4TMA

Crystal structure of gyrase bound to its inhibitor YacG

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8043119	3000068	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8043119	3000068	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	PF00521	e4tmaA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF00521	ECOD (1.6)
A	PF00521	e4tmaA3	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: PF00521	ECOD (1.6)
A	PF00521	e4tmaA2	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: PF00521	ECOD (1.6)
C	PF00521	e4tmaC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF00521	ECOD (1.6)
C	PF00521	e4tmaC2	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: PF00521	ECOD (1.6)
C	PF00521	e4tmaC3	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: PF00521	ECOD (1.6)
E	PF00521	e4tmaE1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF00521	ECOD (1.6)
E	PF00521	e4tmaE3	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: PF00521	ECOD (1.6)
E	PF00521	e4tmaE2	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: PF00521	ECOD (1.6)
G	PF00521	e4tmaG1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF00521	ECOD (1.6)
G	PF00521	e4tmaG3	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: PF00521	ECOD (1.6)
G	PF00521	e4tmaG2	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: PF00521	ECOD (1.6)
B	PF21249	e4tmaB1	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: PF21249	ECOD (1.6)
B	PF18053	e4tmaB2	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: PF18053	ECOD (1.6)
B	PF00986,PF01751	e4tmaB3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PF00986,PF01751	ECOD (1.6)
D	PF18053,PF21249	e4tmaD2	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: PF18053,PF21249	ECOD (1.6)
D	PF00986,PF01751	e4tmaD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PF00986,PF01751	ECOD (1.6)
F	PF21249	e4tmaF1	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: PF21249	ECOD (1.6)
F	PF18053	e4tmaF3	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: PF18053	ECOD (1.6)
F	PF00986,PF01751	e4tmaF2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PF00986,PF01751	ECOD (1.6)
H	PF18053	e4tmaH1	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: PF18053	ECOD (1.6)
H	PF00986,PF01751	e4tmaH2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: PF00986,PF01751	ECOD (1.6)
I	PF03884	e4tmaI1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: PF03884	ECOD (1.6)
J	PF03884	e4tmaJ1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: PF03884	ECOD (1.6)
K	PF03884	e4tmaK1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: PF03884	ECOD (1.6)
L	PF03884	e4tmaL1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: PF03884	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	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)
C	3.90.199.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase II	domain 5	CATH (4.3.0)
C	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)
E	3.90.199.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase II	domain 5	CATH (4.3.0)
E	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)
G	3.90.199.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase II	domain 5	CATH (4.3.0)
G	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)
B	3.30.300.370	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (utative)
B	3.10.20.690	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
B	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
D	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
F	3.30.300.370	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (utative)
F	3.10.20.690	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
F	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
H	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
I	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
J	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
K	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
L	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I, J, K, L	PF03884	DNA gyrase inhibitor YacG (YacG)	DNA gyrase inhibitor YacG	YacG inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. It acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase [1]. YacG has been shown to bind zinc and ...	YacG inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. It acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase [1]. YacG has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins [2]. The conserved four cysteine motif in this protein (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	DNA gyrase subunit A	-	-	-
B, D, F, H	DNA gyrase subunit B	-	-	-
I, J, K, L	DNA gyrase inhibitor YacG	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding enzyme regulator activity molecular function inhibitor activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity molecular function regulator activity enzyme inhibitor activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) regulator activity ATPase inhibitor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding enzyme regulator activity molecular function inhibitor activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity molecular function regulator activity enzyme inhibitor activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) regulator activity ATPase inhibitor activity ATPase regulator activity	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-