Found at: doi:10.1371/journal.pone.0013202.s009 (0.08 PDF) MB Acknowledgments The authors thank Dr. Peter Breuer at Max-Planck-Institute for biochemistry in Germany for generously providing the plasmid pPROEX HTa-ataxin-3. We also thank Drs. Chang-Wen Jin, Xu Shen and Yong- References 1. Hofmann K, Falquet L (2001) A ubiquitin-interacting motif conserved in components of the proteasomal and lysosomal protein degradation systems. Trends Biochem Sci 26: 347–350. 2. Miller SL, Malotky E, O’Bryan JP (2004) Analysis of the role of ubiquitin- interacting motifs in ubiquitin binding and ubiquitylation. J Biol Chem 279: 33528–33537. 3. Young P, Deveraux Q, Beal RE, Pickart CM, Rechsteiner M (1998) Characterization of two polyubiquitin binding sites in the 26 S protease subunit 5a. J Biol Chem 273: 5461–5467. 4. Oldham CE, Mohney RP, Miller SL, Hanes RN, O’Bryan JP (2002) The ubiquitin-interacting motifs target the endocytic adaptor protein epsin for ubiquitination. Curr Biol 12: 1112–1116. 5. Polo S, Sigismund S, Faretta M, Guidi M, Capua MR, et al. (2002) A single motif responsible for ubiquitin recognition and monoubiquitination in endocytic proteins. Nature 416: 451–455. 6. Klapisz E, Sorokina I, Lemeer S, Pijnenburg M, Verkleij AJ, et al. (2002) A ubiquitin-interacting motif (UIM) is essential for Eps15 and Eps15R ubiquitina- tion. J Biol Chem 277: 30746–30753. 7. Shih SC, Katzmann DJ, Schnell JD, Sutanto M, Emr SD, et al. (2002) Epsins and Vps27p/Hrs contain ubiquitin-binding domains that function in receptor endocytosis. Nat Cell Biol 4: 389–393. 8. Urbe S, Sachse M, Row PE, Preisinger C, Barr FA, et al. (2003) The UIM domain of Hrs couples receptor sorting to vesicle formation. J Cell Sci 116: 4169–4179. 9. Kim H, Chen J, Yu X (2007) Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response. Science 316: 1202–1205. 10. Rosenberg RN (1992) Machado-Joseph disease: an autosomal dominant motor system degeneration. Mov Disord 7: 193–203. 11. Berke SJ, Chai Y, Marrs GL, Wen H, Paulson HL (2005) Defining the role of ubiquitin-interacting motifs in the polyglutamine disease protein, ataxin-3. J Biol Chem 280: 32026–32034. 12. Chai Y, Berke SS, Cohen RE, Paulson HL (2004) Poly-ubiquitin binding by the polyglutamine disease protein ataxin-3 links its normal function to protein surveillance pathways. J Biol Chem 279: 3605–3611. 13. Mueller TD, Feigon J (2003) Structural determinants for the binding of ubiquitin-like domains to the proteasome. Embo J 22: 4634–4645. 14. Shekhtman A, Cowburn D (2002) A ubiquitin-interacting motif from Hrs binds to and occludes the ubiquitin surface necessary for polyubiquitination in monoubiquitinated proteins. Biochem Biophys Res Commun 296: 1222–1227. 15. Fisher RD, Wang B, Alam SL, Higginson DS, Robinson H, et al. (2003) Structure and ubiquitin binding of the ubiquitin-interacting motif. J Biol Chem 278: 28976–28984. 16. Swanson KA, Kang RS, Stamenova SD, Hicke L, Radhakrishnan I (2003) Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation. Embo J 22: 4597–4606. 17. Fujiwara K, Tenno T, Sugasawa K, Jee JG, Ohki I, et al. (2004) Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B. J Biol Chem 279: 4760–4767. 18. Wang Q, Young P, Walters KJ (2005) Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition. J Mol Biol 348: 727–739. 19. Sato Y, Yoshikawa A, Mimura H, Yamashita M, Yamagata A, et al. (2009) Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by tandem UIMs of RAP80. Embo J 28: 2461–2468. 20. Hirano S, Kawasaki M, Ura H, Kato R, Raiborg C, et al. (2006) Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting. Nat Struct Mol Biol 13: 272–277. 21. Penengo L, Mapelli M, Murachelli AG, Confalonieri S, Magri L, et al. (2006) Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin. Cell 124: 1183–1195. 22. Prag G, Misra S, Jones EA, Ghirlando R, Davies BA, et al. (2003) Mechanism of ubiquitin recognition by the CUE domain of Vps9p. Cell 113: 609–620. 23. Masino L, Musi V, Menon RP, Fusi P, Kelly G, et al. (2003) Domain architecture of the polyglutamine protein ataxin-3: a globular domain followed by a flexible tail. FEBS Lett 549: 21–25. 24. Goto J, Watanabe M, Ichikawa Y, Yee SB, Ihara N, et al. (1997) Machado- Joseph disease gene products carrying different carboxyl termini. Neurosci Res 28: 373–377. 