6RKW | pdb_00006rkw

CryoEM structure of the complete E. coli DNA Gyrase complex bound to a 130 bp DNA duplex

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)
D	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8034440	3000100	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8036204	3000091	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8036204	3000091	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8034440	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GyrA/ParC C-terminal domain-like	8065316	3002017	SCOP2B (2022-06-29)
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)
B [auth C]	SCOP2B Superfamily	Type II DNA topoisomerase half-clamp domain-like	8037555	3001800	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	GyrA/ParC C-terminal domain-like	8065316	3002017	SCOP2B (2022-06-29)
B [auth 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)
D	DNA_gyraseB	e6rkwD2	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	e6rkwD1	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)
D	gyrB_1st_1	e6rkwD5	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	ECOD (1.6)
D	gyrB_2nd	e6rkwD3	A: a+b complex topology	X: DNA gyrase subunit B insertion domain (From Topology)	H: DNA gyrase subunit B insertion domain (From Topology)	T: DNA gyrase subunit B insertion domain	F: gyrB_2nd	ECOD (1.6)
D	DNA_gyraseB_C	e6rkwD4	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
C [auth B]	DNA_gyraseB	e6rkwB2	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 [auth B]	HATPase_c_1	e6rkwB1	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 [auth B]	gyrB_1st_1	e6rkwB5	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	ECOD (1.6)
C [auth B]	gyrB_2nd	e6rkwB3	A: a+b complex topology	X: DNA gyrase subunit B insertion domain (From Topology)	H: DNA gyrase subunit B insertion domain (From Topology)	T: DNA gyrase subunit B insertion domain	F: gyrB_2nd	ECOD (1.6)
C [auth B]	DNA_gyraseB_C	e6rkwB4	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
A	DNA_gyraseA_C	e6rkwA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-pinwheel (From Topology)	T: beta-pinwheel	F: DNA_gyraseA_C	ECOD (1.6)
A	DNA_topoisoIV_1st	e6rkwA4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
A	DNA_topoisoIV_3rd	e6rkwA2	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	e6rkwA3	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 [auth C]	DNA_gyraseA_C	e6rkwC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-pinwheel (From Topology)	T: beta-pinwheel	F: DNA_gyraseA_C	ECOD (1.6)
B [auth C]	DNA_topoisoIV_1st	e6rkwC4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
B [auth C]	DNA_topoisoIV_3rd	e6rkwC2	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)
B [auth C]	DNA_topoisoIV_2nd_1	e6rkwC3	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B], 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 [auth B], D	PF00986	DNA gyrase B subunit, carboxyl terminus (DNA_gyraseB_C)	DNA gyrase B subunit, carboxyl terminus	-	Family
C [auth B], D	PF18053	DNA gyrase B subunit insert domain (GyrB_insert)	DNA gyrase B subunit insert domain	This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communica ...	This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains [1].	Domain
C [auth B], 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
C [auth B], D	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family
C [auth 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
A, B [auth C]	PF03989	DNA gyrase C-terminal domain, beta-propeller (DNA_gyraseA_C)	DNA gyrase C-terminal domain, beta-propeller	-	Repeat
A, B [auth C]	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
G, H	DNA (62-MER)	-	-	-
E [auth F], F [auth E]	DNA (58-MER)	-	-	-
C [auth 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 anion 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 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 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity DNA negative supercoiling activity DNA topoisomerase activity macromolecular conformation isomerase 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 cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process chromosome organization 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 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 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex
A, B [auth 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 anion 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 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 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity DNA negative supercoiling activity DNA topoisomerase activity macromolecular conformation isomerase 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 cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process chromosome organization 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 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 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 regulation of cellular process negative regulation of biological process regulation of primary metabolic process negative regulation of DNA-templated DNA replication negative regulation of cellular process 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	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

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