Kim T, Hofmann K, von Arnim AG, Chamovitz DA: PCI complexes: pretty complex interactions in diverse signaling pathways. Trends Plant Sci 2001, 6(8):379–386. 10.1016/S1360-1385(01)02015-5
Article
CAS
PubMed
Google Scholar
Hofmann K, Bucher P: The PCI domain: a common theme in three multiprotein complexes. Trends Biochem Sci 1998, 23(6):204–205. 10.1016/S0968-0004(98)01217-1
Article
CAS
PubMed
Google Scholar
Aravind L, Ponting CP: Homologues of 26S proteasome subunits are regulators of transcription and translation. Protein Sci 1998, 7(5):1250–1254.
Article
PubMed Central
CAS
PubMed
Google Scholar
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(5):1169–1178. 10.1006/jmbi.2000.3912
Article
CAS
PubMed
Google Scholar
Fu H, Reis N, Lee Y, Glickman MH, Vierstra RD: Subunit interaction maps for the regulatory particle of the 26S proteasome and the COP9 signalosome. Embo J 2001, 20(24):7096–7107. 10.1093/emboj/20.24.7096
Article
PubMed Central
CAS
PubMed
Google Scholar
Glickman MH, Rubin DM, Coux O, Wefes I, Pfeifer G, Cjeka Z, Baumeister W, Fried VA, 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(5):615–623. 10.1016/S0092-8674(00)81603-7
Article
CAS
PubMed
Google Scholar
Verma R, Aravind L, Oania R, McDonald WH, Yates JR, Koonin EV, Deshaies RJ: Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 2002, 298(5593):611–615. 10.1126/science.1075898
Article
CAS
PubMed
Google Scholar
Maytal-Kivity V, Reis N, Hofmann K, Glickman MH: MPN+, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function. BMC Biochem 2002, 3(1):28. 10.1186/1471-2091-3-28
Article
PubMed Central
PubMed
Google Scholar
Yao T, Cohen RE: A cryptic protease couples deubiquitination and degradation by the proteasome. Nature 2002, 419(6905):403–407. 10.1038/nature01071
Article
CAS
PubMed
Google Scholar
Serino G, Deng XW: The COP9 signalosome: regulating plant development through the control of proteolysis. Annu Rev Plant Biol 2003, 54: 165–182. 10.1146/annurev.arplant.54.031902.134847
Article
CAS
PubMed
Google Scholar
Schwechheimer C, Deng XW: COP9 signalosome revisited: a novel mediator of protein degradation. Trends Cell Biol 2001, 11(10):420–426. 10.1016/S0962-8924(01)02091-8
Article
CAS
PubMed
Google Scholar
Cope GA, Suh GS, Aravind L, Schwarz SE, Zipursky SL, Koonin EV, Deshaies RJ: Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science 2002, 298(5593):608–611. 10.1126/science.1075901
Article
CAS
PubMed
Google Scholar
Asano K, Kinzy TG, Merrick WC, Hershey JW: Conservation and diversity of eukaryotic translation initiation factor eIF3. J Biol Chem 1997, 272(2):1101–1109. 10.1074/jbc.272.28.17668
Article
CAS
PubMed
Google Scholar
Dever TE: Translation initiation: adept at adapting. Trends Biochem Sci 1999, 24(10):398–403. 10.1016/S0968-0004(99)01457-7
Article
CAS
PubMed
Google Scholar
Tran HJ, Allen MD, Lowe J, Bycroft M: Structure of the Jab1/MPN domain and its implications for proteasome function. Biochemistry 2003, 42(39):11460–11465. 10.1021/bi035033g
Article
CAS
PubMed
Google Scholar
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):1–9. 10.1006/jmbi.2000.4288
Article
CAS
PubMed
Google Scholar
Valasek L, Phan L, Schoenfeld LW, Valaskova V, Hinnebusch AG: Related eIF3 subunits TIF32 and HCR1 interact with an RNA recognition motif in PRT1 required for eIF3 integrity and ribosome binding. Embo J 2001, 20(4):891–904. 10.1093/emboj/20.4.891
Article
PubMed Central
CAS
PubMed
Google Scholar
Lier S, Paululat A: The proteasome regulatory particle subunit Rpn6 is required for Drosophila development and interacts physically with signalosome subunit Alien/CSN2. Gene 2002, 298(2):109–119. 10.1016/S0378-1119(02)00930-7
Article
CAS
PubMed
Google Scholar
Freilich S, Oron E, Kapp Y, Nevo-Caspi Y, Orgad S, Segal D, Chamovitz DA: The COP9 signalosome is essential for development of Drosophila melanogaster. Curr Biol 1999, 9(20):1187–1190. 10.1016/S0960-9822(00)80023-8
Article
CAS
PubMed
Google Scholar
Bucher P, Karplus K, Moeri N, Hofmann K: A flexible motif search technique based on generalized profiles. Comput Chem 1996, 20(1):3–23. 10.1016/S0097-8485(96)80003-9
Article
CAS
PubMed
Google Scholar
Maytal-Kivity V, Pick E, Piran R, Hofmann K, Glickman MH: The COP9 signalosome-like complex in S. cerevisiae and links to other PCI complexes. Int J Biochem Cell Biol 2003, 35(5):706–715. 10.1016/S1357-2725(02)00378-3
