Structural Insights into the COP9 Signalosome and Its Common Architecture with the 26S Proteasome Lid and eIF3

Structure

Volumn 18, Issue 4, 2010, Pages 518-527

  Enchev, Radoslav I ^a   Schreiber, Anne ^a   Beuron, Fabienne ^a   Morris, Edward P ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

Cellbio; Proteins

Indexed keywords

COP9 SIGNALOSOME; PROTEASOME; PROTEIN ELF3; PROTEIN LID; RECOMBINANT PROTEIN; UNCLASSIFIED DRUG;

ANIMAL CELL; ANTIBODY LABELING; ARTICLE; CHEMICAL ANALYSIS; CONTROLLED STUDY; ELECTRON MICROSCOPY; ENZYME SUBSTRATE COMPLEX; ERYTHROCYTE; HUMAN; HUMAN CELL; INSECT CELL; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURAL HOMOLOGY; THREE DIMENSIONAL IMAGING;

CLONING, MOLECULAR; ERYTHROCYTES; EUKARYOTIC INITIATION FACTOR-3; HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MULTIPROTEIN COMPLEXES; PEPTIDE HYDROLASES; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; SIGNAL TRANSDUCTION;

HEXAPODA;

EID: 77951639210     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2010.02.008     Document Type: Article

References (45)

