Structural basis of the activation and degradation mechanisms of the E3 ubiquitin ligase Nedd4L

Structure

Volumn 22, Issue 10, 2014, Pages 1446-1457

  Escobedo, Albert ^a   Gomes, Tiago ^a   Aragón, Eric ^a   Martín Malpartida, Pau ^a   Ruiz, Lidia ^a   Macias, Maria J ^a,b  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

INOSITOL 1,4,5 TRISPHOSPHATE; NEDD4L PROTEIN; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG; CALCIUM; ESCRT PROTEIN; NEDD4 UBIQUITIN PROTEIN LIGASES; UBIQUITIN PROTEIN LIGASE;

ARTICLE; BINDING COMPETITION; BINDING SITE; CALCIUM BINDING; CATALYSIS; CONFORMATIONAL TRANSITION; CONSENSUS SEQUENCE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVATION; ENZYME DEGRADATION; ENZYME STRUCTURE; HETERONUCLEAR NUCLEAR MAGNETIC RESONANCE; HETERONUCLEAR SINGLE QUANTUM COHERENCE; HUMAN; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; PROTEIN ANALYSIS; PROTEIN UNFOLDING; PROTON NUCLEAR MAGNETIC RESONANCE; RELAXATION TIME; SECOND MESSENGER; UBIQUITINATION; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; SIGNAL TRANSDUCTION;

AMINO ACID SEQUENCE; BINDING, COMPETITIVE; CALCIUM; ENDOSOMAL SORTING COMPLEXES REQUIRED FOR TRANSPORT; ENZYME ACTIVATION; HUMANS; INOSITOL 1,4,5-TRISPHOSPHATE; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SIGNAL TRANSDUCTION; UBIQUITIN-PROTEIN LIGASES; UBIQUITINATION;

EID: 84908216124     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2014.08.016     Document Type: Article

References (40)

