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PDBsum entry 1fnt
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protein metals Protein-protein interface(s) links
Hydrolase/hydrolase activator PDB id
1fnt

 

 

 

 

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Contents
Protein chains
238 a.a. *
247 a.a. *
241 a.a. *
239 a.a. *
244 a.a. *
233 a.a. *
240 a.a. *
196 a.a. *
222 a.a. *
204 a.a. *
198 a.a. *
212 a.a. *
222 a.a. *
233 a.a. *
(+ 8 more) 198 a.a. *
Metals
_MG ×14
* Residue conservation analysis
PDB id:
1fnt
Name: Hydrolase/hydrolase activator
Title: Crystal structure of the 20s proteasome from yeast in complex with the proteasome activator pa26 from trypanosome brucei at 3.2 angstroms resolution
Structure: Proteasome component c7-alpha. Chain: a, o. Engineered: yes. Proteasome component y7. Chain: b, p. Engineered: yes. Proteasome component y13. Chain: c, q. Engineered: yes.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Trypanosoma brucei. Organism_taxid: 5691. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: 42mer (from PQS)
Resolution:
3.20Å     R-factor:   0.255     R-free:   0.325
Authors: F.G.Whitby,E.Masters,L.Kramer,J.R.Knowlton,Y.Yao,C.C.Wang,C.P.Hill
Key ref:
F.G.Whitby et al. (2000). Structural basis for the activation of 20S proteasomes by 11S regulators. Nature, 408, 115-120. PubMed id: 11081519 DOI: 10.1038/35040607
Date:
23-Aug-00     Release date:   11-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P21243  (PSA1_YEAST) -  Proteasome subunit alpha type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		252 a.a.
238 a.a.
Protein chains
Pfam   ArchSchema ?
P23639  (PSA2_YEAST) -  Proteasome subunit alpha type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		250 a.a.
247 a.a.
Protein chains
Pfam   ArchSchema ?
P23638  (PSA3_YEAST) -  Proteasome subunit alpha type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		258 a.a.
241 a.a.
Protein chains
Pfam   ArchSchema ?
P40303  (PSA4_YEAST) -  Proteasome subunit alpha type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		254 a.a.
239 a.a.
Protein chains
Pfam   ArchSchema ?
P32379  (PSA5_YEAST) -  Proteasome subunit alpha type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		260 a.a.
244 a.a.
Protein chains
Pfam   ArchSchema ?
P40302  (PSA6_YEAST) -  Proteasome subunit alpha type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		234 a.a.
233 a.a.
Protein chains
Pfam   ArchSchema ?
P21242  (PSA7_YEAST) -  Probable proteasome subunit alpha type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		288 a.a.
240 a.a.
Protein chains
Pfam   ArchSchema ?
P38624  (PSB1_YEAST) -  Proteasome subunit beta type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		215 a.a.
196 a.a.
Protein chains
Pfam   ArchSchema ?
P25043  (PSB2_YEAST) -  Proteasome subunit beta type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		261 a.a.
222 a.a.
Protein chains
Pfam   ArchSchema ?
P25451  (PSB3_YEAST) -  Proteasome subunit beta type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		205 a.a.
204 a.a.
Protein chains
Pfam   ArchSchema ?
P22141  (PSB4_YEAST) -  Proteasome subunit beta type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		198 a.a.
198 a.a.
Protein chains
Pfam   ArchSchema ?
P30656  (PSB5_YEAST) -  Proteasome subunit beta type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		287 a.a.
212 a.a.*
Protein chains
Pfam   ArchSchema ?
P23724  (PSB6_YEAST) -  Proteasome subunit beta type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		241 a.a.
222 a.a.
Protein chains
Pfam   ArchSchema ?
P30657  (PSB7_YEAST) -  Proteasome subunit beta type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		266 a.a.
233 a.a.
Protein chains
Pfam   ArchSchema ?
Q9U8G2  (Q9U8G2_9TRYP) -  Proteasome activator protein PA26 (Fragment) from Trypanosoma brucei
Seq:
Struc: 		231 a.a.
198 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chains A, B, C, D, E, F, G, J, K, M, N, O, P, Q, R, S, T, U, X, Y, a, b: E.C.3.4.99.46  - Transferred entry: 3.4.25.1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 3: Chains H, I, L, V, W, Z: E.C.3.4.25.1  - proteasome endopeptidase complex.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cleavage at peptide bonds with very broad specificity.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

 

 
DOI no: 10.1038/35040607 Nature 408:115-120 (2000)
PubMed id: 11081519  
 
 
Structural basis for the activation of 20S proteasomes by 11S regulators.
F.G.Whitby, E.I.Masters, L.Kramer, J.R.Knowlton, Y.Yao, C.C.Wang, C.P.Hill.
 