1. Ambroggio X.I., Rees D.C., Deshaies R.J. JAMM: a metalloprotease-like zinc site in the proteasome and signalosome. PLoS Biol. 2004, 2:E2.
2. Berger I., Fitzgerald D.J., Richmond T.J. Baculovirus expression system for heterologous multiprotein complexes. Nat. Biotechnol. 2004, 22:1583-1587.
3. Ciccarelli F.D., Izaurralde E., Bork P. The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. BMC Bioinformatics 2003, 4:64.
4. Cole C., Barber J.D., Barton G.J. The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 2008, 36:W197-W201.
5. Cope G.A., Suh G.S., Aravind L., Schwarz S.E., Zipursky S.L., Koonin E.V., Deshaies R.J. Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science 2002, 298:608-611.
6. da Fonseca P.C., Morris E.P. Structure of the human 26S proteasome: subunit radial displacements open the gate into the proteolytic core. J. Biol. Chem. 2008, 283:23305-23314.
7. Deng X.W., Dubiel W., Wei N., Hofmann K., Mundt K. Unified nomenclature for the COP9 signalosome and its subunits: an essential regulator of development. Trends Genet. 2000, 16:289.
8. Dessau M., Halimi Y., Erez T., Chomsky-Hecht O., Chamovitz D.A., Hirsch J.A. The Arabidopsis COP9 signalosome subunit 7 is a model PCI domain protein with subdomains involved in COP9 signalosome assembly. Plant Cell 2008, 20:2815-2834.
9. Duda D.M., Borg L.A., Scott D.C., Hunt H.W., Hammel M., Schulman B.A. Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Cell 2008, 134:995-1006.
10. Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., Leith A. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 1996, 116:190-199.
11. Fu H., Reis N., Lee Y., Glickman M.H., Vierstra R.D. Subunit interaction maps for the regulatory particle of the 26S proteasome and the COP9 signalosome. EMBO J. 2001, 20:7096-7107.
12. Glickman M.H., Rubin D.M., Coux O., Wefes I., Pfeifer G., Cjeka Z., Baumeister W., Fried V.A., Finley D. A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3. Cell 1998, 94:615-623.
13. Goddard T.D., Huang C.C., Ferrin T.E. Visualizing density maps with UCSF Chimera. J. Struct. Biol. 2007, 157:281-287.
14. Hetfeld B.K., Bech-Otschir D., Dubiel W. Purification method of the COP9 signalosome from human erythrocytes. Methods Enzymol. 2005, 398:481-491.
15. Hinnebusch A.G. eIF3: a versatile scaffold for translation initiation complexes. Trends Biochem. Sci. 2006, 31:553-562.
16. Holm L., Kaariainen S., Rosenstrom P., Schenkel A. Searching protein structure databases with DaliLite v.3. Bioinformatics 2008, 24:2780-2781.
17. Jones J., Wu K., Yang Y., Guerrero C., Nillegoda N., Pan Z.Q., Huang L. A targeted proteomic analysis of the ubiquitin-like modifier nedd8 and associated proteins. J. Proteome Res. 2008, 7:1274-1287.
18. Kapelari B., Bech-Otschir D., Hegerl R., Schade R., Dumdey R., Dubiel W. Electron microscopy and subunit-subunit interaction studies reveal a first architecture of COP9 signalosome. J. Mol. Biol. 2000, 300:1169-1178.
19. Kelley L.A., Sternberg M.J. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4:363-371.
20. Lanzavecchia S., Cantele F., Bellon P.L. Alignment of 3D structures of macromolecular assemblies. Bioinformatics 2001, 17:58-62.
21. Liakopoulos D., Doenges G., Matuschewski K., Jentsch S. A novel protein modification pathway related to the ubiquitin system. EMBO J. 1998, 17:2208-2214.
22. Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 1999, 128:82-97.
23. Lyapina S., Cope G., Shevchenko A., Serino G., Tsuge T., Zhou C., Wolf D.A., Wei N., Shevchenko A., Deshaies R.J. Promotion of NEDD-CUL1 conjugate cleavage by COP9 signalosome. Science 2001, 292:1382-1385.
24. McGuffin L.J., Bryson K., Jones D.T. The PSIPRED protein structure prediction server. Bioinformatics 2000, 16:404-405.
25. Menon S., Rubio V., Wang X., Deng X.W., Wei N. Purification of the COP9 signalosome from porcine spleen, human cell lines, and Arabidopsis thaliana plants. Methods Enzymol. 2005, 398:468-481.
26. Ohki Y., Funatsu N., Konishi N., Chiba T. The mechanism of poly-NEDD8 chain formation in vitro. Biochem. Biophys. Res. Commun. 2009, 381:443-447.
27. Pick E., Hofmann K., Glickman M. PCI complexes: beyond the proteasome, CSN, and eIF3 troika. Mol. Cell 2009, 35:260-264.
28. Pollastri G., Przybylski D., Rost B., Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002, 47:228-235.
29. Saha A., Deshaies R.J. Multimodal activation of the ubiquitin ligase SCF by Nedd8 conjugation. Mol. Cell 2008, 32:21-31.
30. Sanches M., Alves B.S., Zanchin N.I., Guimaraes B.G. The crystal structure of the human Mov34 MPN domain reveals a metal-free dimer. J. Mol. Biol. 2007, 370:846-855.
31. Scheel H., Hofmann K. Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes. BMC Bioinformatics 2005, 6:71.
32. Schwechheimer C., Serino G., Callis J., Crosby W.L., Lyapina S., Deshaies R.J., Gray W.M., Estelle M., Deng X.W. Interactions of the COP9 signalosome with the E3 ubiquitin ligase SCFTIRI in mediating auxin response. Science 2001, 292:1379-1382.
33. Sharon M., Taverner T., Ambroggio X.I., Deshaies R.J., Robinson C.V. Structural organization of the 19S proteasome lid: insights from MS of intact complexes. PLoS Biol. 2006, 4:e267.
34. Sharon M., Mao H., Boeri Erba E., Stephens E., Zheng N., Robinson C.V. Symmetrical modularity of the COP9 signalosome complex suggests its multifunctionality. Structure 2009, 17:31-40.
35. Siridechadilok B., Fraser C.S., Hall R.J., Doudna J.A., Nogales E. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 2005, 310:1513-1515.
36. Tomoda K., Kubota Y., Arata Y., Mori S., Maeda M., Tanaka T., Yoshida M., Yoneda-Kato N., Kato J.Y. The cytoplasmic shuttling and subsequent degradation of p27Kip1 mediated by Jab1/CSN5 and the COP9 signalosome complex. J. Biol. Chem. 2002, 277:2302-2310.
37. Tsuge T., Matsui M., Wei N. The subunit 1 of the COP9 signalosome suppresses gene expression through its N-terminal domain and incorporates into the complex through the PCI domain. J. Mol. Biol. 2001, 305:1-9.
38. van Heel M., Harauz G., Orlova E.V., Schmidt R., Schatz M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 1996, 116:17-24.
39. Wei N., Deng X.W. The COP9 signalosome. Annu. Rev. Cell Dev. Biol. 2003, 19:261-286.
40. Wei Z., Zhang P., Zhou Z., Cheng Z., Wan M., Gong W. Crystal structure of human eIF3k, the first structure of eIF3 subunits. J. Biol. Chem. 2004, 279:34983-34990.
41. Wolf D.A., Zhou C., Wee S. The COP9 signalosome: an assembly and maintenance platform for cullin ubiquitin ligases?. Nat. Cell Biol. 2003, 5:1029-1033.
42. Yang X., Menon S., Lykke-Andersen K., Tsuge T., Di X., Wang X., Rodriguez-Suarez R.J., Zhang H., Wei N. The COP9 signalosome inhibits p27(kip1) degradation and impedes G1-S phase progression via deneddylation of SCF Cul1. Curr. Biol. 2002, 12:667-672.
43. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008, 9:40.
44. Zheng N., Schulman B.A., Song L., Miller J.J., Jeffrey P.D., Wang P., Chu C., Koepp D.M., Elledge S.J., Pagano M., et al. Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex. Nature 2002, 416:703-709.
45. Zhou M., Sandercock A.M., Fraser C.S., Ridlova G., Stephens E., Schenauer M.R., Yokoi-Fong T., Barsky D., Leary J.A., Hershey J.W., et al. Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. Proc. Natl. Acad. Sci. USA 2008, 105:18139-18144.