Crystal structure of gyrase bound to its inhibitor YacG


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
KSCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain) 8043119 3000068 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain) 8043119 3000068 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
LYacGe4tmaL1 A: alpha arraysX: avirulence protein AvrPiz-t homologsH: avirulence protein AvrPiz-t homologsT: avirulence protein AvrPiz-t homologsF: YacGECOD (v295.2)
KAbhydrolase_1e4tmaK1 A: alpha arraysX: alpha/beta-HydrolasesH: alpha/beta-HydrolasesT: alpha/beta-HydrolasesF: Abhydrolase_1ECOD (v295.2)
JAminotran_4e4tmaJ1 A: alpha arraysX: Immunoglobulin-like beta-sandwichH: a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymesT: a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymesF: Aminotran_4ECOD (v295.2)
IAcetyltransf_16e4tmaI1 A: alpha arraysX: Alpha-beta plaitsH: HTHT: winged helix domainF: Acetyltransf_16ECOD (v295.2)
HORC2e4tmaH1 A: alpha arraysX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: ORC2ECOD (v295.2)
FGlyoxalase_5e4tmaF1 A: alpha arraysX: POZ domainH: POZ domainT: POZ domainF: Glyoxalase_5ECOD (v295.2)
DORC2e4tmaD1 A: alpha arraysX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: ORC2ECOD (v295.2)
Be4tmaB1 A: alpha arraysX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF:ECOD (v295.2)
GAbhydrolase_1e4tmaG1 A: alpha arraysX: alpha/beta-HydrolasesH: alpha/beta-HydrolasesT: alpha/beta-HydrolasesF: Abhydrolase_1ECOD (v295.2)
EAbhydrolase_1e4tmaE1 A: alpha arraysX: alpha/beta-HydrolasesH: alpha/beta-HydrolasesT: alpha/beta-HydrolasesF: Abhydrolase_1ECOD (v295.2)
CCRISPR_Cse2e4tmaC1 A: alpha arraysX: RuvA-CH: post-HMGL domain-likeT: post-HMGL domain-likeF: CRISPR_Cse2ECOD (v295.2)
AAminotran_4e4tmaA1 A: alpha arraysX: Immunoglobulin-like beta-sandwichH: a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymesT: a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymesF: Aminotran_4ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
L3.30.50.10 Alpha Beta 2-Layer Sandwich Erythroid Transcription Factor GATA-1 Chain ACATH (4.3.0)
K3.30.50.10 Alpha Beta 2-Layer Sandwich Erythroid Transcription Factor GATA-1 Chain ACATH (4.3.0)
J3.30.50.10 Alpha Beta 2-Layer Sandwich Erythroid Transcription Factor GATA-1 Chain ACATH (4.3.0)
I3.30.50.10 Alpha Beta 2-Layer Sandwich Erythroid Transcription Factor GATA-1 Chain ACATH (4.3.0)
H3.40.50.670 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (utative)
F3.30.300.370 Alpha Beta 2-Layer Sandwich GMP Synthetase Chain A, domain 3CATH (utative)
F3.10.20.690 Alpha Beta Roll Ubiquitin-like (UB roll) CATH (utative)
F3.40.50.670 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (utative)
D3.40.50.670 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (utative)
B3.30.300.370 Alpha Beta 2-Layer Sandwich GMP Synthetase Chain A, domain 3CATH (utative)
B3.10.20.690 Alpha Beta Roll Ubiquitin-like (UB roll) CATH (utative)
B3.40.50.670 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (utative)
G3.90.199.10 Alpha Beta Alpha-Beta Complex Topoisomerase II domain 5CATH (4.3.0)
G1.10.268.10 Mainly Alpha Orthogonal Bundle Topoisomerase domain 3CATH (4.3.0)
E3.90.199.10 Alpha Beta Alpha-Beta Complex Topoisomerase II domain 5CATH (4.3.0)
E1.10.268.10 Mainly Alpha Orthogonal Bundle Topoisomerase domain 3CATH (4.3.0)
C3.90.199.10 Alpha Beta Alpha-Beta Complex Topoisomerase II domain 5CATH (4.3.0)
C1.10.268.10 Mainly Alpha Orthogonal Bundle Topoisomerase domain 3CATH (4.3.0)
A3.90.199.10 Alpha Beta Alpha-Beta Complex Topoisomerase II domain 5CATH (4.3.0)
A1.10.268.10 Mainly Alpha Orthogonal Bundle Topoisomerase domain 3CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I, J, K, L
PF03884DNA gyrase inhibitor YacG (YacG)DNA gyrase inhibitor YacGYacG 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
B, D, F, H
PF00986DNA gyrase B subunit, carboxyl terminus (DNA_gyraseB_C)DNA gyrase B subunit, carboxyl terminus- Family
B, D, F, H
PF18053DNA gyrase B subunit insert domain (GyrB_insert)DNA gyrase B subunit insert domainThis is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communica ...This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains [1].
