Skip to main content
SpringerLink
Log in

Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop

  • Articles
  • Published:
Science China Chemistry Aims and scope Submit manuscript

Abstract

MINDY-1 is a recently discovered new family of deubiquitinating enzymes (DUB), but one of its yeast homologs, YGL082W, does not show any DUB activity in vitro. Sequence alignment shows that YGL082W possesses the correct catalytic triad, and yet did not catalyze either the hydrolysis of di-ubiquitin, crosslinking with C-terminally propargylated ubiquitin, or hydrolysis of ubiquitin-7-amino-4-methylcoumarin. After obtaining a crystal structure of the catalytic domain of YGL082W, we identified an interesting difference between the catalytic center loop of YGL082W and that of its human homolog MINDY-1. Because the conformation of the catalytic center loop was previously reported to be important for the deubiquitination activity of MINDY-1, we hypothesized that Glu27 (instead of the corresponding Pro136 in MINDY-1) of the catalytic center loop of YGL082W may impair the conformational change and account for the lack of activity. This hypothesis was supported by homology modeling and molecular dynamics simulations, which showed that the Pro-to-Glu mutation (P136E mutation for MINDY-1) creates a hydrogen bond that inhibits the conformation change of the catalytic center loop of MINDY-1. Further experiments through site-directed mutation validated this hypothesis, showing that the P27E mutation caused MIY1 (a homologous active DUB from yeast) to lose activity.

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

Similar content being viewed by others

References

  1. Clague MJ, Urbé S, Komander D. Nat Rev Mol Cell Biol, 2019, 20: 338–352

    CAS  PubMed  Google Scholar 

  2. Jiang X, Chen ZJ. Nat Rev Immunol, 2011, 12: 35–48

    PubMed  Google Scholar 

  3. Damgaard RB, Nachbur U, Yabal M, Wong WWL, Fiil BK, Kastirr M, Rieser E, Rickard JA, Bankovacki A, Peschel C, Ruland J, Bekker-Jensen S, Mailand N, Kaufmann T, Strasser A, Walczak H, Silke J, Jost PJ, Gyrd-Hansen M. Mol Cell, 2012, 46: 746–758

    CAS  PubMed  Google Scholar 

  4. Fiil BK, Damgaard RB, Wagner SA, Keusekotten K, Fritsch M, Bekker-Jensen S, Mailand N, Choudhary C, Komander D, Gyrd-Hansen M. Mol Cell, 2013, 50: 818–830

    CAS  PubMed  PubMed Central  Google Scholar 

  5. van Wijk SJL, Fricke F, Herhaus L, Gupta J, Hötte K, Pampaloni F, Grumati P, Kaulich M, Sou YS, Komatsu M, Greten FR, Fulda S, Heilemann M, Dikic I. Nat Microbiol, 2017, 2: 17066

    CAS  PubMed  Google Scholar 

  6. Zhou Q, Yu X, Demirkaya E, Deuitch N, Stone D, Tsai WL, Kuehn HS, Wang H, Yang D, Park YH, Ombrello AK, Blake M, Romeo T, Remmers EF, Chae JJ, Mullikin JC, Güzel F, Milner JD, Boehm M, Rosenzweig SD, Gadina M, Welch SB, Özen S, Topaloglu R, Abinun M, Kastner DL, Aksentijevich I. Proc Natl Acad Sci USA, 2016, 113: 10127–10132

    CAS  PubMed  Google Scholar 

  7. Catrysse L, Vereecke L, Beyaert R, van Loo G. Trends Immunol, 2014, 35: 22–31

    CAS  PubMed  Google Scholar 

  8. Bett JS, Ibrahim AFM, Garg AK, Kelly V, Pedrioli P, Rocha S, Hay RT. Biochem J, 2013, 451: 185–194

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Sobhian B, Shao G, Lilli DR, Culhane AC, Moreau LA, Xia B, Livingston DM, Greenberg RA. Science, 2007, 316: 1198–1202

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Worden EJ, Padovani C, Martin A. Nat Struct Mol Biol, 2014, 21: 220–227

    CAS  PubMed  Google Scholar 

  11. de Poot SAH, Tian G, Finley D. J Mol Biol, 2017, 429: 3525–3545

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Zheng H, Gupta V, Patterson-Fortin J, Bhattacharya S, Katlinski K, Wu J, Varghese B, Carbone CJ, Aressy B, Fuchs SY, Greenberg RA. Cell Rep, 2013, 5: 180–193

