NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway

  • Gaohua Liu
  • Farhad Forouhar
  • Alexander Eletsky
  • Hanudatta S. Atreya
  • James M. Aramini
  • Rong Xiao
  • Yuanpeng J. Huang
  • Mariam Abashidze
  • Jayaraman Seetharaman
  • Jinfeng Liu
  • Burkhard Rost
  • Thomas Acton
  • Gaetano T. Montelione
  • John F. Hunt
  • Thomas Szyperski
Article

Abstract

For cell regulation, E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1) is involved in the transfer of ubiquitin-fold modifier 1 (Ufm1), a ubiquitin like protein which is activated by E1-like enzyme Uba5, to various target proteins. Thereby, Ufc1 participates in the very recently discovered Ufm1-Uba5-Ufc1 ubiquination pathway which is found in metazoan organisms. The structure of human Ufc1 was solved by using both NMR spectroscopy and X-ray crystallography. The complementary insights obtained with the two techniques provided a unique basis for understanding the function of Ufc1 at atomic resolution. The Ufc1 structure consists of the catalytic core domain conserved in all E2-like enzymes and an additional N-terminal helix. The active site Cys116, which forms a thio-ester bond with Ufm1, is located in a flexible loop that is highly solvent accessible. Based on the Ufc1 and Ufm1 NMR structures, a model could be derived for the Ufc1-Ufm1 complex in which the C-terminal Gly83 of Ufm1 may well form the expected thio-ester with Cys116, suggesting that Ufm1-Ufc1 functions as described for other E1–E2–E3 machineries. α-helix 1 of Ufc1 adopts different conformations in the crystal and in solution, suggesting that this helix plays a key role to mediate specificity.

Keywords

Ufc1 Ufm1 Ubiquitin E2 Ubiquitin conjugating enzyme 

Abbreviations

ASU

Asymmetric unit

E1

Ubiquitin-activating enzyme

E2

Ubiquitin-conjugating enzyme

E3

Ubiquitin-protein ligase

NESG

Northeast Structural Genomics Consortium

NMR

Nuclear magnetic resonance

NSLF

National synchrotron light source

PDB

Protein data bank

SAD

Single-wavelength anomalous diffraction

UBC

Ubiquitin conjugating enzyme

UBL

Ubiquitin-like (Ubl)

