Article

You have full text access to this OnlineOpen article

The crystal structure of the mycobacterium tuberculosis Rv3019c-Rv3020c ESX complex reveals a domain-swapped heterotetramer

  1. Mark A. Arbing1,‡,
  2. Markus Kaufmann1,†,‡,
  3. Tung Phan1,
  4. Sum Chan1,
  5. Duilio Cascio1,
  6. David Eisenberg1,2,3,*

Article first published online: 13 JUL 2010

DOI: 10.1002/pro.451

Issue

Protein Science

Protein Science

Volume 19, Issue 9, pages 1692–1703, September 2010

Additional Information

How to Cite

Arbing, M. A., Kaufmann, M., Phan, T., Chan, S., Cascio, D. and Eisenberg, D. (2010), The crystal structure of the mycobacterium tuberculosis Rv3019c-Rv3020c ESX complex reveals a domain-swapped heterotetramer. Protein Science, 19: 1692–1703. doi: 10.1002/pro.451

Author Information

  1. 1

    UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095-1570

  2. 2

    Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, California 90095-1737

  3. 3

    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569

  1. †

    Swiss Plant Science Web, Department of Botany & Plant Biology, University of Geneva, 1211 Geneva 4, Switzerland

  1. ‡

    Mark A. Arbing and Markus Kaufmann contributed equally to this work.

*Department of Chemistry and Biochemistry, UCLA, 611 Charles E. Young Dr. East, Los Angeles, California 90095-1569

Publication History

  1. Issue published online: 23 AUG 2010
  2. Article first published online: 13 JUL 2010
  3. Manuscript Accepted: 1 JUL 2010
  4. Manuscript Revised: 30 JUN 2010
  5. Manuscript Received: 1 JUN 2010

Funded by

  • Department of Energy. Grant Number: DE-FC02-02ER63421
  • National Institutes of Health. Grant Number: RR-15301 (NCRR)
  • The Department of Energy, Office of Basic Energy Sciences. Grant Number: DE-AC02-06CH11357
  • The Integrated Structure Function Initiative. Grant Number: 2361600206
  • The Tuberculosis Structural Genomics Consortium. Grant Number: A1068135. MK was supported by a postdoctoral fellowship from the Swiss National Science Foundation

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

View Full Article (HTML) Get PDF (522K)