    CAS  PubMed  Google Scholar 

  13. Murphy JM, Mace PD, Eyers PA. Curr Opin Struct Biol, 2017, 47: 95–104

    CAS  PubMed  Google Scholar 

  14. Walden M, Masandi SK, Pawlowski K, Zeqiraj E. Biochm Soc Trans, 2018, 46: 453–466

    CAS  Google Scholar 

  15. Ceccarelli DF, Ivantsiv S, Mullin AA, Coyaud E, Manczyk N, Maisonneuve P, Kurinov I, Zhao L, Go C, Gingras AC, Raught B, Cordes S, Sicheri F. Structure, 2019, 27: 1000–1012.e6

    CAS  PubMed  Google Scholar 

  16. Abdul Rehman SA, Kristariyanto YA, Choi SY, Nkosi PJ, Weidlich S, Labib K, Hofmann K, Kulathu Y. Mol Cell, 2016, 63: 146–155

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Fang GM, Li YM, Shen F, Huang YC, Li JB, Lin Y, Cui HK, Liu L. Angew Chem Int Ed, 2011, 50: 7645–7649

    CAS  Google Scholar 

  18. Fang GM, Wang JX, Liu L. Angew Chem Int Ed, 2012, 51: 10347–10350

    CAS  Google Scholar 

  19. Zheng JS, Tang S, Qi YK, Wang ZP, Liu L. Nat Protoc, 2013, 8: 2483–2495

    CAS  PubMed  Google Scholar 

  20. Li YM, Li YT, Pan M, Kong XQ, Huang YC, Hong ZY, Liu L. Angew Chem Int Ed, 2014, 53: 2198–2202

    CAS  Google Scholar 

  21. Tang S, Si YY, Wang ZP, Mei KR, Chen X, Cheng JY, Zheng JS, Liu L. Angew Chem Int Ed, 2015, 54: 5713–5717

    CAS  Google Scholar 

  22. Pan M, Gao S, Zheng Y, Tan X, Lan H, Tan X, Sun D, Lu L, Wang T, Zheng Q, Huang Y, Wang J, Liu L. J Am Chem Soc, 2016, 138: 7429–7435

    CAS  PubMed  Google Scholar 

  23. Li YT, Yi C, Chen CC, Lan H, Pan M, Zhang SJ, Huang YC, Guan CJ, Li YM, Yu L, Liu L. Nat Commun, 2017, 8: 14846

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Pan M, Zheng Q, Ding S, Zhang L, Qu Q, Wang T, Hong D, Ren Y, Liang L, Chen C, Mei Z, Liu L. Angew Chem Int Ed, 2019, 58: 2627–2631

    CAS  Google Scholar 

  25. Tang S, Liang LJ, Si YY, Gao S, Wang JX, Liang J, Mei Z, Zheng JS, Liu L. Angew Chem Int Ed, 2017, 56: 13333–13337

    CAS  Google Scholar 

  26. He Q, Li J, Qi Y, Wang Z, Huang Y, Liu L. Sci China Chem, 2017, 60: 621–627

    CAS  Google Scholar 

  27. Yang J, Zhao J. Sci China Chem, 2018, 61: 97–112

    CAS  Google Scholar 

  28. Bi X, Pasunooti KK, Liu CF. Sci China Chem, 2018, 61: 251–265

    CAS  Google Scholar 

  29. Li H, Dong S. Sci China Chem, 2017, 60: 201–213

    CAS  Google Scholar 

  30. Si Y, Liang L, Tang S, Qi Y, Huang Y, Liu L. Sci China Chem, 2018, 61: 412–417

    CAS  Google Scholar 

  31. Chen CC, Gao S, Ai HS, Qu Q, Tian CL, Li YM. Sci China Chem, 2018, 61: 702–707

    CAS  Google Scholar 

  32. Qi YK, Si YY, Du SS, Liang J, Wang KW, Zheng JS. Sci China Chem, 2019, 62: 299–312

    CAS  Google Scholar 

  33. Kristariyanto YA, Abdul Rehman SA, Weidlich S, Knebel A, Kulathu Y. EMBO Rep, 2017, 18: 392–402

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Mevissen TET, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SMV, Ovaa H, Komander D. Cell, 2013, 154: 169–184

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Misaghi S, Galardy PJ, Meester WJN, Ovaa H, Ploegh HL, Gaudet R. J Biol Chem, 2005, 280: 1512–1520

    CAS  PubMed  Google Scholar 

  36. Boudreaux DA, Maiti TK, Davies CW, Das C. Proc Natl Acad Sci USA, 2010, 107: 9117–9122

    CAS  PubMed  Google Scholar 

  37. Maiti TK, Permaul M, Boudreaux DA, Mahanic C, Mauney S, Das C. FEBS J, 2011, 278: 4917–4926

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Zhou ZR, Zhang YH, Liu S, Song AX, Hu HY. Biochem J, 2012, 441: 143–149

