Abstract
Bacterial DNA topoisomerases are important drug targets due to their importance in DNA replication and low homology to human topoisomerases. The N-terminal 24 kDa region of E. coli topoisomerase IV E subunit (eParE) contains the ATP binding pocket. Structure—based drug discovery has been proven to be an efficient way to develop potent ATP competitive inhibitors against ParEs. NMR spectroscopy is a powerful tool to understand protein and inhibitor interactions in solution. In this study, we report the backbone assignment for the N-terminal domain of E. coli ParE. The secondary structural information and the assignment will aid in structure—based antibacterial agents development targeting eParE.
Similar content being viewed by others
References
Basarab GS, Manchester JI, Bist S, Boriack-Sjodin PA, Dangel B, Illingworth R, Sherer BA, Sriram S, Uria-Nickelsen M, Eakin AE (2013) Fragment-to-hit-to-lead discovery of a novel pyridylurea scaffold of ATP competitive dual targeting type II topoisomerase inhibiting antibacterial agents. J Med Chem 56:8712–8735
Bellanda M, Peggion E, Otting G, Weigelt J, Perdona E, Domenici E, Marchioro C, Mammi S (2002) Backbone 1H, 13C and 15N resonance assignment of the N-terminal 24 kDa fragment of the gyrase B subunit from E. coli. J Biomol NMR 22:369–370
Bellon S, Parsons JD, Wei Y, Hayakawa K, Swenson LL, Charifson PS, Lippke JA, Aldape R, Gross CH (2004) Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase. Antimicrob Agents Chemother 48:1856–1864
Chen G-Y, Ng FM, Tan YW, Poulsen A, Seetoh W, Lin G, Kang C, Then SW, Ahmad NH, Wong YL, Ng HQ, Chia CSB, Lau QY, Hill J, Hung AW, Keller TH (2015) Application of fragment-based drug discovery against DNA gyrase B. ChemPlusChem 80:1250–1254
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293
Fu G, Wu J, Liu W, Zhu D, Hu Y, Deng J, Zhang XE, Bi L, Wang DC (2009) Crystal structure of DNA gyrase B′ domain sheds lights on the mechanism for T-segment navigation. Nucleic Acids Res 37:5908–5916
Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278:313–352
Klaus W, Ross A, Gsell B, Senn H (2000) Backbone resonance assignment of the N-terminal 24 kDa fragment of the gyrase B subunit from S. aureus complexed with novobiocin. J Biomol NMR 16:357–358
Li Y, Wong YX, Poh ZY, Wong YL, Lee MY, Ng HQ, Liu B, Hung AW, Cherian J, Hill J, Keller TH, Kang C (2015) NMR structural characterization of the N-terminal active domain of the gyrase B subunit from Pseudomonas aeruginosa and its complex with an inhibitor. FEBS Lett 589(19):2683–2689
Miller JR, Waldrop GL (2010) Discovery of novel antibacterials. Expert Opin Drug Discov 5:145–154
Pervushin K, Ono A, Fernandez C, Szyperski T, Kainosho M, Wuthrich K (1998) NMR scalar couplings across Watson–Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Proc Natl Acad Sci USA 95:14147–14151
Reece RJ, Maxwell A (1991) DNA gyrase: structure and function. Crit Rev Biochem Mol Biol 26:335–375
Salzmann M, Pervushin K, Wider G, Senn H, Wuthrich K (1998) TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc Natl Acad Sci USA 95:13585–13590
Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223
Stanger FV, Dehio C, Schirmer T (2014) Structure of the N-terminal Gyrase B fragment in complex with ADPPi reveals rigid-body motion induced by ATP hydrolysis. PLoS One 9:e107289
Tari LW, Li X, Trzoss M, Bensen DC, Chen Z, Lam T, Zhang J, Lee SJ, Hough G, Phillipson D, Akers-Rodriguez S, Cunningham ML, Kwan BP, Nelson KJ, Castellano A, Locke JB, Brown-Driver V, Murphy TM, Ong VS, Pillar CM, Shinabarger DL, Nix J, Lightstone FC, Wong SE, Nguyen TB, Shaw KJ, Finn J (2013) Tricyclic GyrB/ParE (TriBE) inhibitors: a new class of broad-spectrum dual-targeting antibacterial agents. PLoS One 8:e84409
Tsai FT, Singh OM, Skarzynski T, Wonacott AJ, Weston S, Tucker A, Pauptit RA, Breeze AL, Poyser JP, O’Brien R, Ladbury JE, Wigley DB (1997) The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin. Proteins 28:41–52
Tse-Dinh YC (2009) Bacterial topoisomerase I as a target for discovery of antibacterial compounds. Nucleic Acids Res 37:731–737
Wigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G (1991) Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351:624–629
Acknowledgments
We appreciate financial support from A*STAR JCO grants (1331A028, 1231B015). We also thank Prof Ho Sup Yoon and Dr. Hong Ye from Nanyang Technological University for the NMR experiments.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Li, Y., Wong, Y.L., Lee, M.Y. et al. Backbone assignment of the N-terminal 24-kDa fragment of Escherichia coli topoisomerase IV ParE subunit. Biomol NMR Assign 10, 135–138 (2016). https://doi.org/10.1007/s12104-015-9652-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12104-015-9652-9