7UGW | pdb_00007ugw

M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Toprim domain-like	8090033	3000737	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Toprim domain-like	8090033	3000737	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	gyrB_1st_3	e7ugwD2	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_3	ECOD (1.6)
D	DNA_gyraseB_C	e7ugwD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
B	gyrB_1st_3	e7ugwB1	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_3	ECOD (1.6)
B	DNA_gyraseB_C	e7ugwB2	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	DNA_topoisoIV_1st	e7ugwC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
C	DNA_topoisoIV_3rd	e7ugwC3	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_1st,DNA_topoisoIV_2nd_1	e7ugwC2	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_1st,DNA_topoisoIV_2nd_1	ECOD (1.6)
A	DNA_topoisoIV_1st	e7ugwA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
A	DNA_topoisoIV_3rd	e7ugwA2	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_1st,DNA_topoisoIV_2nd_1	e7ugwA3	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_1st,DNA_topoisoIV_2nd_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00986	DNA gyrase B subunit, carboxyl terminus (DNA_gyraseB_C)	DNA gyrase B subunit, carboxyl terminus	-	Family
B, D	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family
A, 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
F [auth E]	evybactin	-	-	-
E [auth V]	DNA (46-MER)	-	-	-
B, D	DNA gyrase subunit B	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide 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	response to stimulus response to chemical 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 response to stimulus response to chemical 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	cell periphery cellular anatomical structure plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome
A, C	DNA gyrase subunit A	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide 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 pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	response to stimulus response to chemical 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 response to stimulus response to chemical 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	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall cytoplasm intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall cytoplasm 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
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	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	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	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
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	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A, C	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A, C	IPR005743	DNA gyrase, subunit A	Family
A, C	IPR006691	DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat	Repeat
A, C	IPR002205	DNA topoisomerase, type IIA, domain A	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
F [auth E]	A1AZ2	Parent Component: HIS
F [auth E]	DAR
F [auth E]	DSN	RESID: AA0195 , AA0624 PSI-MOD : D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987
F [auth E]	IAS	RESID: AA0195 , AA0624
F [auth E]	NLF	Parent Component: TRP RESID: AA0195 , AA0624