UFC1

Ubiquitin-fold modifier conjugating enzyme 1

UFM1

Ubiquitin-fold modifier 1

References

  1. 1.
    Finley D, Chau V (1991) Annu Rev Cell Biol 7:25–69. doi:10.1146/annurev.cb.07.110191.000325 PubMedCrossRefGoogle Scholar
  2. 2.
    VanDemark AP, Hill CP (2002) Curr Opin Struct Biol 12:822–830. doi:10.1016/S0959-440X(02)00389-5 PubMedCrossRefGoogle Scholar
  3. 3.
    Pickart CM, Eddins MJ (2004) Biochim Biophys Acta 1695:55–72. doi:10.1016/j.bbamcr.2004.09.019 PubMedCrossRefGoogle Scholar
  4. 4.
    Kerscher O, Felberbaum R, Hochstrasser M (2006) Annu Rev Cell Dev Biol 22:159–180. doi:10.1146/annurev.cellbio.22.010605.093503 PubMedCrossRefGoogle Scholar
  5. 5.
    Dye BT, Schulman BA (2007) Annu Rev Biophys Biomol Struct 36:131–150. doi:10.1146/annurev.biophys.36.040306.132820 PubMedCrossRefGoogle Scholar
  6. 6.
    Hershko A, Ciechanover A (1998) Annu Rev Biochem 67:425–479. doi:10.1146/annurev.biochem.67.1.425 PubMedCrossRefGoogle Scholar
  7. 7.
    Huang TT, D’Andrea AD (2006) Nat Rev Mol Cell Biol 7:323–334. doi:10.1038/nrm1908 PubMedCrossRefGoogle Scholar
  8. 8.
    Pickart CM (2001) Annu Rev Biochem 70:503–533. doi:10.1146/annurev.biochem.70.1.503 PubMedCrossRefGoogle Scholar
  9. 9.
    VanDemark AP, Hofmann RM, Tsui C, Pickart CM, Wolberger C (2001) Cell 105:711–720. doi:10.1016/S0092-8674(01)00387-7 PubMedCrossRefGoogle Scholar
  10. 10.
    Cort JR, Chiang YW, Zheng DY, Montelione GT, Kennedy MA (2002) Proteins 48:733–736. doi:10.1002/prot.10197 PubMedCrossRefGoogle Scholar
  11. 11.
    Komatsu M, Chiba T, Tatsumi K, Iemura S, Tanida I, Okazaki N, Ueno T, Kominami E, Natsume T, Tanaka K (2004) EMBO J 23:1977–1986. doi:10.1038/sj.emboj.7600205 PubMedCrossRefGoogle Scholar
  12. 12.
    Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer ELL (2002) Nucleic Acids Res 30:276–280. doi:10.1093/nar/30.1.276 PubMedCrossRefGoogle Scholar
  13. 13.
    Liu GH, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, Xiao R, Yee A, Lemak A, Bhattacharya A, Acton TA, Arrowsmith CH, Montelione GT, Szyperski T (2005) Proc Natl Acad Sci USA 102:10487–10492. doi:10.1073/pnas.0504338102 PubMedCrossRefGoogle Scholar
  14. 14.
    Acton TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang YW, Climent T, Cooper B, Denissova NG, Douglas SM, Everett JK, Ho CK, Macapagal D, Rajan PK, Shastry R, Shih LY, Swapna GVT, Wilson M, Wu M, Gerstein M, Inouye M, Hunt JF, Montelione GT (2005) Methods Enzymol 394:210–243. doi:10.1016/S0076-6879(05)94008-1 PubMedCrossRefGoogle Scholar
  15. 15.
    Jansson M, Li YC, Jendeberg L, Anderson S, Montelione GT, Nilsson B (1996) J Biomol NMR 7:131–141. doi:10.1007/BF00203823 PubMedCrossRefGoogle Scholar
  16. 16.
    Liu GH, Aramini J, Atreya HS, Eletsky A, Xiao R, Acton T, Ma LC, Montelione GT, Szyperski T (2005) J Biomol NMR 32:261. doi:10.1007/s10858-005-7941-9 PubMedCrossRefGoogle Scholar
  17. 17.
    Guntert P, Mumenthaler C, Wuthrich K (1997) J Mol Biol 273:283–298. doi:10.1006/jmbi.1997.1284 PubMedCrossRefGoogle Scholar
  18. 18.
    Herrmann T, Guntert P, Wuthrich K (2002) J Mol Biol 319:209–227. doi:10.1016/S0022-2836(02)00241-3 PubMedCrossRefGoogle Scholar
  19. 19.
    Hendrickson WA (1991) Science 254:51–58. doi:10.1126/science.1925561 PubMedCrossRefGoogle Scholar
  20. 20.
    Otwinowski Z, Minor W (1997) Macromol Crystallogr A 276:307–326. doi:10.1016/S0076-6879(97)76066-X CrossRefGoogle Scholar
  21. 21.
    Weeks CM, Miller R (1999) J Appl Crystallogr 32:120–124. doi:10.1107/S0021889898010504 CrossRefGoogle Scholar
  22. 22.
    Terwilliger TC (2003) Acta Crystallogr D 59:38–44. doi:10.1107/S0907444902018036 PubMedCrossRefGoogle Scholar
  23. 23.
    McRee DE (1999) J Struct Biol 125:156–165. doi:10.1006/jsbi.1999.4094 PubMedCrossRefGoogle Scholar
  24. 24.
    Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Acta Crystallogr D 54:905–921. doi:10.1107/S0907444998003254 PubMedCrossRefGoogle Scholar
  25. 25.
    Kleywegt GJ (1996) Acta Crystallogr D Biol Crystallogr 52:842–857PubMedCrossRefGoogle Scholar
  26. 26.
    Kleywegt GJ, Brunger AT (1996) Structure 4:897–904. doi:10.1016/S0969-2126(96)00097-4 PubMedCrossRefGoogle Scholar
  27. 27.