References

  • 1
    WHO ( 2009) Global tuberculosis control–epidemiology, strategy, financing. WHO, Geneva, Switzerland.
  • 2
    Nguyen L, Pieters J ( 2009) Mycobacterial subversion of chemotherapeutic reagents and host defense tactics: challenges in tuberculosis drug development. Annu Rev Pharmacol Toxicol 49: 427–453.
  • 3
    Pym AS, Brodin P, Majlessi L, Brosch R, Demangel C, Williams A, Griffiths KE, Marchal G, Leclerc C, Cole ST ( 2003) Recombinant BCG exporting ESAT-6 confers enhanced protection against tuberculosis. Nat Med 9: 533–539.
  • 4
    Lewis KN, Liao R, Guinn KM, Hickey MJ, Smith S, Behr MA, Sherman DR ( 2003) Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guerin attenuation. J Infect Dis 187: 117–123.
  • 5
    Hsu T, Hingley-Wilson SM, Chen B, Chen M, Dai AZ, Morin PM, Marks CB, Padiyar J, Goulding C, Gingery M, Eisenberg D, Russell RG, Derrick SC, Collins FM, Morris SL, King CH, Jacobs WR Jr ( 2003) The primary mechanism of attenuation of bacillus Calmette-Guerin is a loss of secreted lytic function required for invasion of lung interstitial tissue. Proc Natl Acad Sci USA 100: 12420–12425.
  • 6
    Pym AS, Brodin P, Brosch R, Huerre M, Cole ST ( 2002) Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti. Mol Microbiol 46: 709–717.
    Direct Link:
  • 7
    Koo IC, Wang C, Raghavan S, Morisaki JH, Cox JS, Brown EJ ( 2008) ESX-1-dependent cytolysis in lysosome secretion and inflammasome activation during mycobacterial infection. Cell Microbiol 10: 1866–1878.
    Direct Link:
  • 8
    Smith J, Manoranjan J, Pan M, Bohsali A, Xu J, Liu J, McDonald KL, Szyk A, LaRonde-LeBlanc N, Gao LY ( 2008) Evidence for pore formation in host cell membranes by ESX-1-secreted ESAT-6 and its role in Mycobacterium marinum escape from the vacuole. Infect Immun 76: 5478–5487.
  • 9
    Majlessi L, Brodin P, Brosch R, Rojas MJ, Khun H, Huerre M, Cole ST, Leclerc C ( 2005) Influence of ESAT-6 secretion system 1 (RD1) of Mycobacterium tuberculosis on the interaction between mycobacteria and the host immune system. J Immunol 174: 3570–3579.
  • 10
    Abdallah AM, Gey van Pittius NC, Champion PA, Cox J, Luirink J, Vandenbroucke-Grauls CM, Appelmelk BJ, Bitter W ( 2007) Type VII secretion--mycobacteria show the way. Nat Rev Microbiol 5: 883–891.
  • 11
    Gey Van Pittius NC, Gamieldien J, Hide W, Brown GD, Siezen RJ, Beyers AD ( 2001) The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol 2: RESEARCH 0044.
  • 12
    Tekaia F, Gordon SV, Garnier T, Brosch R, Barrell BG, Cole ST ( 1999) Analysis of the proteome of Mycobacterium tuberculosis in silico. Tuber Lung Dis 79: 329–342.
  • 13
    Pallen MJ ( 2002) The ESAT-6/WXG100 superfamily – and a new Gram-positive secretion system? Trends Microbiol 10: 209–212.
  • 14
    Fortune SM, Jaeger A, Sarracino DA, Chase MR, Sassetti CM, Sherman DR, Bloom BR, Rubin EJ ( 2005) Mutually dependent secretion of proteins required for mycobacterial virulence. Proc Natl Acad Sci USA 102: 10676–10681.
  • 15
    MacGurn JA, Raghavan S, Stanley SA, Cox JS ( 2005) A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis. Mol Microbiol 57: 1653–1663.
    Direct Link:
  • 16
    Coros A, Callahan B, Battaglioli E, Derbyshire KM ( 2008) The specialized secretory apparatus ESX-1 is essential for DNA transfer in Mycobacterium smegmatis. Mol Microbiol 69: 794–808.
  • 17
    Renshaw PS, Lightbody KL, Veverka V, Muskett FW, Kelly G, Frenkiel TA, Gordon SV, Hewinson RG, Burke B, Norman J, Williamson RA, Carr MD ( 2005) Structure and function of the complex formed by the tuberculosis virulence factors CFP-10 and ESAT-6. EMBO J 24: 2491–2498.
  • 18
    Renshaw PS, Panagiotidou P, Whelan A, Gordon SV, Hewinson RG, Williamson RA, Carr MD ( 2002) Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. J Biol Chem 277: 21598–21603.
  • 19
