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CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage.

<div class='caption-title'>Proposed mechanism of supercoiling of DNA by gyrase.</div>
<div class='caption-title'>Cryo-EM volumes of the Tetrahedral and Dihedral complexes.</div>
<div class='caption-title'>The Dihedral complexes do not require antibiotics or cross-linkers for assembly.</div>
Soczek KM, Grant T, Rosenthal PB, Mondragón A
OpenAccess logo Elife 7 (2018)
Related entries: 6n1p, 6n1r

Cited: 15 times
EuropePMC logo PMID: 30457554

Abstract

Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.2 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.

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  1. Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly. He J, Lin P, Chen J, Cao H, Huang SY. Nat Commun 13 4066 (2022)


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  1. Structure-Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System. Brieba LG. Plants (Basel) 8 E533 (2019)
  2. DNA Gyrase as a Target for Quinolones. Spencer AC, Panda SS. Biomedicines 11 371 (2023)
  3. Natural and Synthetic Oligoarylamides: Privileged Structures for Medical Applications. Seedorf T, Kirschning A, Solga D. Chemistry 27 7321-7339 (2021)
  4. What's on the Other Side of the Gate: A Structural Perspective on DNA Gate Opening of Type IA and IIA DNA Topoisomerases. Vidmar V, Vayssières M, Lamour V. Int J Mol Sci 24 3986 (2023)

Articles citing this publication (10)

  1. Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Vanden Broeck A, Lotz C, Ortiz J, Lamour V. Nat Commun 10 4935 (2019)
  2. Structural basis for allosteric regulation of Human Topoisomerase IIα. Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V. Nat Commun 12 2962 (2021)
  3. Protein Side-Chain-DNA Contacts Probed by Fast Magic-Angle Spinning NMR. Lacabanne D, Boudet J, Malär AA, Wu P, Cadalbert R, Salmon L, Allain FH, Meier BH, Wiegand T. J Phys Chem B 124 11089-11097 (2020)
  4. Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin. Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stępień Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Süssmuth RD, Ghilarov D. Nat Catal 6 52-67 (2023)
  5. Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea. Villain P, Catchpole R, Forterre P, Oberto J, da Cunha V, Basta T. Mol Biol Evol 39 msac155 (2022)
  6. Basic residues at the C-gate of DNA gyrase are involved in DNA supercoiling. Smith EM, Mondragón A. J Biol Chem 297 101000 (2021)
  7. A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase. Chang CM, Wang SC, Wang CH, Pang AH, Yang CH, Chang YK, Wu WJ, Tsai MD. Commun Chem 7 45 (2024)
  8. Cryo-EM structures of African swine fever virus topoisomerase. Zhao Y, Kuang W, An Q, Li J, Wang Y, Deng Z. mBio 14 e0122823 (2023)
  9. Escherichia coli GyrA Tower Domain Interacts with QnrB1 Loop B and Plays an Important Role in QnrB1 Protection from Quinolone Inhibition. Chen C, Wang Y, Nakaminami H, Kim ES, Jacoby GA, Hooper DC. Antimicrob Agents Chemother 65 e0040221 (2021)
  10. Intracellular Experimental Evolution of Francisella tularensis Subsp. holarctica Live Vaccine Strain (LVS) to Antimicrobial Resistance. Mehta HH, Song X, Shamoo Y. ACS Infect Dis 9 308-321 (2023)


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