4TMA | pdb_00004tma

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	DNA_topoisoIV_1st	e4tmaA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
A	DNA_topoisoIV_3rd	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: DNA_topoisoIV_3rd	ECOD (1.6)
A	DNA_topoisoIV_2nd_1	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: DNA_topoisoIV_2nd_1	ECOD (1.6)
C	DNA_topoisoIV_1st	e4tmaC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
C	DNA_topoisoIV_3rd	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: DNA_topoisoIV_3rd	ECOD (1.6)
C	DNA_topoisoIV_2nd_1	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: DNA_topoisoIV_2nd_1	ECOD (1.6)
E	DNA_topoisoIV_1st	e4tmaE1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
E	DNA_topoisoIV_3rd	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: DNA_topoisoIV_3rd	ECOD (1.6)
E	DNA_topoisoIV_2nd_1	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: DNA_topoisoIV_2nd_1	ECOD (1.6)
G	DNA_topoisoIV_1st	e4tmaG1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
G	DNA_topoisoIV_3rd	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: DNA_topoisoIV_3rd	ECOD (1.6)
G	DNA_topoisoIV_2nd_1	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: DNA_topoisoIV_2nd_1	ECOD (1.6)
B	gyrB_1st_1	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: gyrB_1st_1	ECOD (1.6)
B	gyrB_2nd	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: gyrB_2nd	ECOD (1.6)
B	DNA_gyraseB_C	e4tmaB3	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	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: gyrB_1st	ECOD (1.6)
D	DNA_gyraseB_C	e4tmaD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
F	gyrB_1st_1	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: gyrB_1st_1	ECOD (1.6)
F	gyrB_2nd	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: gyrB_2nd	ECOD (1.6)
F	DNA_gyraseB_C	e4tmaF2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
H	gyrB_2nd,gyrB_1st_1,gyrB_1st_2	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: gyrB_2nd,gyrB_1st_1,gyrB_1st_2	ECOD (1.6)
H	DNA_gyraseB_C	e4tmaH2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
I	YacG	e4tmaI1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: YacG	ECOD (1.6)
J	YacG	e4tmaJ1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: YacG	ECOD (1.6)
K	YacG	e4tmaK1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: YacG	ECOD (1.6)
L	YacG	e4tmaL1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: YacG	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 (4.3.0)
B	3.10.20.690	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
B	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
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 (4.3.0)
F	3.10.20.690	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
F	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
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 nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid enzyme inhibitor activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ATPase regulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding enzyme regulator activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid enzyme inhibitor activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ATPase regulator activity ATP-dependent activity ATP-dependent activity, acting on DNA molecular function inhibitor activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity catalytic activity, acting on DNA DNA topoisomerase activity molecular function regulator activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) regulator activity ATPase inhibitor activity catalytic activity macromolecular conformation isomerase activity	regulation of cellular 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-