Intrinsic disorder in ubiquitination substrates

Journal of Molecular Biology

Volumn 412, Issue 3, 2011, Pages 319-324

  Hagai, Tzachi ^a   Azia, Ariel ^a   Tóth Petróczy, Ágnes ^a   Levy, Yaakov ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

acetylation; intrinsically disordered; proteasomal degradation; SUMOylation; ubiquitination

Indexed keywords

PROTEASOME; PROTEIN P97;

ACETYLATION; ARTICLE; COMPLEX FORMATION; INTRINSICALLY DISORDERED; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN UNFOLDING; REGULATORY SEQUENCE; SUMOYLATION; UBIQUITINATION;

EUKARYOTA;

EID: 80052349174     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.07.024     Document Type: Article

References (33)

1. Schrader E.K., Harstad K.G., and Matouschek A. Targeting proteins for degradation Nat. Chem. Biol. 5 2009 815 822
2. Peth A., Uchiki T., and Goldberg A.L. ATP-dependent steps in the binding of ubiquitin conjugates to the 26S proteasome that commit to degradation Mol. Cell 40 2010 671 681
3. Zhao M., Zhang N.Y., Zurawel A., Hansen K.C., and Liu C.W. Degradation of some polyubiquitinated proteins requires an intrinsic proteasomal binding element in the substrates J. Biol. Chem. 285 2010 4771 4780
4. Inobe T., Fishbain S., Prakash S., and Matouschek A. Defining the geometry of the two-component proteasome degron Nat. Chem. Biol. 7 2011 161 167
5. Liu C.W., Corboy M.J., DeMartino G.N., and Thomas P.J. Endoproteolytic activity of the proteasome Science 299 2003 408 411 (Pubitemid 36120047)
6. Piwko W., and Jentsch S. Proteasome-mediated protein processing by bidirectional degradation initiated from an internal site Nat. Struct. Mol. Biol. 13 2006 691 697 (Pubitemid 44175161)
7. Fishbain S., Prakash S., Herrig A., Elsasser S., and Matouschek A. Rad23 escapes degradation because it lacks a proteasome initiation region Nat. Commun. 2 2011 192
8. Grabbe C., Husnjak K., and Dikic I. The spatial and temporal organization of ubiquitin networks Nat. Rev., Mol. Cell Biol. 12 2011 295 307
9. Dosztanyi Z., Csizmok V., Tompa P., and Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content Bioinformatics 21 2005 3433 3434 (Pubitemid 41222453)
10. Xue B., Dunbrack R.L., Williams R.W., Dunker A.K., and Uversky V.N. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids Biochim. Biophys. Acta 1804 2010 996 1010
11. Iakoucheva L.M., Radivojac P., Brown C.J., O'Connor T.R., Sikes J.G., Obradovic Z., and Dunker A.K. The importance of intrinsic disorder for protein phosphorylation Nucleic Acids Res. 32 2004 1037 1049 (Pubitemid 38854704)
12. Dyson H.J., and Wright P.E. Intrinsically unstructured proteins and their functions Nat. Rev., Mol. Cell Biol. 6 2005 197 208 (Pubitemid 40314921)
13. Tompa P. Intrinsically unstructured proteins Trends Biochem. Sci. 27 2002 527 533 (Pubitemid 35279598)
14. P. Tompa Structure and Function of Intrinsically Disordered Proteins 1st edit 2009 Taylor & Francis Group Boca Raton, FL
15. Radivojac P., Iakoucheva L.M., Oldfield C.J., Obradovic Z., Uversky V.N., and Dunker A.K. Intrinsic disorder and functional proteomics Biophys. J. 92 2007 1439 1456 (Pubitemid 46393458)
16. Babu M.M., van der Lee R., de Groot N.S., and Gsponer J. Intrinsically disordered proteins: regulation and disease Curr. Opin. Struct. Biol. 21 2011 432 440
17. Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., and Walther T.C. Lysine acetylation targets protein complexes and co-regulates major cellular functions Science 325 2009 834 840
18. Radivojac P., Vacic V., Haynes C., Cocklin R.R., Mohan A., and Heyen J.W. Identification, analysis, and prediction of protein ubiquitination sites Proteins 78 2009 365 380
19. Ward J.J., Sodhi J.S., McGuffin L.J., Buxton B.F., and Jones D.T. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life J. Mol. Biol. 337 2004 635 645 (Pubitemid 38326883)
20. Vucetic S., Brown C.J., Dunker A.K., and Obradovic Z. Flavors of protein disorder Proteins 52 2003 573 584 (Pubitemid 37034155)
21. Gsponer J., Futschik M.E., Teichmann S.A., and Babu M.M. Tight regulation of unstructured proteins: from transcript synthesis to protein degradation Science 322 2008 1365 1368 (Pubitemid 352775246)
22. Henderson A., Erales J., Hoyt M.A., and Coffino P. Dependence of proteasome processing rate on substrate unfolding J. Biol. Chem. 286 2011 17495 17502
23. Beskow A., Grimberg K.B., Bott L.C., Salomons F.A., Dantuma N.P., and Young P. A conserved unfoldase activity for the p97 AAA-ATPase in proteasomal degradation J. Mol. Biol. 394 2009 732 746
24. Johnson L.N., and Lewis R.J. Structural basis for control by phosphorylation Chem. Rev. 101 2001 2209 2242 (Pubitemid 35373017)
25. Hunter T. The age of crosstalk: phosphorylation, ubiquitination, and beyond Mol. Cell 28 2007 730 738 (Pubitemid 350217067)
26. Barrick D. Biological regulation via ankyrin repeat folding ACS Chem. Biol. 4 2009 19 22
27. Han J.H., Batey S., Nickson A.A., Teichmann S.A., and Clarke J. The folding and evolution of multidomain proteins Nat. Rev., Mol. Cell Biol. 8 2007 319 330 (Pubitemid 46474660)
28. Kim Y.H., and Stites W.E. Effects of excluded volume upon protein stability in covalently cross-linked proteins with variable linker lengths Biochemistry 47 2008 8804 8814
29. Varshavsky A. The N-end rule Cell 69 1992 725 735
30. Hagai T., and Levy Y. Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding Proc. Natl Acad. Sci. USA 107 2010 2001 2006
31. Ravid T., and Hochstrasser M. Autoregulation of an E2 enzyme by ubiquitin-chain assembly on its catalytic residue Nat. Cell Biol. 9 2007 422 427 (Pubitemid 46511075)
32. Baugh J.M., Viktorova E.G., and Pilipenko E.V. Proteasomes can degrade a significant proportion of cellular proteins independent of ubiquitination J. Mol. Biol. 386 2009 814 827
33. Tsvetkov P., Reuven N., and Shaul Y. The nanny model for IDPs Nat. Chem. Biol. 5 2009 778 781