Domain
B, D, F, H
PF01751Toprim domain (Toprim)Toprim domain- Family
B, D, F, H
PF21249GyrB, hook (GyrB_hook)GyrB, hookThis entry represents the N-terminal section of the 'Toprim hook' as described in [1], which is localised between the Toprim (Pfam:PF01751) and the insert (Pfam:PF18053) domains [1-3]. The C-terminal section of the hook is included in (Pfam:PF00986). ...This entry represents the N-terminal section of the 'Toprim hook' as described in [1], which is localised between the Toprim (Pfam:PF01751) and the insert (Pfam:PF18053) domains [1-3]. The C-terminal section of the hook is included in (Pfam:PF00986). The hook is flexible towards the Toprim domain.
Domain
A, C, E, G
PF00521DNA gyrase/topoisomerase IV, subunit A (DNA_topoisoIV)DNA gyrase/topoisomerase IV, subunit AThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I, J, K, L
DNA gyrase inhibitor YacG -
B, D, F, H
DNA gyrase subunit B
A, C, E, G
DNA gyrase subunit A

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I, J, K, L
IPR005584DNA gyrase inhibitor YacGFamily
I, J, K, L
IPR013088Zinc finger, NHR/GATA-typeHomologous Superfamily
B, D, F, H
IPR011557DNA gyrase, subunit BFamily
B, D, F, H
IPR018522DNA topoisomerase, type IIA, conserved siteConserved Site
B, D, F, H
IPR013506DNA topoisomerase, type IIA, subunit B, domain 2Domain
B, D, F, H
IPR049353DNA gyrase subunit B, hookDomain
B, D, F, H
IPR013760DNA topoisomerase, type IIA-like domain superfamilyHomologous Superfamily
B, D, F, H
IPR036890Histidine kinase/HSP90-like ATPase superfamilyHomologous Superfamily
B, D, F, H
IPR006171TOPRIM domainDomain
B, D, F, H
IPR000565DNA topoisomerase, type IIA, subunit BFamily
B, D, F, H
IPR003594Histidine kinase/HSP90-like ATPase domainDomain
B, D, F, H
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
B, D, F, H
IPR001241DNA topoisomerase, type IIAFamily
B, D, F, H
IPR002288DNA gyrase B subunit, C-terminalDomain
B, D, F, H
IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
B, D, F, H
IPR034160DNA gyrase subunit B, TOPRIM domainDomain
B, D, F, H
IPR041423DNA gyrase subunit B insert domainDomain
B, D, F, H
IPR013759DNA topoisomerase, type IIA, subunit B, C-terminalHomologous Superfamily
A, C, E, G
IPR035516DNA gyrase/topoisomerase IV, subunit A, C-terminalHomologous Superfamily
A, C, E, G
IPR050220Type II DNA TopoisomerasesFamily
A, C, E, G
IPR013760DNA topoisomerase, type IIA-like domain superfamilyHomologous Superfamily
A, C, E, G
IPR013758DNA topoisomerase, type IIA, domain A, alpha-betaHomologous Superfamily
A, C, E, G
IPR006691DNA gyrase/topoisomerase IV, subunit A, C-terminal repeatRepeat
A, C, E, G
IPR013757DNA topoisomerase, type IIA, alpha-helical domain superfamilyHomologous Superfamily
A, C, E, G
IPR005743DNA gyrase, subunit AFamily
A, C, E, G
IPR002205DNA topoisomerase, type IIA, domain ADomain