An Archaeal Homolog of Proteasome Assembly Factor Functions as a Proteasome Activator

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Kumoi, Kentaro ^a   Satoh, Tadashi ^a   Murata, Kazuyoshi ^b   Hiromoto, Takeshi ^a   Mizushima, Tsunehiro ^a,c   Kamiya, Yukiko ^d   Noda, Masanori ^e   Uchiyama, Susumu ^e   Yagi, Hirokazu ^a   Kato, Koichi ^a,d  

^a NAGOYA CITY UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE FOR PHYSIOLOGICAL SCIENCES   (Japan)

^c UNIVERSITY OF HYOGO   (Japan)

^d OKAZAKI INSTITUTE FOR INTEGRATIVE BIOSCIENCE   (Japan)

^e OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

20S PROTEASOME; ARCHAEAL PROTEIN; CHAPERONE; PBAA PROTEIN; PBAB PROTEIN; PROTEASOME; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; MOLECULAR EVOLUTION; MOLECULAR RECOGNITION; PROTEIN AGGREGATION; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN UNFOLDING; PYROCOCCUS FURIOSUS;

ARCHAEA; ARCHAEAL PROTEINS; EVOLUTION, MOLECULAR; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN BINDING;

EID: 84875290826     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060294     Document Type: Article

References (46)