    Kleywegt GJ, Jones TA (1996) Acta Crystallogr D Biol Crystallogr 52:826–828PubMedCrossRefGoogle Scholar
  28. 28.
    Mizushima T, Tatsumi K, Ozaki Y, Kawakami T, Suzuki A, Ogasahara K, Komatsu M, Kominami E, Tanaka K, Yamane T (2007) Biochem Biophys Res Commun 362:1079–1084. doi:10.1016/j.bbrc.2007.08.129 PubMedCrossRefGoogle Scholar
  29. 29.
    Holm L, Sander C (1996) Nucleic Acids Res 24:206–209. doi:10.1093/nar/24.1.206 PubMedCrossRefGoogle Scholar
  30. 30.
    Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) J Mol Biol 247:536–540PubMedGoogle Scholar
  31. 31.
    Gille C, Frommel C (2001) Bioinformatics 17:377–378. doi:10.1093/bioinformatics/17.4.377 PubMedCrossRefGoogle Scholar
  32. 32.
    Miura T, Klaus W, Gsell B, Miyamoto C, Senn H (1999) J Mol Biol 290:213–228. doi:10.1006/jmbi.1999.2859 PubMedCrossRefGoogle Scholar
  33. 33.
    Hamilton KS, Ellison MJ, Barber KR, Williams RS, Huzil JT, McKenna S, Ptak C, Glover M, Shaw GS (2001) Structure 9:897–904. doi:10.1016/S0969-2126(01)00657-8 PubMedCrossRefGoogle Scholar
  34. 34.
    Huang DT, Paydar A, Zhuang M, Waddell MB, Holton JM, Schulman BA (2005) Mol Cell 17:341–350. doi:10.1016/j.molcel.2004.12.020 PubMedCrossRefGoogle Scholar
  35. 35.
    Bencsath KP, Podgorski MS, Pagala VR, Slaughter CA, Schulman BA (2002) J Biol Chem 277:47938–47945. doi:10.1074/jbc.M207442200 PubMedCrossRefGoogle Scholar
  36. 36.
    Huang DT, Hunt HW, Zhuang M, Ohi MD, Holton JM, Schulman BA (2007) Nature 445:394–398. doi:10.1038/nature05490 PubMedCrossRefGoogle Scholar
  37. 37.
    Huang L, Kinnucan E, Wang GL, Beaudenon S, Howley PM, Huibregtse JM, Pavletich NP (1999) Science 286:1321–1326. doi:10.1126/science.286.5443.1321 PubMedCrossRefGoogle Scholar
  38. 38.
    Zheng N, Wang P, Jeffrey PD, Pavletich NP (2000) Cell 102:533–539. doi:10.1016/S0092-8674(00)00057-X PubMedCrossRefGoogle Scholar
  39. 39.
    Zhang MH, Windheim M, Roe SM, Peggie M, Cohen P, Prodromou C, Pearl LH (2005) Mol Cell 20:525–538. doi:10.1016/j.molcel.2005.09.023 PubMedCrossRefGoogle Scholar
  40. 40.
    Eletsky A, Atreya HS, Liu GH, Szyperski T (2005) J Am Chem Soc 127:14578–14579. doi:10.1021/ja054895x PubMedCrossRefGoogle Scholar
  41. 41.
    Wagner G (1983) Q Rev Biophys 16:1–57PubMedCrossRefGoogle Scholar
  42. 42.
    Skalicky JJ, Mills JL, Sharma S, Szyperski T (2001) J Am Chem Soc 123:388–397. doi:10.1021/ja003220l PubMedCrossRefGoogle Scholar
  43. 43.
    Koradi R, Billeter M, Wuthrich K (1996) J Mol Graph 14:51–55. doi:10.1016/0263-7855(96)00009-4 PubMedCrossRefGoogle Scholar
  44. 44.
    Kraulis PJ (1991) J Appl Crystallogr 24:946–950. doi:10.1107/S0021889891004399 CrossRefGoogle Scholar
  45. 45.
    Merritt EA, Bacon DJ (1997) Macromol Crystallogr B 277:505–524. doi:10.1016/S0076-6879(97)77028-9 CrossRefGoogle Scholar
  46. 46.
    Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283–291. doi:10.1107/S0021889892009944 CrossRefGoogle Scholar
  47. 47.
    Word JM, Bateman RC, Presley BK, Lovell SC, Richardson DC (2000) Protein Sci 9:2251–2259PubMedCrossRefGoogle Scholar
  48. 48.
    Huang YJ, Powers R, Montelione GT (2005) J Am Chem Soc 127:1665–1674. doi:10.1021/ja047109h PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Gaohua Liu
    • 1
  • Farhad Forouhar
    • 2
  • Alexander Eletsky
    • 1
  • Hanudatta S. Atreya
    • 1
  • James M. Aramini
    • 3
  • Rong Xiao
    • 3
  • Yuanpeng J. Huang
    • 3
  • Mariam Abashidze
    • 2
  • Jayaraman Seetharaman
    • 2
  • Jinfeng Liu
    • 4
  • Burkhard Rost
    • 4
  • Thomas Acton
    • 3
  • Gaetano T. Montelione
    • 3
  • John F. Hunt
    • 2
  • Thomas Szyperski
    • 1
  1. 1.Department of Chemistry, Northeast Structural Genomics ConsortiumThe State University of New York at BuffaloBuffaloUSA
  2. 2.Department of Biological Sciences, Northeast Structural Genomics ConsortiumColumbia UniversityNew YorkUSA
  3. 3.The Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics ConsortiumRutgers UniversityPiscatawayUSA
  4. 4.Department of Biochemistry and Molecular Biophysics, Northeast Structural Genomics ConsortiumColumbia UniversityNew YorkUSA

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