Skip to main content
SpringerLink
Log in

Crystal structure of a putative transcriptional regulator SCO0520 from Streptomyces coelicolor A3(2) reveals an unusual dimer among TetR family proteins

  • Published:
Journal of Structural and Functional Genomics

Abstract

A structure of the apo-form of the putative transcriptional regulator SCO0520 from Streptomyces coelicolor A3(2) was determined at 1.8 Å resolution. SCO0520 belongs to the TetR family of regulators. In the crystal lattice, the asymmetric unit contains two monomers that form an Ω-shaped dimer. The distance between the two DNA-recognition domains is much longer than the corresponding distances in the known structures of other TetR family proteins. In addition, the subunits in the dimer have different conformational states, resulting in different relative positions of the DNA-binding and regulatory domains. Similar conformational modifications are observed in other TetR regulators and result from ligand binding. These studies provide information about the flexibility of SCO0520 molecule and its putative biological function.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Abbreviations

DLS:

Dynamic light scattering

HTH:

Helix-turn-helix

MCSG:

Midwest Center for Structural Genomics

PDB:

Protein Data Bank

RMSD:

Root mean square deviation

SDR:

Short-chain dehydrogenase/reductase

TCEP:

Tris (2-carboxyethyl) phosphine

TetRs:

Tetracycline family of regulators

References

  1. Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O’Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147

    Article  PubMed  Google Scholar 

  2. Chater KF (1993) Genetics of differentiation in Streptomyces. Annu Rev Microbiol 47:685–713

    Article  PubMed  CAS  Google Scholar 

  3. Redenbach M, Kieser HM, Denapaite D, Eichner A, Cullum J, Kinashi H, Hopwood DA (1996) A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Mol Microbiol 21:77–96

    Article  PubMed  CAS  Google Scholar 

  4. Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R (2005) The TetR family of transcriptional repressors. Microbiol Mol Biol Rev 69:326–356

    Article  PubMed  CAS  Google Scholar 

  5. Orth P, Cordes F, Schnappinger D, Hillen W, Saenger W, Hinrichs W (1998) Conformational changes of the Tet repressor induced by tetracycline trapping. J Mol Biol 279:439–447

    Article  PubMed  CAS  Google Scholar 

  6. Orth P, Schnappinger D, Hillen W, Saenger W, Hinrichs W (2000) Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat Struct Biol 7:215–219

    Article  PubMed  CAS  Google Scholar 

  7. Kisker C, Hinrichs W, Tovar K, Hillen W, Saenger W (1995) The complex formed between Tet repressor and tetracycline-Mg2+ reveals mechanism of antibiotic resistance. J Mol Biol 247:260–280

    Article  PubMed  CAS  Google Scholar 

  8. Hinrichs W, Kisker C, Duvel M, Muller A, Tovar K, Hillen W, Saenger W (1994) Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance. Science 264:418–420

    Article  PubMed  CAS  Google Scholar 

  9. Schumacher MA, Miller MC, Grkovic S, Brown MH, Skurray RA, Brennan RG (2001) Structural mechanisms of QacR induction and multidrug recognition. Science 294:2158–2163

    Article  PubMed  CAS  Google Scholar 

  10. Schumacher MA, Miller MC, Grkovic S, Brown MH, Skurray RA, Brennan RG (2002) Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR. EMBO J 21:1210–1218

    Article  PubMed  CAS  Google Scholar 

  11. Schumacher MA, Miller MC, Brennan RG (2004) Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein. EMBO J 23:2923–2930

    Article  PubMed  CAS  Google Scholar 

  12. Murray DS, Schumacher MA, Brennan RG (2004) Crystal structures of QacR-diamidine complexes reveal additional multidrug-binding modes and a novel mechanism of drug charge neutralization. J Biol Chem 279:14365–14371

    Article  PubMed  CAS  Google Scholar 

  13. Natsume R, Ohnishi Y, Senda T, Horinouchi S (2004) Crystal structure of a gamma-butyrolactone autoregulator receptor protein in Streptomyces coelicolor A3(2). J Mol Biol 336:409–419

    Article  PubMed  CAS  Google Scholar 

  14. Dover LG, Corsino PE, Daniels IR, Cocklin SL, Tatituri V, Besra GS, Futterer K (2004) Crystal structure of the TetR/CamR family repressor Mycobacterium tuberculosis EthR implicated in ethionamide resistance. J Mol Biol 340:1095–1105

    Article  PubMed  CAS  Google Scholar 

  15. Frenois F, Engohang-Ndong J, Locht C, Baulard AR, Villeret V (2004) Structure of EthR in a ligand bound conformation reveals therapeutic perspectives against tuberculosis. Mol Cell 16:301–307

    Article  PubMed  CAS  Google Scholar 

  16. Willand N, Dirie B, Carette X, Bifani P, Singhal A, Desroses M, Leroux F, Willery E, Mathys V, Deprez-Poulain R, Delcroix G, Frenois F, Aumercier M, Locht C, Villeret V, Deprez B, Baulard AR (2009) Synthetic EthR inhibitors boost antituberculous activity of ethionamide. Nat Med 15:537–544

    Article  PubMed  CAS  Google Scholar 

  17. Rajan SS, Yang X, Shuvalova L, Collart F, Anderson WF (2006) Crystal structure of Yfir, an unusual TetR/CamR-type putative transcriptional regulator from Bacillus subtilis. Proteins 65:255–257

    Article  PubMed  CAS  Google Scholar 

  18. Li M, Gu R, Su CC, Routh MD, Harris KC, Jewell ES, McDermott G, Yu EW (2007) Crystal structure of the transcriptional regulator AcrR from Escherichia coli. J Mol Biol 374:591–603

    Article  PubMed  CAS  Google Scholar 

  19. Willems AR, Tahlan K, Taguchi T, Zhang K, Lee ZZ, Ichinose K, Junop MS, Nodwell JR (2008) Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA. J Mol Biol 376:1377–1387

    Article  PubMed  CAS  Google Scholar 

  20. Koclega KD, Chruszcz M, Zimmerman MD, Cymborowski M, Evdokimova E, Minor W (2007) Crystal structure of a transcriptional regulator TM1030 from Thermotoga maritima solved by an unusual MAD experiment. J Struct Biol 159:424–432

    Article  PubMed  CAS  Google Scholar 

  21. Premkumar L, Rife CL, Krishna SS, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Floyd R, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kovarik JS, Kreusch A, Levin I, McPhillips TM, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rezezadeh F, Rodionov D, Schwarzenbacher R, Spraggon G, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA (2007) Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function. Proteins 68:418–424

    Article  PubMed  CAS  Google Scholar 

  22. Okada U, Kondo K, Hayashi T, Watanabe N, Yao M, Tamura T, Tanaka I (2008) Structural and functional analysis of the TetR-family transcriptional regulator SCO0332 from Streptomyces coelicolor. Acta Crystallogr D 64:198–205

    Article  PubMed  Google Scholar 

  23. Zhang RG, Skarina T, Katz JE, Beasley S, Khachatryan A, Vyas S, Arrowsmith CH, Clarke S, Edwards A, Joachimiak A, Savchenko A (2001) Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase. Structure 9:1095–1106

    Article  PubMed  CAS  Google Scholar 

  24. Rosenbaum G, Alkire R, Evans G, Rotella FJ, Lazarski K, Zhang R, Ginell SL, Duke N, Naday I, Lazarz J, Molitsky MJ, Keefe L, Gonczy J, Rock L, Sanishvili R, Walsh MA, Westbrook E, Joachimiak A (2006) The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results. J Synchrotron Radiat 13:30–45

    Article  PubMed  CAS  Google Scholar 

  25. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Macromol Crystallogr A 276:307–326

    Article  CAS  Google Scholar 

  26. Minor W, Cymborowski M, Otwinowski Z, Chruszcz M (2006) HKL-3000: the integration of data reduction and structure solution—from diffraction images to an initial model in minutes. Acta Crystallogr D 62:859–866

    Article  PubMed  Google Scholar 

  27. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112–122

    Article  PubMed  Google Scholar 

  28. Otwinowski Z (1991) Proceedings of the CCP4 study weekend, isomorphous replacement and anomalous scattering. Wolf W, Evans PR, Leslie AGW (eds). Daresbury Laboratory, Warrington, pp 80–86

  29. Cowtan KD, Main P (1993) Improvement of macromolecular electron-density maps by the simultaneous application of real and reciprocal space constraints. Acta Crystallogr A 49:148–157

    Article  CAS  Google Scholar 

  30. Cowtan KD, Zhang KYJ (1999) Density modification for macromolecular phase improvement. Progr Biophys Mol Biol 72:245–270

    Article  CAS  Google Scholar 

  31. CCP4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D 50:760–763

    Article  Google Scholar 

  32. Terwilliger TC, Berendzen J (1999) Automated MAD and MIR structure solution. Acta Crystallogr D 55:849–861

    Article  PubMed  CAS  Google Scholar 

  33. Terwilliger TC (2002) Automated structure solution, density modification and model building. Acta Crystallogr D 58:1937–1940

    Article  PubMed  Google Scholar 

  34. Perrakis A, Morris R, Lamzin VS (1999) Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6:458–463

    Article  PubMed  CAS  Google Scholar 

  35. Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Crystallogr A 47:110–119

    Article  PubMed  Google Scholar 

  36. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D 60:2126–2132

    Article  PubMed  Google Scholar 

  37. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53:240–255

    Article  PubMed  CAS  Google Scholar 

  38. Vaguine AA, Richelle J, Wodak SJ (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D 55:191–205

    Article  PubMed  CAS  Google Scholar 

  39. 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

    Article  CAS  Google Scholar 

  40. Yang H, Guranovic V, Dutta S, Berman HM, Westbrook JD (2004) Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D 60:1833–1839

    Article  PubMed  Google Scholar 

  41. Lovell SC, Davis IW, Arendall WB, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50:437–450

    Article  PubMed  CAS  Google Scholar 

  42. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242

    Article  PubMed  CAS  Google Scholar 

  43. Delano WL (2002) The Pymol molecular graphics system. DeLano Scientific, San Carlos, CA

    Google Scholar 

  44. Potterton L, McNicholas S, Krissinel E, Gruber J, Cowtan K, Emsley P, Murshudov GN, Cohen S, Perrakis A, Noble M (2004) Developments in the CCP4 molecular-graphics project. Acta Crystallogr D 60:2288–2294

    Article  PubMed  Google Scholar 

  45. Altschul SF, Gish W, Miller W, Meyers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  46. Thompson JD, Higgins DG, Gibson TJ (1994) ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  47. Gouet P, Robert X, Courcelle E (2003) ESPript/ENDscript: Extracting and 23 rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31:3320–3323

    Article  PubMed  CAS  Google Scholar 

  48. Holm L, Sander C. (1995) 3-D lookup: fast protein structure database searches at 90% reliability. In: Proceedings of 3rd international conference on intelligent systems for molecular biology (ISMB’95), pp179–187

  49. Gibrat JF, Madej T, Bryant SH (1996) Surprising similarities in structure comparison. Curr Opin Struct Biol 6:377–385

    Article  PubMed  CAS  Google Scholar 

  50. Madej T, Gibrat JF, Bryant SH (1995) Threading a database of protein cores. Proteins 23:356–3690

    Article  PubMed  CAS  Google Scholar 

  51. Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33:89–93

    Article  Google Scholar 

  52. Wang S, Kirillova O, Chruszcz M, Gront D, Zimmerman MD, Cymborowski MT, Shumilin IA, Skarina T, Gorodichtchenskaia E, Savchenko A, Edwards AM, Minor W (2009) The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold. Protein Sci 18:2410–2419

    Article  PubMed  CAS  Google Scholar 

  53. Ponstingl H, Henrick K, Thornton JM (2000) Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 41:47–57

    Article  PubMed  CAS  Google Scholar 

  54. Ponstingl H, Kabir T, Thornton JM (2003) Automatic inference of protein quaternary structure from crystals. J Appl Crystal 36:1116–1122

    Article  CAS  Google Scholar 

  55. Yu Z, Reichheld SE, Savchenko A, Parkinson J, Davidson AR (2010) A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators. J Mol Biol 400:847–864

    Article  PubMed  CAS  Google Scholar 

  56. Jornvall H, Persson B, Krook M, Atrian S, Gonzalez-Duarte R, Jeffery J, Ghosh D (1995) Short-chain dehydrogenases/reductases (SDR). Biochemistry 34:6003–6013

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The results shown in this report are derived from work performed at Argonne National Laboratory, at the Structural Biology Center of the Advanced Photon Source. Argonne is operated by University of Chicago Argonne, LLC, for the US Department of Energy, Office of Biological and Environmental Research under contract DE-AC02-06CH11357. The authors would like to thank Andrzej Joachimiak and members of the Structural Biology Center and the Midwest Center for Structural Genomics for help and discussions, and Matthew Zimmerman for critically reading the manuscript. The work described in the paper was supported by NIH PSI grants GM62414 and GM074942.

Author information

Author notes

  1. Ekaterina V. Filippova

    Present address: Department of Molecular Pharmacology and Biological Chemistry, Northwestern Feinberg School of Medicine, Chicago, IL, 60611, USA

Authors and Affiliations

  1. Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA

    Ekaterina V. Filippova, Maksymilian Chruszcz, Marcin Cymborowski & Wladek Minor

  2. The Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5G 2C4, Canada

    Jun Gu, Alexei Savchenko & Aled Edwards

  3. Midwest Center for Structural Genomics http://www.mcsg.anl.gov/

    Ekaterina V. Filippova, Maksymilian Chruszcz, Marcin Cymborowski, Jun Gu, Alexei Savchenko, Aled Edwards & Wladek Minor

Authors
  1. Ekaterina V. Filippova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Maksymilian Chruszcz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marcin Cymborowski
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jun Gu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Alexei Savchenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Aled Edwards
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wladek Minor
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wladek Minor.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 44 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Filippova, E.V., Chruszcz, M., Cymborowski, M. et al. Crystal structure of a putative transcriptional regulator SCO0520 from Streptomyces coelicolor A3(2) reveals an unusual dimer among TetR family proteins. J Struct Funct Genomics 12, 149–157 (2011). https://doi.org/10.1007/s10969-011-9112-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10969-011-9112-4

Keywords

Search

Navigation