Promiscuous interactions of gp78 E3 ligase CUE domain with polyubiquitin chains

Structure

Volumn 20, Issue 12, 2012, Pages 2138-2150

  Liu, Shan ^a   Chen, Yinghua ^a   Li, Jess ^a   Huang, Tao ^a   Tarasov, Sergey ^a   King, Aaren ^a   Weissman, Allan M ^a   Byrd, R Andrew ^a   Das, Ranabir ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIUBIQUITIN; POLYUBIQUITIN; UBIQUITIN; UBIQUITIN PROTEIN LIGASE E3; UBIQUITIN PROTEIN LIGASE E3 GP78; UNCLASSIFIED DRUG;

ARTICLE; ATOM; ESCHERICHIA COLI; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; UBIQUITINATION;

AMINO ACID SEQUENCE; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; POLYUBIQUITIN; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, AUTOCRINE MOTILITY FACTOR; THERMODYNAMICS;

EID: 84870562001     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2012.09.020     Document Type: Article

References (42)

1. B. Chen, J. Mariano, Y.C. Tsai, A.H. Chan, M. Cohen, and A.M. Weissman The activity of a human endoplasmic reticulum-associated degradation E3, gp78, requires its Cue domain, RING finger, and an E2-binding site Proc. Natl. Acad. Sci. USA 103 2006 341 346
2. Z.J. Chen, and L.J. Sun Nonproteolytic functions of ubiquitin in cell signaling Mol. Cell 33 2009 275 286
3. D.E. Christensen, P.S. Brzovic, and R.E. Klevit E2-BRCA1 RING interactions dictate synthesis of mono- or specific polyubiquitin chain linkages Nat. Struct. Mol. Biol. 14 2007 941 948
4. R. Das, J. Mariano, Y.C. Tsai, R.C. Kalathur, Z. Kostova, J. Li, S.G. Tarasov, R.L. McFeeters, A.S. Altieri, and X. Ji Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78 Mol. Cell 34 2009 674 685
5. A.B. Datta, G.L. Hura, and C. Wolberger The structure and conformation of Lys63-linked tetraubiquitin J. Mol. Biol. 392 2009 1117 1124
6. S.J. de Vries, A.D. van Dijk, M. Krzeminski, M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar, and A.M. Bonvin HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets Proteins 69 2007 726 733
7. 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
8. C. Dominguez, R. Boelens, and A.M. Bonvin HADDOCK: a protein-protein docking approach based on biochemical or biophysical information J. Am. Chem. Soc. 125 2003 1731 1737
9. M.T. Haldeman, G. Xia, E.M. Kasperek, and C.M. Pickart Structure and function of ubiquitin conjugating enzyme E2-25K: the tail is a core-dependent activity element Biochemistry 36 1997 10526 10537
10. T. Hirano, O. Serve, M. Yagi-Utsumi, E. Takemoto, T. Hiromoto, T. Satoh, T. Mizushima, and K. Kato Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution J. Biol. Chem. 286 2011 37496 37502
11. R.M. Hofmann, and C.M. Pickart In vitro assembly and recognition of Lys-63 polyubiquitin chains J. Biol. Chem. 276 2001 27936 27943
12. J.H. Hurley, S. Lee, and G. Prag Ubiquitin-binding domains Biochem. J. 399 2006 361 372
13. K. Husnjak, S. Elsasser, N. Zhang, X. Chen, L. Randles, Y. Shi, K. Hofmann, K.J. Walters, D. Finley, and I. Dikic Proteasome subunit Rpn13 is a novel ubiquitin receptor Nature 453 2008 481 488
14. F. Ikeda, and I. Dikic Atypical ubiquitin chains: new molecular signals. 'Protein Modifications: Beyond the Usual Suspects' review series EMBO Rep. 9 2008 536 542
15. J. Iwahara, C.D. Schwieters, and G.M. Clore Ensemble approach for NMR structure refinement against (1)H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule J. Am. Chem. Soc. 126 2004 5879 5896
16. B.A. Johnson Using NMRView to visualize and analyze the NMR spectra of macromolecules Methods Mol. Biol. 278 2004 313 352
17. R.S. Kang, C.M. Daniels, S.A. Francis, S.C. Shih, W.J. Salerno, L. Hicke, and I. Radhakrishnan Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding Cell 113 2003 621 630
18. D. Komander, and M. Rape The ubiquitin code Annu. Rev. Biochem. 81 2012 203 229
19. M.Y. Lai, D. Zhang, N. Laronde-Leblanc, and D. Fushman Structural and biochemical studies of the open state of Lys48-linked diubiquitin Biochim. Biophys. Acta 1823 2012 2046 2056