1. Baumeister W, Walz J, Zühl F, Seemüller E, (1998) The proteasome: paradigm of a self-compartmentalizing protease. Cell 92: 367-380.
2. Coux O, Tanaka K, Goldberg AL, (1996) Structure and functions of the 20S and 26S proteasomes. Annu Rev Biochem 65: 801-847.
3. Tanaka K, (2009) The proteasome: overview of structure and functions. Proc Jpn Acad Ser B Phys Biol Sci 85: 12-36.
4. Löwe J, Stock D, Jap B, Zwickl P, Baumeister W, et al. (1995) Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution. Science 268: 533-539.
5. Unno M, Mizushima T, Morimoto Y, Tomisugi Y, Tanaka K, et al. (2002) The structure of the mammalian 20S proteasome at 2.75 Å resolution. Structure 10: 609-618.
6. Stadtmueller BM, Hill CP, (2011) Proteasome activators. Mol Cell 41: 8-19.
7. Förster A, Masters EI, Whitby FG, Robinson H, Hill CP, (2005) The 1.9 Å structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. Mol Cell 18: 589-599.
8. Sadre-Bazzaz K, Whitby FG, Robinson H, Formosa T, Hill CP, (2010) Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening. Mol Cell 37: 728-735.
9. Ma CP, Slaughter CA, DeMartino GN, (1992) Identification, purification, and characterization of a protein activator (PA28) of the 20 S proteasome (macropain). J Biol Chem 267: 10515-10523.
10. Ustrell V, Hoffman L, Pratt G, Rechsteiner M, (2002) PA200, a nuclear proteasome activator involved in DNA repair. EMBO J 21: 3516-3525.
11. Benaroudj N, Goldberg AL, (2000) PAN, the proteasome-activating nucleotidase from archaebacteria, is a protein-unfolding molecular chaperone. Nat Cell Biol 2: 833-839.
12. Benaroudj N, Zwickl P, Seemüller E, Baumeister W, Goldberg AL, (2003) ATP hydrolysis by the proteasome regulatory complex PAN serves multiple functions in protein degradation. Mol Cell 11: 69-78.
13. Maupin-Furlow J, (2012) Proteasomes and protein conjugation across domains of life. Nat Rev Microbiol 10: 100-111.
14. Rabl J, Smith DM, Yu Y, Chang SC, Goldberg AL, et al. (2008) Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. Mol Cell 30: 360-368.
15. Smith DM, Chang SC, Park S, Finley D, Cheng Y, et al. (2007) Docking of the proteasomal ATPases' carboxyl termini in the 20S proteasome's α ring opens the gate for substrate entry. Mol Cell 27: 731-744.
16. Yu Y, Smith DM, Kim HM, Rodriguez V, Goldberg AL, et al. (2010) Interactions of PAN's C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions. EMBO J 29: 692-702.
17. Barthelme D, Sauer RT, (2012) Identification of the Cdc48*20S proteasome as an ancient AAA+ proteolytic machine. Science 337: 843-846.
18. Murata S, Yashiroda H, Tanaka K, (2009) Molecular mechanisms of proteasome assembly. Nat Rev Mol Cell Biol 10: 104-115.
19. Ramos PC, Dohmen RJ, (2008) PACemakers of proteasome core particle assembly. Structure 16: 1296-1304.
20. Kusmierczyk AR, Kunjappu MJ, Kim RY, Hochstrasser M, (2011) A conserved 20S proteasome assembly factor requires a C-terminal HbYX motif for proteasomal precursor binding. Nat Struct Mol Biol 18: 622-629.
21. Madding LS, Michel JK, Shockley KR, Conners SB, Epting KL, et al. (2007) Role of the β1 subunit in the function and stability of the 20S proteasome in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 189: 583-590.
22. Menon AL, Poole FL, 2nd, Cvetkovic A, Trauger SA, Kalisiak E, et al (2009) Novel multiprotein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome. Mol Cell Proteomics 8: 735-751.
23. Zwickl P, Kleinz J, Baumeister W, (1994) Critical elements in proteasome assembly. Nat Struct Biol 1: 765-770.
24. Smith DM, Kafri G, Cheng Y, Ng D, Walz T, et al. (2005) ATP binding to PAN or the 26S ATPases causes association with the 20S proteasome, gate opening, and translocation of unfolded proteins. Mol Cell 20: 687-698.
25. Li X, Lonard DM, Jung SY, Malovannaya A, Feng Q, et al. (2006) The SRC-3/AIB1 coactivator is degraded in a ubiquitin- and ATP-independent manner by the REGγ proteasome. Cell 124: 381-392.
26. Li X, Amazit L, Long W, Lonard DM, Monaco JJ, et al. (2007) Ubiquitin- and ATP-independent proteolytic turnover of p21 by the REGγ-proteasome pathway. Mol Cell 26: 831-842.
27. Liu CW, Corboy MJ, DeMartino GN, Thomas PJ, (2003) Endoproteolytic activity of the proteasome. Science 299: 408-411.
28. Hirano Y, Hendil KB, Yashiroda H, Iemura S, Nagane R, et al. (2005) A heterodimeric complex that promotes the assembly of mammalian 20S proteasomes. Nature 437: 1381-1385.
29. Holm L, Rosenström P, (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38: W545-549.
30. Djuranovic S, Hartmann MD, Habeck M, Ursinus A, Zwickl P, et al. (2009) Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases. Mol Cell 34: 580-590.
31. Zhang F, Hu M, Tian G, Zhang P, Finley D, et al. (2009) Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Mol Cell 34: 473-484.
32. Zhang F, Wu Z, Zhang P, Tian G, Finley D, et al. (2009) Mechanism of substrate unfolding and translocation by the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Mol Cell 34: 485-496.
33. Stadtmueller BM, Kish-Trier E, Ferrell K, Petersen CN, Robinson H, et al. (2012) Structure of a Proteasome Pba1-Pba2 Complex: Implications for proteasome assembly, activation, and biological function. J Biol Chem 287: 37371-37382.
34. Sasakawa H, Sakata E, Yamaguchi Y, Masuda M, Mori T, et al. (2007) Ultra-high field NMR studies of antibody binding and site-specific phosphorylation of α-synuclein. Biochem Biophys Res Commun 363: 795-799.
35. Schuck P, (2000) Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys J 78: 1606-1619.
36. Otwinowski Z, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods in Enzymology 276: 307-326.
37. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213-221.
38. Langer G, Cohen SX, Lamzin VS, Perrakis A, (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3: 1171-1179.
39. Emsley P, Lohkamp B, Scott WG, Cowtan K, (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486-501.
40. Murshudov GN, Vagin AA, Dodson EJ, (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240-255.
41. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, et al (2003) Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 50: 437-450.
42. Murata K, Liu X, Danev R, Jakana J, Schmid MF, et al. (2010) Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions. Structure 18: 903-912.
43. Murata K, Nishimura S, Kuniyasu A, Nakayama H, (2010) Three-dimensional structure of the α1-β complex in the skeletal muscle dihydropyridine receptor by single-particle electron microscopy. J Electron Microsc (Tokyo) 59: 215-226.
44. Kremer JR, Mastronarde DN, McIntosh JR, (1996) Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116: 71-76.
45. Ludtke SJ, Baldwin PR, Chiu W, (1999) EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128: 82-97.
46. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.