    Lightbody KL, Ilghari D, Waters LC, Carey G, Bailey MA, Williamson RA, Renshaw PS, Carr MD ( 2008) Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. J Biol Chem 283: 17681–17690.
  • 20
    Lightbody KL, Renshaw PS, Collins ML, Wright RL, Hunt DM, Gordon SV, Hewinson RG, Buxton RS, Williamson RA, Carr MD ( 2004) Characterisation of complex formation between members of the Mycobacterium tuberculosis complex CFP-10/ESAT-6 protein family: towards an understanding of the rules governing complex formation and thereby functional flexibility. FEMS Microbiol Lett 238: 255–262.
  • 21
    Champion PA, Stanley SA, Champion MM, Brown EJ, Cox JS ( 2006) C-terminal signal sequence promotes virulence factor secretion in Mycobacterium tuberculosis. Science 313: 1632–1636.
  • 22
    Stanley SA, Raghavan S, Hwang WW, Cox JS ( 2003) Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system. Proc Natl Acad Sci USA 100: 13001–13006.
  • 23
    Pathak SK, Basu S, Basu KK, Banerjee A, Pathak S, Bhattacharyya A, Kaisho T, Kundu M, Basu J ( 2007) Direct extracellular interaction between the early secreted antigen ESAT-6 of Mycobacterium tuberculosis and TLR2 inhibits TLR signaling in macrophages. Nat Immunol 8: 610–618.
  • 24
    de Jonge MI, Pehau-Arnaudet G, Fretz MM, Romain F, Bottai D, Brodin P, Honore N, Marchal G, Jiskoot W, England P, Cole ST, Brosch R ( 2007) ESAT-6 from Mycobacterium tuberculosis dissociates from its putative chaperone CFP-10 under acidic conditions and exhibits membrane-lysing activity. J Bacteriol 189: 6028–6034.
  • 25
    Meher AK, Bal NC, Chary KV, Arora A ( 2006) Mycobacterium tuberculosis H37Rv ESAT-6-CFP-10 complex formation confers thermodynamic and biochemical stability. FEBS J 273: 1445–1462.
    Direct Link:
  • 26
    Skjot RL, Brock I, Arend SM, Munk ME, Theisen M, Ottenhoff TH, Andersen P ( 2002) Epitope mapping of the immunodominant antigen TB10.4 and the two homologous proteins TB10.3 and TB12.9, which constitute a subfamily of the esat-6 gene family. Infect Immun 70: 5446–5453.
  • 27
    Rosenkrands I, Weldingh K, Jacobsen S, Hansen CV, Florio W, Gianetri I, Andersen P ( 2000) Mapping and identification of Mycobacterium tuberculosis proteins by two-dimensional gel electrophoresis, microsequencing and immunodetection. Electrophoresis 21: 935–948.
    Direct Link:
  • 28
    Skjot RL, Oettinger T, Rosenkrands I, Ravn P, Brock I, Jacobsen S, Andersen P ( 2000) Comparative evaluation of low-molecular-mass proteins from Mycobacterium tuberculosis identifies members of the ESAT-6 family as immunodominant T-cell antigens. Infect Immun 68: 214–220.
  • 29
    Maciag A, Dainese E, Rodriguez GM, Milano A, Provvedi R, Pasca MR, Smith I, Palu G, Riccardi G, Manganelli R ( 2007) Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J Bacteriol 189: 730–740.
  • 30
    Rodriguez GM, Voskuil MI, Gold B, Schoolnik GK, Smith I ( 2002) ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect Immun 70: 3371–3381.
  • 31
    Serafini A, Boldrin F, Palu G, Manganelli R ( 2009) Characterization of a Mycobacterium tuberculosis ESX-3 conditional mutant: essentiality and rescue by iron and zinc. J Bacteriol 191: 6340–6344.
  • 32
    Siegrist MS, Unnikrishnan M, McConnell MJ, Borowsky M, Cheng TY, Siddiqi N, Fortune SM, Moody DB, Rubin EJ ( 2009) Mycobacterial Esx-3 is required for mycobactin-mediated iron acquisition. Proc Natl Acad Sci USA 106: 18792–18797.
  • 33
    Rost B, Yachdav G, Liu J ( 2004) The PredictProtein server. Nucleic Acids Res 32: W321–326.
  • 34
    Lawrence MC, Colman PM ( 1993) Shape complementarity at protein/protein interfaces. J Mol Biol 234: 946–950.
  • 35
    Ilghari D, Waters LC, Veverka V, Muskett FW, Carr MD ( 2009) 15N, 13C and 1H resonance assignments and secondary structure determination of the Mycobacterium tuberculosis Rv0287–Rv0288 protein complex. Biomol NMR Assign 3: 171–174.
  • 36
    Sundaramoorthy R, Fyfe PK, Hunter WN ( 2008) Structure of Staphylococcus aureus EsxA suggests a contribution to virulence by action as a transport chaperone and/or adaptor protein. J Mol Biol 383: 603–614.
  • 37
    Liu Y, Eisenberg D ( 2002) 3D domain swapping: as domains continue to swap. Protein Sci 11: 1285–1299.
    Direct Link:
  • 38
    Guo Z, Eisenberg D ( 2006) Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I. Proc Natl Acad Sci USA 103: 8042–8047.
  • 39
    Bennett MJ, Sawaya MR, Eisenberg D ( 2006) Deposition diseases and 3D domain swapping. Structure 14: 811–824.
  • 40
    Louie GV, Yang W, Bowman ME, Choe S ( 1997) Crystal structure of the complex of diphtheria toxin with an extracellular fragment of its receptor. Mol Cell 1: 67–78.
  • 41
    Johnson PD, Stuart RL, Grayson ML, Olden D, Clancy A, Ravn P, Andersen P, Britton WJ, Rothel JS ( 1999) Tuberculin-purified protein derivative-, MPT-64-, and ESAT-6-stimulated gamma interferon responses in medical students before and after Mycobacterium bovis BCG vaccination and in patients with tuberculosis. Clin Diagn Lab Immunol 6: 934–937.
  • 42
    Brodin P, de Jonge MI, Majlessi L, Leclerc C, Nilges M, Cole ST, Brosch R ( 2005) Functional analysis of early secreted antigenic target-6, the dominant T-cell antigen of Mycobacterium tuberculosis, reveals key residues involved in secretion, complex formation, virulence, and immunogenicity. J Biol Chem 280: 33953–33959.
  • 43
    Meher AK, Lella RK, Sharma C, Arora A ( 2007) Analysis of complex formation and immune response of CFP-10 and ESAT-6 mutants. Vaccine 25: 6098–6106.
  • 44
    Otwinowski Z, Minor W ( 1997) Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307–326.
  • 45
    Terwilliger TC, Berendzen J ( 1999) Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 55: 849–861.
    Direct Link:
  • 46
    Terwilliger TC ( 2001) Maximum-likelihood density modification using pattern recognition of structural motifs. Acta Crystallogr D Biol Crystallogr 57: 1755–1762.
    Direct Link:
  • 47
    Perrakis A, Morris R, Lamzin VS ( 1999) Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6: 458–463.
  • 48
    Collaborative Computational Project N ( 1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50: 760–763.
    Direct Link:
  • 49
    Emsley P, Cowtan K ( 2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126–2132.
    Direct Link:
  • 50
    Murshudov GN, Vagin AA, Dodson EJ ( 1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240–255.
    Direct Link:
  • 51
    Painter J, Merritt E ( 2006) TLSMD web server for the generation of multi-group TLS models. J Appl Crystallogr 39: 109–111.
    Direct Link:
  • 52
    Painter J, Merritt EA ( 2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D Biol Crystallogr 62: 439–450.
    Direct Link:
  • 53
    Colovos C, Yeates TO ( 1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2: 1511–1519.
    Direct Link:
  • 54
    Laskowski RA, MacArthur MW, Moss DS, Thornton JM ( 1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26: 283–291.
    Direct Link:
  • 55
    Vriend G, Sander C ( 1993) Quality control of protein models: directional atomic contact analysis. J Appl Crystallogr 26: 47–60.
    Direct Link:
  • 56
    DeLano WL ( 2002) The PyMOL Molecular Graphics System. Palo Alto, CA: DeLano Scientific.
  • 57
    Holm L, Park J ( 2000) DaliLite workbench for protein structure comparison. Bioinformatics 16: 566–567.
  • 58
    Davis ME, Madura JD, Luty BA, McCammon JA ( 1991) Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comput Phys Commun 62: 187–197.
  • 59
    Krissinel E, Henrick K ( 2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774–797.
  • 60
    Lee B, Richards FM ( 1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55: 379–400.
View Full Article (HTML) Get PDF (522K)