20. W. Li, D. Tu, A.T. Brunger, and Y. Ye A ubiquitin ligase transfers preformed polyubiquitin chains from a conjugating enzyme to a substrate Nature 446 2007 333 337
21. W. Li, D. Tu, L. Li, T. Wollert, R. Ghirlando, A.T. Brunger, and Y. Ye Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2 Proc. Natl. Acad. Sci. USA 106 2009 3722 3727
22. D. Morito, K. Hirao, Y. Oda, N. Hosokawa, F. Tokunaga, D.M. Cyr, K. Tanaka, K. Iwai, and K. Nagata Gp78 cooperates with RMA1 in endoplasmic reticulum-associated degradation of CFTRDeltaF508 Mol. Biol. Cell 19 2008 1328 1336
23. K. Newton, M.L. Matsumoto, I.E. Wertz, D.S. Kirkpatrick, J.R. Lill, J. Tan, D. Dugger, N. Gordon, S.S. Sidhu, and F.A. Fellouse Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies Cell 134 2008 668 678
24. L.A. Passmore, and D. Barford Getting into position: the catalytic mechanisms of protein ubiquitylation Biochem. J. 379 2004 513 525
25. P. Peschard, G. Kozlov, T. Lin, I.A. Mirza, A.M. Berghuis, S. Lipkowitz, M. Park, and K. Gehring Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b Mol. Cell 27 2007 474 485
26. J. Piotrowski, R. Beal, L. Hoffman, K.D. Wilkinson, R.E. Cohen, and C.M. Pickart Inhibition of the 26 S proteasome by polyubiquitin chains synthesized to have defined lengths J. Biol. Chem. 272 1997 23712 23721
27. C.P. Ponting Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction Biochem. J. 351 2000 527 535
28. G. Prag, S. Misra, E.A. Jones, R. Ghirlando, B.A. Davies, B.F. Horazdovsky, and J.H. Hurley Mechanism of ubiquitin recognition by the CUE domain of Vps9p Cell 113 2003 609 620
29. S. Raasi, R. Varadan, D. Fushman, and C.M. Pickart Diverse polyubiquitin interaction properties of ubiquitin-associated domains Nat. Struct. Mol. Biol. 12 2005 708 714
30. M.C. Rodrigo-Brenni, and D.O. Morgan Sequential E2s drive polyubiquitin chain assembly on APC targets Cell 130 2007 127 139
31. M. Sattler, J. Schleucher, and C. Griesinger Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients Prog. Nucl. Magn. Reson. Spectrosc. 34 1999 93 158
32. S.C. Shih, G. Prag, S.A. Francis, M.A. Sutanto, J.H. Hurley, and L. Hicke A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain EMBO J. 22 2003 1273 1281
33. B.L. Song, N. Sever, and R.A. DeBose-Boyd Gp78, a membrane-anchored ubiquitin ligase, associates with Insig-1 and couples sterol-regulated ubiquitination to degradation of HMG CoA reductase Mol. Cell 19 2005 829 840
34. J.S. Thrower, L. Hoffman, M. Rechsteiner, and C.M. Pickart Recognition of the polyubiquitin proteolytic signal EMBO J. 19 2000 94 102
35. Y.C. Tsai, A. Mendoza, J.M. Mariano, M. Zhou, Z. Kostova, B. Chen, T. Veenstra, S.M. Hewitt, L.J. Helman, C. Khanna, and A.M. Weissman The ubiquitin ligase gp78 promotes sarcoma metastasis by targeting KAI1 for degradation Nat. Med. 13 2007 1504 1509
36. H.D. Ulrich, and S. Jentsch Two RING finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repair EMBO J. 19 2000 3388 3397
37. R. Varadan, M. Assfalg, S. Raasi, C. Pickart, and D. Fushman Structural determinants for selective recognition of a Lys48-linked polyubiquitin chain by a UBA domain Mol. Cell 18 2005 687 698
38. J.M. Winget, and T. Mayor The diversity of ubiquitin recognition: hot spots and varied specificity Mol. Cell 38 2010 627 635
39. H. Wu, Y.C. Lo, and S.C. Lin Recent advances in polyubiquitin chain recognition F1000 Biol. Rep. 2 2010 1 5
40. D. Zhang, S. Raasi, and D. Fushman Affinity makes the difference: nonselective interaction of the UBA domain of Ubiquilin-1 with monomeric ubiquitin and polyubiquitin chains J. Mol. Biol. 377 2008 162 180
41. N. Zhang, Q. Wang, A. Ehlinger, L. Randles, J.W. Lary, Y. Kang, A. Haririnia, A.J. Storaska, J.L. Cole, D. Fushman, and K.J. Walters Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13 Mol. Cell 35 2009 280 290
42. C. Zwahlen, P. Legault, S.J.F. Vincent, J. Greenblatt, R. Konrat, and L.E. Kay Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: application to a bacteriophage λ N-peptide/boxB RNA nomplex J. Am. Chem. Soc. 119 1997 6711 6721