Article
CAS
PubMed
Google Scholar
Hulo N, Sigrist CJ, Le Saux V, Langendijk-Genevaux PS, Bordoli L, Gattiker A, De Castro E, Bucher P, Bairoch A: Recent improvements to the PROSITE database. Nucleic Acids Res 2004, 32 Database issue: D134–7. 10.1093/nar/gkh044
Article
Google Scholar
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. Nucleic Acids Res 2004, 32 Database issue: D138–41. 10.1093/nar/gkh121
Article
Google Scholar
Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P: SMART 4.0: towards genomic data integration. Nucleic Acids Res 2004, 32 Database issue: D142–4. 10.1093/nar/gkh088
Article
Google Scholar
Mayeur GL, Fraser CS, Peiretti F, Block KL, Hershey JW: Characterization of eIF3k: a newly discovered subunit of mammalian translation initiation factor elF3. Eur J Biochem 2003, 270(20):4133–4139. 10.1046/j.1432-1033.2003.03807.x
Article
CAS
PubMed
Google Scholar
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(33):34983–34990. 10.1074/jbc.M405158200
Article
CAS
PubMed
Google Scholar
Hofmann K, Bucher P, Falquet L, Bairoch A: The PROSITE database, its status in 1999. Nucleic Acids Res 1999, 27(1):215–219. 10.1093/nar/27.1.215
Article
PubMed Central
CAS
PubMed
Google Scholar
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423(6937):241–254. 10.1038/nature01644
Article
CAS
PubMed
Google Scholar
D'Andrea LD, Regan L: TPR proteins: the versatile helix. Trends Biochem Sci 2003, 28(12):655–662. 10.1016/j.tibs.2003.10.007
Article
PubMed
Google Scholar
Rost B, Liu J: The PredictProtein server. Nucleic Acids Res 2003, 31(13):3300–3304. 10.1093/nar/gkg508
Article
PubMed Central
CAS
PubMed
Google Scholar
Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ: JPred: a consensus secondary structure prediction server. Bioinformatics 1998, 14(10):892–893. 10.1093/bioinformatics/14.10.892
Article
CAS
PubMed
Google Scholar
Gough J, Karplus K, Hughey R, Chothia C: Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001, 313(4):903–919. 10.1006/jmbi.2001.5080
Article
CAS
PubMed
Google Scholar
Valasek L, Hasek J, Nielsen KH, Hinnebusch AG: Dual function of eIF3j/Hcr1p in processing 20 S pre-rRNA and translation initiation. J Biol Chem 2001, 276(46):43351–43360. 10.1074/jbc.M106887200
Article
CAS
PubMed
Google Scholar
Morris-Desbois C, Rety S, Ferro M, Garin J, Jalinot P: The human protein HSPC021 interacts with Int-6 and is associated with eukaryotic translation initiation factor 3. J Biol Chem 2001, 276(49):45988–45995. 10.1074/jbc.M104966200
Article
CAS
PubMed
Google Scholar
Holm L, Sander C: Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997, 25(1):231–234. 10.1093/nar/25.1.231
Article
PubMed Central
CAS
PubMed
Google Scholar
Ciccarelli FD, Izaurralde E, Bork P: The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. BMC Bioinformatics 2003, 4(1):64. 10.1186/1471-2105-4-64
Article
PubMed Central
PubMed
Google Scholar
Kajava AV: What curves alpha-solenoids? Evidence for an alpha-helical toroid structure of Rpn1 and Rpn2 proteins of the 26 S proteasome. J Biol Chem 2002, 277(51):49791–49798. 10.1074/jbc.M204982200
Article
CAS
PubMed
Google Scholar
Chang EC, Schwechheimer C: ZOMES III: the interface between signalling and proteolysis. EMBO Rep 2004, 5(11):1041–1045. 10.1038/sj.embor.7400275
Article
PubMed Central
CAS
PubMed
Google Scholar
Isono E, Saeki Y, Yokosawa H, Toh-e A: Rpn7 Is required for the structural integrity of the 26 S proteasome of Saccharomyces cerevisiae. J Biol Chem 2004, 279(26):27168–27176. 10.1074/jbc.M314231200
Article
CAS
PubMed
Google Scholar
Bairoch A, Apweiler R: The Swiss-Prot Protein Sequence Data Bank and Its Supplement Trembl. Nucleic Acids Research 1997, 25(1):31–36. 10.1093/nar/25.1.31
Article
PubMed Central
CAS
PubMed
Google Scholar
Benton D: Recent changes in the GenBank On-line Service. Nucleic Acids Research 1990, 18(6):1517–1520.
Article
PubMed Central
CAS
PubMed
Google Scholar
Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences of the United States of America 1992, 89(22):10915–10919.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hofmann K: Sensitive protein comparisons with profiles and hidden Markov models. Brief Bioinform 2000, 1(2):167–178.
Article
CAS
PubMed
Google Scholar
Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302(1):205–217. 10.1006/jmbi.2000.4042
Article
CAS
PubMed
Google Scholar