    CAS  PubMed  Google Scholar 

  39. Yin ST, Huang H, Zhang YH, Zhou ZR, Song AX, Hong FS, Hu HY. Biochem Biophys Res Commun, 2011, 416: 76–79

    CAS  PubMed  Google Scholar 

  40. Ekkebus R, van Kasteren SI, Kulathu Y, Scholten A, Berlin I, Geurink PP, de Jong A, Goerdayal S, Neefjes J, Heck AJR, Komander D, Ovaa H. J Am Chem Soc, 2013, 135: 2867–2870

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Gersch M, Wagstaff JL, Toms AV, Graves B, Freund SMV, Komander D. Mol Cell, 2019, 74: 436–451.e7

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Kim RQ, Geurink PP, Mulder MPC, Fish A, Ekkebus R, El Oualid F, van Dijk WJ, van Dalen D, Ovaa H, van Ingen H, Sixma TK. Nat Commun, 2019, 10: 231

    PubMed  PubMed Central  Google Scholar 

  43. Liang LJ, Si Y, Tang S, Huang D, Wang ZA, Tian C, Zheng JS. Chin Chem Lett, 2018, 29: 1155–1159

    CAS  Google Scholar 

  44. Mali SM, Singh SK, Eid E, Brik A. J Am Chem Soc, 2017, 139: 4971–4986

    CAS  PubMed  Google Scholar 

  45. Wu J, Kumar S, Wang F, Wang H, Chen L, Arsenault P, Mattern M, Weinstock J. J Med Chem, 2018, 61: 422–443

    CAS  PubMed  Google Scholar 

  46. El Oualid F, Merkx R, Ekkebus R, Hameed DS, Smit JJ, de Jong A, Hilkmann H, Sixma TK, Ovaa H. Angew Chem Int Ed, 2010, 49: 10149–10153

    CAS  Google Scholar 

  47. Kong L, Shaw N, Yan L, Lou Z, Rao Z. J Biol Chem, 2015, 290: 7160–7168

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Webb B, Sali A. Protein structure modeling with MODELLER. In: Kaufmann M, Klinger C, Savelsbergh A, Eds. Functional Genomics. Methods in Molecular Biology. Vol 1654. New York: Humana Press, 2017. 39–54

    Google Scholar 

  49. Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Šali A. Annu Rev Biophys Biomol Struct, 2000, 29: 291–325

    PubMed  Google Scholar 

  50. Sali A, Blundell TL. J Mol Biol, 1993, 234: 779–815

    CAS  PubMed  Google Scholar 

  51. Fiser A, Do RKG, Šali A. Protein Sci, 2000, 9: 1753–1773

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Ortiz AR, Strauss CEM, Olmea O. Protein Sci, 2002, 11: 2606–2621

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Siew N, Elofsson A, Rychlewski L, Fischer D. Bioinformatics, 2000, 16: 776–785

    CAS  PubMed  Google Scholar 

  54. Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. Proteins, 2003, 53: 76–87

    CAS  PubMed  Google Scholar 

  55. Ye Y, Godzik A. Nucleic Acids Res, 2004, 32: W582–W585

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Zhang Y, Skolnick J. Nucleic Acids Res, 2005, 33: 2302–2309

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Shaw DE. J Comput Chem, 2005, 26: 1318–1328

    CAS  PubMed  Google Scholar 

  58. Bowers KJ, Dror RO, Shaw DE. J Chem Phys, 2006, 124: 184109

    PubMed  Google Scholar 

  59. Bowers KJ, Dror RO, Shaw DE. J Comput Phys, 2007, 221: 303–329

    Google Scholar 

Download references

Acknowledgements

The work was supported by the National Key Research and Development Program of China (2017YFA0505200), the National Natural Science Foundation of China (21532004, 91753205, 81621002, 21621003) and ShanghaiTech University.

Author information

Authors and Affiliations

  1. Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China

    Lining Lu, Tian Wang, Lujun Liang & Lei Liu

  2. School of Life Science, Beijing Institute of Technology, Beijing, 100081, China

    Feng Wang

  3. Human Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China

    Yu Guo & Suwen Zhao

Authors
  1. Lining Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yu Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tian Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lujun Liang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Suwen Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Feng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Lei Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Suwen Zhao, Feng Wang or Lei Liu.

Ethics declarations

Conflict of interest The authors declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lu, L., Guo, Y., Wang, T. et al. Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop. Sci. China Chem. 63, 237–243 (2020). https://doi.org/10.1007/s11426-019-9623-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11426-019-9623-0

Keywords

Search

Navigation