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- EMDB-19782: M. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403 -

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Basic information

Entry
Database: EMDB / ID: EMD-19782
TitleM. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403
Map data
Sample
  • Complex: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403
    • Complex: DNA gyrase
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: DNA
      • DNA: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')
      • DNA: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')
  • Ligand: 6-[[2-[1-(6-methoxy-1,5-naphthyridin-4-yl)-1,2,3-triazol-4-yl]ethylamino]methyl]-4H-1,4-benzothiazin-3-one
KeywordsMycobacterium tuberculosis / DNA gyrase / Novel Bacterial Topoisomerase II Inhibitors / antibiotic resistance / structure-activity relation / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus ...DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / EF-hand calcium-binding domain. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGedeon A / Yab E / Dinut A / Sadowski E / Capton E / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E ...Gedeon A / Yab E / Dinut A / Sadowski E / Capton E / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E / Wehenkel AM / Gubellini F / Mechaly A / Alzari PM / Deprez B / Baulard A / Aubry A / Willand N / Petrella S
Funding support France, 3 items
OrganizationGrant numberCountry
IdEx Universite Paris Cite France
Agence Nationale de la Recherche (ANR)ANR-18-IDEX-0001 France
Fondation pour la Recherche Medicale (FRM)EQU202303016284 France
CitationJournal: iScience / Year: 2024
Title: Molecular mechanism of a triazole-containing inhibitor of DNA gyrase.
Authors: Antoine Gedeon / Emilie Yab / Aurelia Dinut / Elodie Sadowski / Estelle Capton / Aurore Dreneau / Julienne Petit / Bruna Gioia / Catherine Piveteau / Kamel Djaout / Estelle Lecat / Anne ...Authors: Antoine Gedeon / Emilie Yab / Aurelia Dinut / Elodie Sadowski / Estelle Capton / Aurore Dreneau / Julienne Petit / Bruna Gioia / Catherine Piveteau / Kamel Djaout / Estelle Lecat / Anne Marie Wehenkel / Francesca Gubellini / Ariel Mechaly / Pedro M Alzari / Benoît Deprez / Alain Baulard / Alexandra Aubry / Nicolas Willand / Stéphanie Petrella /
Abstract: Antimicrobial resistance remains a persistent and pressing public health concern. Here, we describe the synthesis of original triazole-containing inhibitors targeting the DNA gyrase, a well-validated ...Antimicrobial resistance remains a persistent and pressing public health concern. Here, we describe the synthesis of original triazole-containing inhibitors targeting the DNA gyrase, a well-validated drug target for developing new antibiotics. Our compounds demonstrate potent antibacterial activity against various pathogenic bacteria, with notable potency against (). Moreover, one hit, compound , named BDM71403, was shown to be more potent in than the NBTI of reference, gepotidacin. Mechanistic enzymology assays reveal a competitive interaction of BDM71403 with fluoroquinolones within the gyrase cleavage core. High-resolution cryo-electron microscopy structural analysis provides detailed insights into the ternary complex formed by the gyrase, double-stranded DNA, and either BDM71403 or gepotidacin, providing a rational framework to understand the superior efficacy on . This study highlights the potential of triazole-based scaffolds as promising gyrase inhibitors, offering new avenues for drug development in the fight against antimicrobial resistance.
History
DepositionMar 4, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19782.png

Downloads & links

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Map

FileDownload / File: emd_19782.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.223
Minimum - Maximum-0.4665563 - 1.3601288
Average (Standard dev.)-0.0006629095 (±0.024735129)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_19782_additional_1.map
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Half map: #1

Fileemd_19782_half_map_1.map
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Half map: #2

Fileemd_19782_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403

EntireName: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403
Components
  • Complex: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403
    • Complex: DNA gyrase
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: DNA
      • DNA: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')
      • DNA: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')
  • Ligand: 6-[[2-[1-(6-methoxy-1,5-naphthyridin-4-yl)-1,2,3-triazol-4-yl]ethylamino]methyl]-4H-1,4-benzothiazin-3-one

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Supramolecule #1: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403

SupramoleculeName: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: DNA gyrase

SupramoleculeName: DNA gyrase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DNA gyrase subunit A

MacromoleculeName: DNA gyrase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 92.30418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TDTTLPPDDS LDRIEPVDIE QEMQRSYIDY AMSVIVGRAL PEVRDGLKPV HRRVLYAMFD SGFRPDRSHA KSARSVAETM GNYHPHGDA SIYDSLVRMA QPWSLRYPLV DGQGNFGSPG NDPPAAMRYT EARLTPLAME MLREIDEETV DFIPNYDGRV Q EPTVLPSR ...String:
TDTTLPPDDS LDRIEPVDIE QEMQRSYIDY AMSVIVGRAL PEVRDGLKPV HRRVLYAMFD SGFRPDRSHA KSARSVAETM GNYHPHGDA SIYDSLVRMA QPWSLRYPLV DGQGNFGSPG NDPPAAMRYT EARLTPLAME MLREIDEETV DFIPNYDGRV Q EPTVLPSR FPNLLANGSG GIAVGMATNI PPHNLRELAD AVFWALENHD ADEEETLAAV MGRVKGPDFP TAGLIVGSQG TA DAYKTGR GSIRMRGVVE VEEDSRGRTS LVITELPYQV NHDNFITSIA EQVRDGKLAG ISNIEDQSSD RVGLRIVIEI KRD AVAKVV INNLYKHTQL QTSFGANMLA IVDGVPRTLR LDQLIRYYVD HQLDVIVRRT TYRLRKANER AHILRGLVKA LDAL DEVIA LIRASETVDI ARAGLIELLD IDEIQAQAIL DMQLRRLAAL ERQRIIDDLA KIEAEIADLE DILAKPERQR GIVRD ELAE IVDRHGDDRR TRIIAIDGDV SDEDLIARED VVVTITETGY AKRTKTDLYR SQKRGGKGVQ GAGLKQDDIV AHFFVC STH DLILFFTTQG RVYRAKAYDL PEASRTARGQ HVANLLAFQP EERIAQVIQI RGYTDAPYLV LATRNGLVKK SKLTDFD SN RSGGIVAVNL RDNDELVGAV LCSAGDDLLL VSANGQSIRF SATDEALRPM GRATSGVQGM RFNIDDRLLS LNVVREGT Y LLVATSGGYA KRTAIEEYPV QGRGGKGVLT VMYDRRRGRL VGALIVDDDS ELYAVTSGGG VIRTAARQVR KAGRQTKGV RLMNLGEGDT LLAIARNAEE SGDDNAVDAN GADQTGN

UniProtKB: DNA gyrase subunit A

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Macromolecule #2: DNA gyrase subunit B

MacromoleculeName: DNA gyrase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 74.423953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMVAAQKKK AQDEYGAASI TILEGLEAVR KRPGMYIGST GERGLHHLIW EVVDNAVDEA MAGYATTVNV VLLEDGGVEV ADDGRGIPV ATHASGIPTV DVVMTQLHAG GKFDSDAYAI SGGLHGVGVS VVNALSTRLE VEIKRDGYEW SQVYEKSEPL G LKQGAPTK ...String:
GAMVAAQKKK AQDEYGAASI TILEGLEAVR KRPGMYIGST GERGLHHLIW EVVDNAVDEA MAGYATTVNV VLLEDGGVEV ADDGRGIPV ATHASGIPTV DVVMTQLHAG GKFDSDAYAI SGGLHGVGVS VVNALSTRLE VEIKRDGYEW SQVYEKSEPL G LKQGAPTK KTGSTVRFWA DPAVFETTEY DFETVARRLQ EMAFLNKGLT INLTDERVTQ DEVVDEVVSD VAEAPKSASE RA AESTAPH KVKSRTFHYP GGLVDFVKHI NRTKNAIHSS IVDFSGKGTG HEVEIAMQWN AGYSESVHTF ANTINTHEGG THE EGFRSA LTSVVNKYAK DRKLLKDKDP NLTGDDIREG LAAVISVKVS EPQFEGQTKT KLGNTEVKSF VQKVCNEQLT HWFE ANPTD AKVVVNKAVS SAQARIAARK ARELVRRKSA TDIGGLPGKL ADCRSTDPRK SELYVVEGDS AGGSAKSGRD SMFQA ILPL RGKIINVEKA RIDRVLKNTE VQAIITALGT GIHDEFDIGK LRYHKIVLMA DADVDGQHIS TLLLTLLFRF MRPLIE NGH VFLAQPPLYK LKWQRSDPEF AYSDRERDGL LEAGLKAGKK INKEDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVT LD DAAAADELFS ILMGEDVDAR RSFITRNAKD VRFLDV

UniProtKB: DNA gyrase subunit B

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Macromolecule #3: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')

MacromoleculeName: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.325371 KDa
SequenceString: (DG)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DC)(DG) (DT)(DT)(DG)(DC)(DG)(DC)(DC)(DC)(DG)(DT) (DA)(DG)(DG)(DG)(DC)(DT)(DA)(DC)(DG) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DG) (DC) (DT)(DC)(DT)(DT)(DC)(DT) ...String:
(DG)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DC)(DG) (DT)(DT)(DG)(DC)(DG)(DC)(DC)(DC)(DG)(DT) (DA)(DG)(DG)(DG)(DC)(DT)(DA)(DC)(DG) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DG) (DC) (DT)(DC)(DT)(DT)(DC)(DT)(DT)(DA) (DG)(DT)(DA)(DT)(DT)(DA)(DC)(DC)(DC)(DC) (DT)(DT) (DC)(DC)(DG)(DG)(DT)(DA)(DG) (DG)(DT)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DC) (DA)(DG)(DC) (DG)(DC)(DT)(DT)(DG)(DC) (DG)(DG)(DT)(DC)(DG)(DT)(DT)(DC)(DT)(DG) (DC)(DA)(DT)(DC) (DG)(DG)(DG)(DT)(DC) (DG)(DC)(DG)(DC)(DA)(DG)(DC)(DC)(DG)(DG) (DC)(DG)(DG)(DT)(DA) (DC)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DA)(DT)(DT)(DA)(DC)(DC) (DG)(DG)(DA)(DC)(DG)(DA) (DA)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DT)(DT)

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Macromolecule #4: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')

MacromoleculeName: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.29148 KDa
SequenceString: (DA)(DA)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DT) (DT)(DC)(DG)(DT)(DC)(DC)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DG)(DT)(DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG) (DC) (DT)(DG)(DC)(DG)(DC)(DG) ...String:
(DA)(DA)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DT) (DT)(DC)(DG)(DT)(DC)(DC)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DG)(DT)(DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG) (DC) (DT)(DG)(DC)(DG)(DC)(DG)(DA)(DC) (DC)(DC)(DG)(DA)(DT)(DG)(DC)(DA)(DG)(DA) (DA)(DC) (DG)(DA)(DC)(DC)(DG)(DC)(DA) (DA)(DG)(DC)(DG)(DC)(DT)(DG)(DC)(DG)(DC) (DT)(DC)(DC) (DG)(DA)(DC)(DC)(DT)(DA) (DC)(DC)(DG)(DG)(DA)(DA)(DG)(DG)(DG)(DG) (DT)(DA)(DA)(DT) (DA)(DC)(DT)(DA)(DA) (DG)(DA)(DA)(DG)(DA)(DG)(DC)(DG)(DA)(DA) (DG)(DG)(DC)(DC)(DG) (DC)(DC)(DG)(DT) (DA)(DG)(DC)(DC)(DC)(DT)(DA)(DC)(DG)(DG) (DG)(DC)(DG)(DC)(DA)(DA) (DC)(DG)(DT) (DC)(DC)(DG)(DG)(DT)(DA)(DC)

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Macromolecule #5: 6-[[2-[1-(6-methoxy-1,5-naphthyridin-4-yl)-1,2,3-triazol-4-yl]eth...

MacromoleculeName: 6-[[2-[1-(6-methoxy-1,5-naphthyridin-4-yl)-1,2,3-triazol-4-yl]ethylamino]methyl]-4H-1,4-benzothiazin-3-one
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1H5Q
Molecular weightTheoretical: 447.513 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 987000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8s7o:
M. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403

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