOD (1.6)
A	DNA_gyraseB	e5j5qA2	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: DNA_gyraseB	ECOD (1.6)
A	HATPase_c_1	e5j5qA1	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_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
C	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	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	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
A	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
A	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, B, 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
A, B, 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	DNA (5'-D(GPCPAPTPAPTPAPTPAPTPAPTPGPC)-3')	-	-	-
A, B, C, D	DNA topoisomerase 4 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 nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA negative supercoiling activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity macromolecular conformation isomerase activity cation binding metal ion binding	cellular process cell cycle chromosome segregation cell cycle process 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 metabolic process cellular process cell cycle chromosome segregation cell cycle process 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 metabolic process cellular component organization or biogenesis macromolecule metabolic process	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, C, D	IPR018522	DNA topoisomerase, type IIA, conserved site	Conserved Site
A, B, C, D	IPR013506	DNA topoisomerase, type IIA, subunit B, domain 2	Domain
A, B, C, D	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B, C, D	IPR006171	TOPRIM domain	Domain
A, B, C, D	IPR000565	DNA topoisomerase, type IIA, subunit B	Family
A, B, C, D	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
A, B, C, D	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, B, C, D	IPR001241	DNA topoisomerase, type IIA	Family
A, B, C, D	IPR005740	DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes	Family
A, B, C, D	IPR002288	DNA gyrase B subunit, C-terminal	Domain
A, B, C, D	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily

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.