25. Wang Q, Li L, Ye Y (2006) Regulation of retrotranslocation by p97-associated deubiquitinating enzyme ataxin-3. J Cell Biol 174: 963–971. AT3-UIM/Ub Interaction Gang Chang, and Ms. Xiao-Jing Lin for technical assistance, and Mr. Si- Tao Yin for preparing the K63-linked diUb protein. Author Contributions Conceived and designed the experiments: AXS HYH. Performed the experiments: AXS CJZ YP XCG ZRZ JH. Analyzed the data: AXS CJZ ZRZ QSF JH DL HYH. Contributed reagents/materials/analysis tools: YP DL. Wrote the paper: AXS HYH. 26. Mao Y, Senic-Matuglia F, Di Fiore PP, Polo S, Hodsdon ME, et al. (2005) Deubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain. Proc Natl Acad Sci U S A 102: 12700–12705. 27. Chai Y, Koppenhafer SL, Shoesmith SJ, Perez MK, Paulson HL (1999) Evidence for proteasome involvement in polyglutamine disease: localization to nuclear inclusions in SCA3/MJD and suppression of polyglutamine aggregation in vitro. Hum Mol Genet 8: 673–682. 28. Tarlac V, Storey E (2003) Role of proteolysis in polyglutamine disorders. J Neurosci Res 74: 406–416. 29. Khan LA, Bauer PO, Miyazaki H, Lindenberg KS, Landwehrmeyer BG, et al. (2006) Expanded polyglutamines impair synaptic transmission and ubiquitin- proteasome system in Caenorhabditis elegans. J Neurochem 98: 576–587. 30. Farrow NA, Muhandiram R, Singer AU, Pascal SM, Kay CM, et al. (1994) Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33: 5984–6003. 31. Ogura K, Nobuhisa I, Yuzawa S, Takeya R, Torikai S, et al. (2006) NMR solution structure of the tandem Src homology 3 domains of p47phox complexed with a p22phox-derived proline-rich peptide. J Biol Chem 281: 3660–3668. 32. Hurley JH, Lee S, Prag G (2006) Ubiquitin-binding domains. Biochem J 399: 361–372. 33. Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 194: 531–544. 34. Choi JY, Ryu JH, Kim HS, Park SG, Bae KH, et al. (2007) Co-chaperone CHIP promotes aggregation of ataxin-1. Mol Cell Neurosci 34: 69–79. 35. Mueller TD, Kamionka M, Feigon J (2004) Specificity of the interaction between ubiquitin-associated domains and ubiquitin. J Biol Chem 279: 11926–11936. 36. Ohno A, Jee J, Fujiwara K, Tenno T, Goda N, et al. (2005) Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition. Structure 13: 521–532. 37. Chang YG, Song AX, Gao YG, Shi YH, Lin XJ, et al. (2006) Solution structure of the ubiquitin-associated domain of human BMSC-UbP and its complex with ubiquitin. Protein Sci 15: 1248–1259. 38. Winborn BJ, Travis SM, Todi SV, Scaglione KM, Xu P, et al. (2008) The deubiquitinating enzyme ataxin-3, a polyglutamine disease protein, edits Lys63 linkages in mixed linkage ubiquitin chains. J Biol Chem 283: 26436–26443. 39. Burnett B, Li F, Pittman RN (2003) The polyglutamine neurodegenerative protein ataxin-3 binds polyubiquitylated proteins and has ubiquitin protease activity. Hum Mol Genet 12: 3195–3205. 40. Faber PW, Barnes GT, Srinidhi J, Chen J, Gusella JF, et al. (1998) Huntingtin interacts with a family of WW domain proteins. Hum Mol Genet 7: 1463–1474. 41. Gao YG, Yan XZ, Song AX, Chang YG, Gao XC, et al. (2006) Structural insights into the specific binding of huntingtin proline-rich region with the SH3 and WW domains. Structure 14: 1755–1765. 42. Narasimhan J, Wang M, Fu Z, Klein JM, Haas AL, et al. (2005) Crystal structure of the interferon-induced ubiquitin-like protein ISG15. J Biol Chem 280: 27356–27365. 43. Chang YG, Yan XZ, Xie YY, Gao XC, Song AX, et al. (2008) Different roles for two ubiquitin-like domains of ISG15 in protein modification. J Biol Chem 283: 13370–13377. 44. Flick K, Raasi S, Zhang H, Yen JL, Kaiser P (2006) A ubiquitin-interacting motif protects polyubiquitinated Met4 from degradation by the 26S proteasome. Nat Cell Biol 8: 509–515. 45. Raiborg C, Bache KG, Gillooly DJ, Madshus IH, Stang E, et al. (2002) Hrs sorts ubiquitinated proteins into clathrin-coated microdomains of early endosomes. Nat Cell Biol 4: 394–398. 46. Sims JJ, Cohen RE (2009) Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80. Mol Cell 33: 775–783. 47. Zhang N, Wang Q, Ehlinger A, Randles L, Lary JW, et al. (2009) Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13. Mol Cell 35: 280–290. 48. Sims JJ, Haririnia A, Dickinson BC, Fushman D, Cohen RE (2009) Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains. Nat Struct Mol Biol 16: 883–889. 49. Ivanov AV, Peng H, Yurchenko V, Yap KL, Negorev DG, et al. (2007) PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing. Mol Cell 28: 823–837. 50. Miller SL, Scappini EL, O’Bryan J (2007) Ubiquitin-interacting motifs inhibit aggregation of polyQ-expanded huntingtin. J Biol Chem 282: 10096–10103. PLoS ONE | www.plosone.org 12 October 2010 | Volume 5 | Issue 10 | e13202