Annotations: 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)
K	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8043119	3000068	SCOP2B (2022-06-29)
J	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)
L	YacG	e4tmaL1	A: a/b three-layered sandwiches	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T: avirulence protein AvrPiz-t homologs	F: YacG	ECOD (v294.1)
K	Abhydrolase_1	e4tmaK1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: Abhydrolase_1	ECOD (v294.1)
J	Ribosomal_S8e	e4tmaJ1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.1)
I	Acetyltransf_16	e4tmaI1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Acetyltransf_16	ECOD (v294.1)
H	HLH	e4tmaH1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: HLH	ECOD (v294.1)
F	Glyoxalase_5	e4tmaF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Glyoxalase_5	ECOD (v294.1)
D	ORC2	e4tmaD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ORC2	ECOD (v294.1)
B	YadA_stalk	e4tmaB1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: YadA_stalk	ECOD (v294.1)
G	Abhydrolase_1	e4tmaG1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: Abhydrolase_1	ECOD (v294.1)
E	Abhydrolase_1	e4tmaE1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: Abhydrolase_1	ECOD (v294.1)
C	Acetyltransf_9	e4tmaC1	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Acetyltransf_9	ECOD (v294.1)
A	Ribosomal_S8e	e4tmaA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	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)
J	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
I	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
H	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)
D	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
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)
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)
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)
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)
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)

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
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	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	-
B, D, F, H	DNA gyrase subunit B	-	-	-
A, C, E, G	DNA gyrase subunit A	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I, J, K, L	IPR005584	DNA gyrase inhibitor YacG	Family
I, J, K, L	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily

4TMA | pdb_00004tma

Crystal structure of gyrase bound to its inhibitor YacG

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage