Journal of Structural and Functional Genomics

, Volume 12, Issue 3, pp 149–157 | Cite as

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

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


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.


Helix-turn-helix DNA-binding motif Structural genomics TetR transcriptional regulator X-ray crystal structure 



Dynamic light scattering




Midwest Center for Structural Genomics


Protein Data Bank


Root mean square deviation


Short-chain dehydrogenase/reductase


Tris (2-carboxyethyl) phosphine


Tetracycline family of regulators



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.

Supplementary material

10969_2011_9112_MOESM1_ESM.pdf (44 kb)
Supplementary material 1 (PDF 44 kb)


  1. 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 417:141–147PubMedCrossRefGoogle Scholar
  2. 2.
    Chater KF (1993) Genetics of differentiation in Streptomyces. Annu Rev Microbiol 47:685–713PubMedCrossRefGoogle Scholar
  3. 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 21:77–96PubMedCrossRefGoogle Scholar
  4. 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 69:326–356PubMedCrossRefGoogle Scholar
  5. 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 279:439–447PubMedCrossRefGoogle Scholar
  6. 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 7:215–219PubMedCrossRefGoogle Scholar
  7. 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 247:260–280PubMedCrossRefGoogle Scholar
  8. 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 264:418–420PubMedCrossRefGoogle Scholar
  9. 9.
    Schumacher MA, Miller MC, Grkovic S, Brown MH, Skurray RA, Brennan RG (2001) Structural mechanisms of QacR induction and multidrug recognition. Science 294:2158–2163PubMedCrossRefGoogle Scholar
  10. 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 21:1210–1218PubMedCrossRefGoogle Scholar
  11. 11.
    Schumacher MA, Miller MC, Brennan RG (2004) Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein. EMBO J 23:2923–2930PubMedCrossRefGoogle Scholar
  12. 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 279:14365–14371PubMedCrossRefGoogle Scholar
  13. 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 336:409–419PubMedCrossRefGoogle Scholar
  14. 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 340:1095–1105PubMedCrossRefGoogle Scholar
  15. 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 16:301–307PubMedCrossRefGoogle Scholar
  16. 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 15:537–544PubMedCrossRefGoogle Scholar
  17. 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 65:255–257PubMedCrossRefGoogle Scholar
  18. 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 374:591–603PubMedCrossRefGoogle Scholar
  19. 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 376:1377–1387PubMedCrossRefGoogle Scholar
  20. 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 159:424–432PubMedCrossRefGoogle Scholar
  21. 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 68:418–424PubMedCrossRefGoogle Scholar
  22. 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 64:198–205PubMedCrossRefGoogle Scholar
  23. 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 9:1095–1106PubMedCrossRefGoogle Scholar
  24. 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 13:30–45PubMedCrossRefGoogle Scholar
  25. 25.
    Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Macromol Crystallogr A 276:307–326CrossRefGoogle Scholar
  26. 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 62:859–866PubMedCrossRefGoogle Scholar
  27. 27.
    Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112–122PubMedCrossRefGoogle Scholar
  28. 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 80–86Google Scholar
  29. 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 49:148–157CrossRefGoogle Scholar
  30. 30.
    Cowtan KD, Zhang KYJ (1999) Density modification for macromolecular phase improvement. Progr Biophys Mol Biol 72:245–270CrossRefGoogle Scholar
  31. 31.
    CCP4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D 50:760–763CrossRefGoogle Scholar
  32. 32.
    Terwilliger TC, Berendzen J (1999) Automated MAD and MIR structure solution. Acta Crystallogr D 55:849–861PubMedCrossRefGoogle Scholar
  33. 33.
    Terwilliger TC (2002) Automated structure solution, density modification and model building. Acta Crystallogr D 58:1937–1940PubMedCrossRefGoogle Scholar
  34. 34.
    Perrakis A, Morris R, Lamzin VS (1999) Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6:458–463PubMedCrossRefGoogle Scholar
  35. 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 47:110–119PubMedCrossRefGoogle Scholar
  36. 36.
    Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D 60:2126–2132PubMedCrossRefGoogle Scholar
  37. 37.
    Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53:240–255PubMedCrossRefGoogle Scholar
  38. 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 55:191–205PubMedCrossRefGoogle Scholar
  39. 39.
    Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) Procheck—a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291CrossRefGoogle Scholar
  40. 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 60:1833–1839PubMedCrossRefGoogle Scholar
  41. 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 50:437–450PubMedCrossRefGoogle Scholar
  42. 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 28:235–242PubMedCrossRefGoogle Scholar
  43. 43.
    Delano WL (2002) The Pymol molecular graphics system. DeLano Scientific, San Carlos, CAGoogle Scholar
  44. 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 60:2288–2294PubMedCrossRefGoogle Scholar
  45. 45.
    Altschul SF, Gish W, Miller W, Meyers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  46. 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 22:4673–4680PubMedCrossRefGoogle Scholar
  47. 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 31:3320–3323PubMedCrossRefGoogle Scholar
  48. 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), pp179–187Google Scholar
  49. 49.
    Gibrat JF, Madej T, Bryant SH (1996) Surprising similarities in structure comparison. Curr Opin Struct Biol 6:377–385PubMedCrossRefGoogle Scholar
  50. 50.
    Madej T, Gibrat JF, Bryant SH (1995) Threading a database of protein cores. Proteins 23:356–3690PubMedCrossRefGoogle Scholar
  51. 51.
    Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33:89–93CrossRefGoogle Scholar
  52. 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 18:2410–2419PubMedCrossRefGoogle Scholar
  53. 53.
    Ponstingl H, Henrick K, Thornton JM (2000) Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 41:47–57PubMedCrossRefGoogle Scholar
  54. 54.
    Ponstingl H, Kabir T, Thornton JM (2003) Automatic inference of protein quaternary structure from crystals. J Appl Crystal 36:1116–1122CrossRefGoogle Scholar
  55. 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 400:847–864PubMedCrossRefGoogle Scholar
  56. 56.
    Jornvall H, Persson B, Krook M, Atrian S, Gonzalez-Duarte R, Jeffery J, Ghosh D (1995) Short-chain dehydrogenases/reductases (SDR). Biochemistry 34:6003–6013PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Ekaterina V. Filippova
    • 1
    • 3
    • 4
  • Maksymilian Chruszcz
    • 1
    • 4
  • Marcin Cymborowski
    • 1
    • 4
  • Jun Gu
    • 2
    • 4
  • Alexei Savchenko
    • 2
    • 4
  • Aled Edwards
    • 2
    • 4
  • Wladek Minor
    • 1
    • 4
  1. 1.Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleUSA
  2. 2.The Banting and Best Department of Medical ResearchUniversity of TorontoTorontoCanada
  3. 3.Department of Molecular Pharmacology and Biological ChemistryNorthwestern Feinberg School of MedicineChicagoUSA
  4. 4.Midwest Center for Structural Genomics

Personalised recommendations