Biomolecular NMR Assignments

, Volume 8, Issue 1, pp 145–148 | Cite as

1H, 13C, and 15N backbone and side-chain chemical shift assignment of the toxin Doc in the unbound state

  • Steven De Gieter
  • Remy Loris
  • Nico A. J. van NulandEmail author
  • Abel Garcia-Pino


Toxin–antitoxin (TA) modules in bacteria are involved in pathogenesis, antibiotic stress response, persister formation and programmed cell death. The toxin Doc, from the phd/doc module, blocks protein synthesis by targeting the translation machinery. Despite a large wealth of biophysical and biochemical data on the regulatory aspects of the operon transcription and role of Doc co-activator and co-repressor, little is still know on the molecular basis of Doc toxicity. Structural information about this toxin is only available for its inhibited state bound to the antitoxin Phd. Here we report the 1H, 15N and 13C backbone and side chain chemical shift assignments of the toxin Doc from of bacteriophage P1 (the model protein from this family of TA modules) in its free state. The BMRB accession number is 18899.


Toxin–antitoxin module Macromolecular complex NMR Doc Bacteriophage P1 



This work received financial support from the VIB, FWO-Vlaanderen, the Onderzoeksfonds of the Vrije Universiteit Brussel (OZR-VUB) and the Hercules Foundation. A.G.P. is a post-doctoral fellow of the FWO-Vlaanderen.


  1. Anantharaman V, Aravind L (2003) New connections in the prokaryotic toxin–antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol 4:R81CrossRefGoogle Scholar
  2. Arbing MA, Handelman SK, Kuzin AP, Verdon G, Wang C, Su M, Rothenbacher FP, Abashidze M, Liu M, Hurley JM et al (2010) Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin–antitoxin systems. Structure 18:996–1010CrossRefGoogle Scholar
  3. Buts L, Lah J, Dao-Thi MH, Wyns L, Loris R (2005) Toxin–antitoxin modules as bacterial metabolic stress managers. Trends Biochem Sci 30:672–679CrossRefGoogle Scholar
  4. De Jonge N, Garcia-Pino A, Buts L, Haesaerts S, Charlier D, Zangger K, Wyns L, De Greve H, Loris R (2009) Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain. Mol Cell 35:154–163CrossRefGoogle Scholar
  5. 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 6:277–293CrossRefGoogle Scholar
  6. Garcia-Pino A, Christensen-Dalsgaard M, Wyns L, Yarmolinsky M, Magnuson RD, Gerdes K, Loris R (2008) Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation. J Biol Chem 283:30821–30827CrossRefGoogle Scholar
  7. Garcia-Pino A, Balasubramanian S, Wyns L, Gazit E, De Greve H, Magnuson RD, Charlier D, van Nuland NA, Loris R (2010) Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity. Cell 142:101–111CrossRefGoogle Scholar
  8. Gerdes K, Christensen SK, Lobner-Olesen A (2005) Prokaryotic toxin–antitoxin stress response loci. Nat Rev Microbiol 3:371–382CrossRefGoogle Scholar
  9. Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278:313–352Google Scholar
  10. Magnuson RD (2007) Hypothetical functions of toxin–antitoxin systems. J Bacteriol 189:6089–6092CrossRefGoogle Scholar
  11. Overgaard M, Borch J, Jorgensen MG, Gerdes K (2008) Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Mol Microbiol 69:841–857CrossRefGoogle Scholar
  12. Pandey DP, Gerdes K (2005) Toxin–antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 33:966–976CrossRefGoogle Scholar
  13. Sattler M, Schleucher J, Griesinger C (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog Nucl Magn Reson Spectrosc 34:93–158CrossRefGoogle Scholar
  14. 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 44:213–223CrossRefGoogle Scholar
  15. Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59:687–696CrossRefGoogle Scholar
  16. Winther KS, Gerdes K (2012) Regulation of enteric vapBC transcription: induction by VapC toxin dimer-breaking. Nucleic Acids Res 40:4347–4357CrossRefGoogle Scholar
  17. Wishart DS, Sykes BD (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171–180CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Steven De Gieter
    • 1
    • 2
  • Remy Loris
    • 1
    • 2
  • Nico A. J. van Nuland
    • 1
    • 2
    Email author
  • Abel Garcia-Pino
    • 1
    • 2
  1. 1.Jean Jeener NMR Centre, Structural Biology BrusselsVrije Universiteit BrusselBrusselBelgium
  2. 2.Molecular Recognition Unit, Department of Structural BiologyVIBBrusselBelgium

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