6RKS

E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Type II DNA topoisomerase half-clamp domain-like	8037555	3001800	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8055745	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type II DNA topoisomerase half-clamp domain-like	8037555	3001800	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8055745	3000034	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DNA_topoisoIV_1st	e6rksA3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
A	DNA_topoisoIV_3rd	e6rksA2	A: alpha bundles	X: alpha-helical domain in type II DNA topoisomerase (From Topology)	H: alpha-helical domain in type II DNA topoisomerase (From Topology)	T: alpha-helical domain in type II DNA topoisomerase	F: DNA_topoisoIV_3rd	ECOD (1.6)
A	DNA_topoisoIV_2nd_1	e6rksA1	A: a+b two layers	X: a+b domain in type II DNA topoisomerase (From Topology)	H: a+b domain in type II DNA topoisomerase (From Topology)	T: a+b domain in type II DNA topoisomerase	F: DNA_topoisoIV_2nd_1	ECOD (1.6)
C	DNA_topoisoIV_1st	e6rksC2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
C	DNA_topoisoIV_3rd	e6rksC1	A: alpha bundles	X: alpha-helical domain in type II DNA topoisomerase (From Topology)	H: alpha-helical domain in type II DNA topoisomerase (From Topology)	T: alpha-helical domain in type II DNA topoisomerase	F: DNA_topoisoIV_3rd	ECOD (1.6)
C	DNA_topoisoIV_2nd_1	e6rksC3	A: a+b two layers	X: a+b domain in type II DNA topoisomerase (From Topology)	H: a+b domain in type II DNA topoisomerase (From Topology)	T: a+b domain in type II DNA topoisomerase	F: DNA_topoisoIV_2nd_1	ECOD (1.6)
B	gyrB_1st_1,gyrB_1st_2	e6rksB2	A: a+b two layers	X: SSHS domain	H: SSHS domain in type II DNA topoisomerase (From Topology)	T: SSHS domain in type II DNA topoisomerase	F: gyrB_1st_1,gyrB_1st_2	ECOD (1.6)
B	DNA_gyraseB_C	e6rksB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
D	gyrB_1st_1,gyrB_1st_2	e6rksD1	A: a+b two layers	X: SSHS domain	H: SSHS domain in type II DNA topoisomerase (From Topology)	T: SSHS domain in type II DNA topoisomerase	F: gyrB_1st_1,gyrB_1st_2	ECOD (1.6)
D	DNA_gyraseB_C	e6rksD2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00521	DNA gyrase/topoisomerase IV, subunit A (DNA_topoisoIV)	DNA gyrase/topoisomerase IV, subunit A	-	Family
B, D	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family
B, D	PF21249	GyrB, hook (GyrB_hook)	GyrB, hook	This entry represents the N-terminal section of the 'Toprim hook' as described in [1], which is localised between the Toprim (Pfam:PF01751) and the insert (Pfam:PF18053) domains [1-3]. The C-terminal section of the hook is included in (Pfam:PF00986). ...	This entry represents the N-terminal section of the 'Toprim hook' as described in [1], which is localised between the Toprim (Pfam:PF01751) and the insert (Pfam:PF18053) domains [1-3]. The C-terminal section of the hook is included in (Pfam:PF00986). The hook is flexible towards the Toprim domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	DNA gyrase subunit A	ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity 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 ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity 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 isomerase activity DNA negative supercoiling activity DNA topoisomerase activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity identical protein binding protein binding	response to stimulus response to chemical response to xenobiotic stimulus response to antibiotic nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process chromosome organization DNA conformation change response to stimulus response to chemical response to xenobiotic stimulus response to antibiotic nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic 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 process cellular component organization or biogenesis cellular biosynthetic process cellular metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process negative regulation of biological process regulation of primary metabolic process negative regulation of DNA-templated DNA replication negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of DNA replication negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of DNA-templated DNA replication negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication	membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome non-membrane-bounded organelle DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex
B, D	DNA gyrase subunit B	ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity 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 ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity 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 isomerase activity DNA negative supercoiling activity DNA topoisomerase activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity cation binding metal ion binding	response to stimulus response to chemical response to xenobiotic stimulus response to antibiotic nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process chromosome organization DNA conformation change response to stimulus response to chemical response to xenobiotic stimulus response to antibiotic nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic 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 process cellular component organization or biogenesis cellular biosynthetic process cellular metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome non-membrane-bounded organelle DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex
E [auth F], F [auth E]	DNA Strand 1	-	-	-
G, H	DNA Strand 2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR035516	DNA gyrase/topoisomerase IV, subunit A, C-terminal	Homologous Superfamily
A, C	IPR050220	Type II DNA Topoisomerases	Family
A, C	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A, C	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A, C	IPR006691	DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat	Repeat
A, C	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A, C	IPR005743	DNA gyrase, subunit A	Family
A, C	IPR002205	DNA topoisomerase, type IIA, domain A	Domain
B, D	IPR011557	DNA gyrase, subunit B	Family
B, D	IPR018522	DNA topoisomerase, type IIA, conserved site	Conserved Site
B, D	IPR013506	DNA topoisomerase, type IIA, subunit B, domain 2	Domain
B, D	IPR049353	DNA gyrase subunit B, hook	Domain
B, D	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
B, D	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
B, D	IPR006171	TOPRIM domain	Domain
B, D	IPR000565	DNA topoisomerase, type IIA, subunit B	Family
B, D	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
B, D	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
B, D	IPR001241	DNA topoisomerase, type IIA	Family
B, D	IPR002288	DNA gyrase B subunit, C-terminal	Domain
B, D	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
B, D	IPR034160	DNA gyrase subunit B, TOPRIM domain	Domain
B, D	IPR041423	DNA gyrase subunit B insert domain	Domain
B, D	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily