3K9F | pdb_00003k9f

Detailed structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3k9fa_	Multi-domain proteins (alpha and beta)	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	DNA Gyrase A	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
B	d3k9fb_	Multi-domain proteins (alpha and beta)	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	DNA Gyrase A	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
C	d3k9fc_	Multi-domain proteins (alpha and beta)	DNA gyrase B, C-terminal domain-like	DNA gyrase B, C-terminal domain-like	DNA gyrase B, C-terminal domain	DNA gyrase beta-prime domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
D	d3k9fd_	Multi-domain proteins (alpha and beta)	DNA gyrase B, C-terminal domain-like	DNA gyrase B, C-terminal domain-like	DNA gyrase B, C-terminal domain	DNA gyrase beta-prime domain	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Toprim domain-like	8090034	3000737	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Toprim domain-like	8090034	3000737	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	e3k9fA4	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: BRCT	F:	ECOD (20:10:01)
B	e3k9fB4	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: BRCT	F:	ECOD (20:10:01)
C	e3k9fC1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: Peptidase_S26	F:	ECOD (20:10:01)
D	e3k9fD1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: Peptidase_S26	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
C, D	PF00986	DNA gyrase B subunit, carboxyl terminus (DNA_gyraseB_C)	DNA gyrase B subunit, carboxyl terminus	-	Family
C, D	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA topoisomerase 4 subunit A	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	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 cytoplasm DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex cell periphery extrinsic component of plasma membrane membrane intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex cell periphery extrinsic component of plasma membrane membrane plasma membrane extrinsic component of membrane
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
H	DNA (5'-D(PGPAPCPTPAPTPGPCPAPCPGPTPAPAPAPAPCPAP*G)-3')	-	-	-
G	DNA (5'-D(CPTPGPTPTPTPTPACPGPTPGPCPAP*T)-3')	-	-	-
F	DNA (5'-D(PAPGPTPCPAPTPTPCPAPTPGPAPCPCPTPTPGPGP*T)-3')	-	-	-
E	DNA (5'-D(APCPCPAPAPGPGPTCPAPTPGPAPAP*T)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035516	DNA gyrase/topoisomerase IV, subunit A, C-terminal	Homologous Superfamily
A, B	IPR050220	Type II DNA Topoisomerases	Family
A, B	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
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	IPR006691	DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat	Repeat
A, B	IPR005741	DNA topoisomerase IV subunit A, Gram-positive	Family
A, B	IPR002205	DNA topoisomerase, type IIA, domain A	Domain
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	IPR006171	TOPRIM domain	Domain
C, D	IPR000565	DNA topoisomerase, type IIA, subunit B	Family
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	IPR005740	DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes	Family
C, D	IPR002288	DNA gyrase B subunit, C-terminal	Domain
C, D	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily