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Structure paper

TitleCryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex.
Journal, issue, pagesNat Commun, Vol. 10, Issue 1, Page 4935, Year 2019
Publish dateOct 30, 2019
AuthorsArnaud Vanden Broeck / Christophe Lotz / Julio Ortiz / Valérie Lamour /
PubMed AbstractDNA gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, a detailed architecture of ...DNA gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, a detailed architecture of the full-length DNA gyrase from the model organism E. coli is still missing. Herein, we report the complete structure of the E. coli DNA gyrase nucleoprotein complex trapped by the antibiotic gepotidacin, using phase-plate single-particle cryo-electron microscopy. Our data unveil the structural and spatial organization of the functional domains, their connections and the position of the conserved GyrA-box motif. The deconvolution of two states of the DNA-binding/cleavage domain provides a better understanding of the allosteric movements of the enzyme complex. The local atomic resolution in the DNA-bound area reaching up to 3.0 Å enables the identification of the antibiotic density. Altogether, this study paves the way for the cryo-EM determination of gyrase complexes with antibiotics and opens perspectives for targeting conformational intermediates.
External linksNat Commun / PubMed:31666516 / PubMed Central
MethodsEM (single particle)
Resolution4.0 - 6.6 Å
Structure data

4909

6rks

EMDB-4909, PDB-6rks:
E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion
Method: EM (single particle) / Resolution: 4.0 Å

4910

6rku

EMDB-4910, PDB-6rku:
E. coli DNA Gyrase - DNA binding and cleavage domain in State 1
Method: EM (single particle) / Resolution: 4.0 Å

4912

6rkv

EMDB-4912, PDB-6rkv:
E. coli DNA Gyrase - DNA binding and cleavage domain in State 2
Method: EM (single particle) / Resolution: 4.6 Å

4913

6rkw

EMDB-4913, PDB-6rkw:
CryoEM structure of the complete E. coli DNA Gyrase complex bound to a 130 bp DNA duplex
Method: EM (single particle) / Resolution: 6.6 Å

EMDB-4914:
E. coli DNA Gyrase - ATPase & DNA binding and cleavage domains
Method: EM (single particle) / Resolution: 5.9 Å

EMDB-4915:
E. coli DNA Gyrase - CTD & DNA binding and cleavage domain
Method: EM (single particle) / Resolution: 6.3 Å

Chemicals

ChemComp-JHN:
(3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione / antibiotic, inhibitor*YM

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

Source
  • escherichia coli k-12 (bacteria)
  • Escherichia coli O157:H7 str. SS52 (bacteria)
  • escherichia coli (E. coli)
  • escherichia coli (strain k12) (bacteria)
KeywordsISOMERASE / Complex / DNA Gyrase / Inhibitor / DNA BINDING PROTEIN

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