1AB4

59KDA FRAGMENT OF GYRASE A FROM E. COLI

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ab4a_	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	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Type II DNA topoisomerase half-clamp domain-like	8025176	4002825	SCOP2 (2022-06-29)
A	SCOP2 Family	Toprim C-terminal associated domain-like	8055744	4007653	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type II DNA topoisomerase half-clamp domain-like	8037555	3001800	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8055745	3000034	SCOP2 (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	e1ab4A1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
A	DNA_topoisoIV_3rd	e1ab4A2	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	e1ab4A3	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.199.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase II	domain 5	CATH (4.3.0)
A	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00521	DNA gyrase/topoisomerase IV, subunit A (DNA_topoisoIV)	DNA gyrase/topoisomerase IV, subunit A	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	GYRASE 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR035516	DNA gyrase/topoisomerase IV, subunit A, C-terminal	Homologous Superfamily
A	IPR050220	Type II DNA Topoisomerases	Family
A	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A	IPR006691	DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat	Repeat
A	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A	IPR005743	DNA gyrase, subunit A	Family
A	IPR002205	DNA topoisomerase, type IIA, domain A	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	DNA topoisomerase (ATP-hydrolysing) M-CSA #745	E. coli DNA gyrase is a member of the family of type II topoisomerases, which change the topology of DNA by cleaving both the phosphodiester backbones of the double-stranded DNA, transporting another double-stranded segement through the enzyme bridged gap, and then religating the DNA. Therefore, E. coli DNA gyrase catalyses the relaxation of negatively supercoiled DNA, and is uniquely also able to introduce negative supercoils into DNA at the expense of ATP hydrolysis. By introducing a transient break into the DNA substrate, pasing another piece of DNA though the gap and releasing it, the enzyme relieves topological contraints caused by replication and transcription complexes moving along the DNA. The enzyme consists of 2 GyrA and 2 GyrB subunits. The catalytic domain is found on the GyrA subunit, whilst the ATP hydrolysis site is found on GyrB.	Defined by 3 residues: ARG:A-3 [auth A-32]HIS:A-49 [auth A-78]TYR:A_2-93 [auth A_2-122] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.99.1.3 (PDB Primary Data) Search M-CSA Motif + EC 5.99.1.3 EC: 5.6.2.2 (UniProt) Search M-CSA Motif + EC 5.6.2.2

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.