1. E. Aragón, N. Goerner, A.I. Zaromytidou, Q. Xi, A. Escobedo, J. Massagué, and M.J. Macias A Smad action turnover switch operated by WW domain readers of a phosphoserine code Genes Dev. 25 2011 1275 1288
2. E. Aragón, N. Goerner, Q. Xi, T. Gomes, S. Gao, J. Massagué, and M.J. Macias Structural basis for the versatile interactions of Smad7 with regulator WW domains in TGF-β Pathways Structure 20 2012 1726 1736
3. G. Barbato, M. Ikura, L.E. Kay, R.W. Pastor, and A. Bax Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible Biochemistry 31 1992 5269 5278
4. C. Bartels, T.H. Xia, M. Billeter, P. Güntert, and K. Wüthrich The program XEASY for computer-supported NMR spectral analysis of biological macromolecules J. Biomol. NMR 6 1995 1 10
5. M.J. Berridge Inositol trisphosphate and calcium signalling mechanisms Biochim. Biophys. Acta 1793 2009 933 940
6. M.C. Bruce, V. Kanelis, F. Fouladkou, A. Debonneville, O. Staub, and D. Rotin Regulation of Nedd4-2 self-ubiquitination and stability by a PY motif located within its HECT-domain Biochem. J. 415 2008 155 163
7. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, and N.S. Pannu Crystallography & NMR system: A new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54 1998 905 921
8. W. Cho, and R.V. Stahelin Membrane binding and subcellular targeting of C2 domains Biochim. Biophys. Acta 1761 2006 838 849
9. P. de Bie, and A. Ciechanover Ubiquitination of E3 ligases: self-regulation of the ubiquitin system via proteolytic and non-proteolytic mechanisms Cell Death Differ. 18 2011 1393 1402
10. F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer, and A. Bax NMRPipe: a multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6 1995 277 293
11. J.F. Doreleijers, W.F. Vranken, C. Schulte, J.L. Markley, E.L. Ulrich, G. Vriend, and G.W. Vuister NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB Nucleic Acids Res. 40 2012 D519 D524
12. R. Dunn, D.A. Klos, A.S. Adler, and L. Hicke The C2 domain of the Rsp5 ubiquitin ligase binds membrane phosphoinositides and directs ubiquitination of endosomal cargo J. Cell Biol. 165 2004 135 144
13. N.A. Farrow, R. Muhandiram, A.U. Singer, S.M. Pascal, C.M. Kay, G. Gish, S.E. Shoelson, T. Pawson, J.D. Forman-Kay, and L.E. Kay Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation Biochemistry 33 1994 5984 6003
14. E. Gallagher, M. Gao, Y.C. Liu, and M. Karin Activation of the E3 ubiquitin ligase Itch through a phosphorylation-induced conformational change Proc. Natl. Acad. Sci. USA 103 2006 1717 1722
15. S. Gao, C. Alarcón, G. Sapkota, S. Rahman, P.Y. Chen, N. Goerner, M.J. Macias, H. Erdjument-Bromage, P. Tempst, and J. Massagué Ubiquitin ligase Nedd4L targets activated Smad2/3 to limit TGF-beta signaling Mol. Cell 36 2009 457 468
16. N.F. Garrone, B.L. Blazer-Yost, R.B. Weiss, J.M. Lalouel, and A. Rohrwasser A human polymorphism affects NEDD4L subcellular targeting by leading to two isoforms that contain or lack a C2 domain BMC Cell Biol. 10 2009 26
17. M. Guerrero-Valero, C. Ferrer-Orta, J. Querol-Audí, C. Marin-Vicente, I. Fita, J.C. Gómez-Fernández, N. Verdaguer, and S. Corbalán-García Structural and mechanistic insights into the association of PKCalpha-C2 domain to PtdIns(4,5)P2 Proc. Natl. Acad. Sci. USA 106 2009 6603 6607
18. A. Hershko, A. Ciechanover, and I.A. Rose Resolution of the ATP-dependent proteolytic system from reticulocytes: a component that interacts with ATP Proc. Natl. Acad. Sci. USA 76 1979 3107 3110
19. B. Hess, C. Kutzner, D. Van Der Spoel, and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 2008 435 447
20. D. Hoeller, C.M. Hecker, and I. Dikic Ubiquitin and ubiquitin-like proteins in cancer pathogenesis Nat. Rev. Cancer 6 2006 776 788
21. J.M. Huibregtse, M. Scheffner, S. Beaudenon, and P.M. Howley A family of proteins structurally and functionally related to the E6-AP ubiquitin-protein ligase Proc. Natl. Acad. Sci. USA 92 1995 5249
22. M. Hyvönen, M.J. Macias, M. Nilges, H. Oschkinat, M. Saraste, and M. Wilmanns Structure of the binding site for inositol phosphates in a PH domain EMBO J. 14 1995 4676 4685
23. H.B. Kamadurai, J. Souphron, D.C. Scott, D.M. Duda, D.J. Miller, D. Stringer, R.C. Piper, and B.A. Schulman Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex Mol. Cell 36 2009 1095 1102
24. D. Komander, M.J. Clague, and S. Urbé Breaking the chains: structure and function of the deubiquitinases Nat. Rev. Mol. Cell Biol. 10 2009 550 563
25. M.J. Macias, S. Wiesner, and M. Sudol WW and SH3 domains, two different scaffolds to recognize proline-rich ligands FEBS Lett. 513 2002 30 37
26. J. Massagué TGFβ signalling in context Nat. Rev. Mol. Cell Biol. 13 2012 616 630
27. M. Nilges, M.J. Macias, S.I. O'Donoghue, and H. Oschkinat Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin J. Mol. Biol. 269 1997 408 422
28. M.D. Petroski The ubiquitin system, disease, and drug discovery BMC Biochem. 9 Suppl 1 2008 S7
29. P.J. Plant, H. Yeger, O. Staub, P. Howard, and D. Rotin The C2 domain of the ubiquitin protein ligase Nedd4 mediates Ca2+-dependent plasma membrane localization J. Biol. Chem. 272 1997 32329 32336
30. J. Rizo, and T.C. Südhof C2-domains, structure and function of a universal Ca2+-binding domain J. Biol. Chem. 273 1998 15879 15882
31. Y. Shen, F. Delaglio, G. Cornilescu, and A. Bax TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts J. Biomol. NMR 44 2009 213 223
32. O. Staub, S. Dho, P. Henry, J. Correa, T. Ishikawa, J. McGlade, and D. Rotin WW domains of Nedd4 bind to the proline-rich PY motifs in the epithelial Na+ channel deleted in Liddle's syndrome EMBO J. 15 1996 2371 2380
33. M. Sudol, H.I. Chen, C. Bougeret, A. Einbond, and P. Bork Characterization of a novel protein-binding module - the WW domain FEBS Lett. 369 1995 67 71
34. B.C. Suh, and B. Hille Regulation of ion channels by phosphatidylinositol 4,5-bisphosphate Curr. Opin. Neurobiol. 15 2005 370 378
35. M.A. Verdecia, C.A. Joazeiro, N.J. Wells, J.L. Ferrer, M.E. Bowman, T. Hunter, and J.P. Noel Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase Mol. Cell 11 2003 249 259
36. W.F. Vranken, W. Boucher, T.J. Stevens, R.H. Fogh, A. Pajon, M. Llinas, E.L. Ulrich, J.L. Markley, J. Ionides, and E.D. Laue The CCPN data model for NMR spectroscopy: development of a software pipeline Proteins 59 2005 687 696
37. L. Wan, W. Zou, D. Gao, H. Inuzuka, H. Fukushima, A.H. Berg, R. Drapp, S. Shaik, D. Hu, and C. Lester Cdh1 regulates osteoblast function through an APC/C-independent modulation of Smurf1 Mol. Cell 44 2011 721 733
38. J. Wang, Q. Peng, Q. Lin, C. Childress, D. Carey, and W. Yang Calcium activates Nedd4 E3 ubiquitin ligases by releasing the C2 domain-mediated auto-inhibition J. Biol. Chem. 285 2010 12279 12288
39. S. Wiesner, A.A. Ogunjimi, H.R. Wang, D. Rotin, F. Sicheri, J.L. Wrana, and J.D. Forman-Kay Autoinhibition of the HECT-type ubiquitin ligase Smurf2 through its C2 domain Cell 130 2007 651 662
40. W. Zou, X. Chen, J.H. Shim, Z. Huang, N. Brady, D. Hu, R. Drapp, K. Sigrist, L.H. Glimcher, and D. Jones The E3 ubiquitin ligase Wwp2 regulates craniofacial development through mono-ubiquitylation of Goosecoid Nat. Cell Biol. 13 2011 59 65