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The structure of a resuscitation-promoting factor domain from Mycobacterium tuberculosis shows homology to lysozymes

Nature Structural & Molecular Biology volume 12, pages 270–273 (2005)Cite this article

Abstract

Resuscitation-promoting factor (RPF) proteins reactivate stationary-phase cultures of (G+C)-rich Gram-positive bacteria including the causative agent of tuberculosis, Mycobacterium tuberculosis. We report the solution structure of the RPF domain from M. tuberculosis Rv1009 (RpfB) solved by heteronuclear multidimensional NMR. Structural homology with various glycoside hydrolases suggested that RpfB cleaved oligosaccharides. Biochemical studies indicate that a conserved active site glutamate is important for resuscitation activity. These data, as well as the presence of a clear binding pocket for a large molecule, indicate that oligosaccharide cleavage is probably the signal for revival from dormancy.

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Figure 1: Solution structure and oligosaccharide binding to RpfBc.
Figure 2: Comparison of RpfBc with other glycoside hydrolases.
Figure 3: Resuscitation activity assays of recombinant M. tuberculosis RpfC and RpfC E80A.

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References

  1. Tufariello, J.M., Chan, J. & Flynn, J.L. Latent tuberculosis: mechanisms of host and bacillus that contribute to persistent infection. Lancet Infect. Dis. 3, 578–590 (2003).

    Article  CAS  Google Scholar 

  2. Mukamolova, G.V., Kaprelyants, A.S., Young, D.I., Young, M. & Kell, D.B. A bacterial cytokine. Proc. Natl. Acad. Sci. USA 95, 8916–8921 (1998).

    Article  CAS  Google Scholar 

  3. Mukamolova, G.V. et al. A family of autocrine growth factors in Mycobacterium tuberculosis. Mol. Microbiol. 46, 623–635 (2002).

    Article  CAS  Google Scholar 

  4. Cohen-Gonsaud, M. et al. Resuscitation-promoting factors possess a lysozyme-like domain. Trends Biochem. Sci. 29, 7–10 (2004).

    Article  CAS  Google Scholar 

  5. Cohen-Gonsaud, M. et al. 1H, 15N and 13C chemical shift assignments of the Resuscitation Promoting Factor domain of Rv1009 from Mycobacterium tuberculosis. J. Biomol. NMR 30, 373–374 (2004).

    Article  CAS  Google Scholar 

  6. Mukamolova, G.V. et al. The rpf gene of Micrococcus luteus encodes an essential secreted growth factor. Mol. Microbiol. 46, 611–621 (2002).

    Article  CAS  Google Scholar 

  7. Holm, L. & Sander, C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26, 316–319 (1998).

    Article  CAS  Google Scholar 

  8. Song, H., Inaka, K., Maenaka, K. & Matsushima, M. Structural changes of active site cleft and different saccharide binding modes in human lysozyme co-crystallized with hexa-N-acetyl-chitohexaose at pH 4.0. J. Mol. Biol. 244, 522–540 (1994).

    Article  CAS  Google Scholar 

  9. van Asselt, E.J. et al. Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand. Structure Fold. Des. 7, 1167–1180 (1999).

    Article  CAS  Google Scholar 

  10. van Asselt, E.J., Thunnissen, A.M. & Dijkstra, B.W. High resolution crystal structures of the Escherichia coli lytic transglycosylase Slt70 and its complex with a peptidoglycan fragment. J. Mol. Biol. 291, 877–898 (1999).

    Article  CAS  Google Scholar 

  11. Hartmann, M. et al. The glycosylated cell surface protein Rpf2, containing a resuscitation-promoting factor motif, is involved in intercellular communication of Corynebacterium glutamicum. Arch. Microbiol. 182, 299–312 (2004).

    Article  CAS  Google Scholar 

  12. Raymond J.B., Mahapatra, S., Crick, D.C. & Pavelka, M.S. Jr. Identification of the namH gene, encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan. J. Biol. Chem. 280, 326–333 (2005).

    Article  CAS  Google Scholar 

  13. Pons, J.L., Malliavin, T.E. & Delsuc, M.A. Gifa V 4: a complete package for NMR data set processing. J. Biomol. NMR 8, 445–452 (1996).

    Article  CAS  Google Scholar 

  14. Johnson, B.A. & R.A., B. NMRView: a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603–614 (1994).

    Article  CAS  Google Scholar 

  15. Cornilescu, G., Delaglio, F. & Bax, A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289–302 (1999).

    Article  CAS  Google Scholar 

  16. Sharma, D. & Rajarathnam, K. 13C NMR chemical shifts can predict disulfide bond formation. J. Biomol. NMR 18, 165–171 (2000).

    Article  CAS  Google Scholar 

  17. Linge, J.P., O'Donoghue, S.I. & Nilges, M. Automated assignment of ambiguous nuclear overhauser effects with ARIA. Methods Enzymol. 339, 71–90 (2001).

    Article  CAS  Google Scholar 

  18. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr. D 54, 905–921 (1998).

    Article  CAS  Google Scholar 

  19. Laskowski, R.A., MacArthur, M.W., Hutchinson, E.G. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  20. Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–55 (1996).

    Article  CAS  Google Scholar 

  21. Lees, J.G., Smith, B., Wien, F., Miles, A. and Wallace, B.A. CDTool: an integrated software package for circular dichroism spectroscopic data processing, analysis, and archiving. Anal. Biochem. 332, 285–289 (2004).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by European Union grant QLK2-2001-02018 (M.C-G. and N.H.K.). NMR experiments were recorded and analyzed using the facilities of the structural biology platform RIO (Centre de Biochimie Structurale, Montpellier, France). We thank B. Sarra for help with CD.

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Authors and Affiliations

  1. School of Crystallography and Institute for Structural Molecular Biology, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK

    Martin Cohen-Gonsaud, Claire Bagnéris & Nicholas H Keep

  2. Centre de Biochimie Structurale, CNRS UMR5048, INSERM UMR554, UMI, Faculté de Pharmacie, BP 14491, 15 Avenue Charles Flahault, Montpellier, 34093 Cedex 5, France

    Philippe Barthe & Christian Roumestand

  3. Division of Microbial Diseases, Eastman Dental Institute, University College London, 256 Gray's Inn Road, London, WC1X 8LD, UK

    Brian Henderson

  4. Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK

    John Ward

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  1. Martin Cohen-Gonsaud
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Correspondence to Nicholas H Keep.

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Supplementary information

Supplementary Fig. 1

Chemical shift change against residue. (PDF 1496 kb)

Supplementary Fig. 2

R.m.s. deviation on addition of (NAG)4 to lysozyme by residue. (PDF 928 kb)

Supplementary Fig. 3

CD spectra of recombinant unmutated and E80A mutant protein. (PDF 278 kb)

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Cohen-Gonsaud, M., Barthe, P., Bagnéris, C. et al. The structure of a resuscitation-promoting factor domain from Mycobacterium tuberculosis shows homology to lysozymes. Nat Struct Mol Biol 12, 270–273 (2005). https://doi.org/10.1038/nsmb905

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