  ABSTRACT  
 
Most of the non-lysosomal proteolysis that occurs in eukaryotic cells is performed by a nonspecific and abundant barrel-shaped complex called the 20S proteasome. Substrates access the active sites, which are sequestered in an internal chamber, by traversing a narrow opening (alpha-annulus) that is blocked in the unliganded 20S proteasome by amino-terminal sequences of alpha-subunits. Peptide products probably exit the 20S proteasome through the same opening. 11S regulators (also called PA26 (ref. 4), PA28 (ref. 5) and REG) are heptamers that stimulate 20S proteasome peptidase activity in vitro and may facilitate product release in vivo. Here we report the co-crystal structure of yeast 20S proteasome with the 11S regulator from Trypanosoma brucei (PA26). PA26 carboxy-terminal tails provide binding affinity by inserting into pockets on the 20S proteasome, and PA26 activation loops induce conformational changes in alpha-subunits that open the gate separating the proteasome interior from the intracellular environment. The reduction in processivity expected for an open conformation of the exit gate may explain the role of 11S regulators in the production of ligands for major histocompatibility complex class I molecules.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Structure of PA26. a, PA26 heptamer coloured by monomer. b, Monomer coloured by secondary structure. This orientation corresponds to the magenta monomer in a. c, Proteasome-binding surface of the PA26 heptamer. Activation loops are yellow, C-terminal helix is red. View direction is from below structure in a. d, Alignment of T. brucei PA26 and human REG amino-acid sequences. Identical residues are shaded in pink. Disordered residues are indicated with a thin line. PA26/REG residues are structurally equivalent from the start of helix 2 to the C terminus as indicated. The alignment for helix 1 is tentative. The hexahistidine affinity tag inserted after the initiator methionine of PA26 is shown. Every tenth residue is marked with a dash (the first PA26 residue marked is Gln10). Residues that contact the 20S proteasome are indicated with blue triangles. The PA26 construct used in this study has a threonine in place of the authentic serine^4 at position 226. 		Figure 4.
Figure 4: Mechanism of binding. a, Top view of the 20S proteasome -subunits with the molecular surface shown as a purple net. The seven pockets that receive PA26 C termini surround the central open gate. b, Side view of PA26 C-terminal residues (yellow) binding into a pocket. This view is a close up of the interface at the top left of Fig. 1b. The PA26 C-terminal carboxylate approaches the N terminus of 5 helix 1, which is in a vertical orientation in the lower part of this figure. 2F[o] - F[ c] density (0.8 times the r.m.s. deviation) was computed following torsion angle dynamics refinement in which the last 30 residues of PA26 were set to zero occupancy. Density for the last well-defined side chain of PA26, Arg 223, appears to connect the two segments of PA26 near the top of this figure.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 408, 115-120) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21499243 A.R.Kusmierczyk, M.J.Kunjappu, R.Y.Kim, and M.Hochstrasser (2011).
A conserved 20S proteasome assembly factor requires a C-terminal HbYX motif for proteasomal precursor binding.
  Nat Struct Mol Biol, 18, 622-629.  
21387144 E.J.Sijts, and P.M.Kloetzel (2011).
The role of the proteasome in the generation of MHC class I ligands and immune responses.
  Cell Mol Life Sci, 68, 1491-1502.  
22037170 G.Tian, S.Park, M.J.Lee, B.Huck, F.McAllister, C.P.Hill, S.P.Gygi, and D.Finley (2011).
An asymmetric interface between the regulatory and core particles of the proteasome.
  Nat Struct Mol Biol, 18, 1259-1267.  
21529711 M.Bader, S.Benjamin, O.L.Wapinski, D.M.Smith, A.L.Goldberg, and H.Steller (2011).
A conserved f box regulatory complex controls proteasome activity in Drosophila.
  Cell, 145, 371-382.  
20536393 A.De Leo, G.Matusali, G.Arena, L.Di Renzo, and E.Mattia (2010).
Epstein-Barr virus lytic cycle activation alters proteasome subunit expression in Burkitt's lymphoma cells.
  Biol Chem, 391, 1041-1046.  
20305655 B.G.Lee, E.Y.Park, K.E.Lee, H.Jeon, K.H.Sung, H.Paulsen, H.Rübsamen-Schaeff, H.Brötz-Oesterhelt, and H.K.Song (2010).
Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism.
  Nat Struct Mol Biol, 17, 471-478.
PDB codes: 3ktg 3kth 3kti 3ktj 3ktk
19889631 B.M.Stadtmueller, K.Ferrell, F.G.Whitby, A.Heroux, H.Robinson, D.G.Myszka, and C.P.Hill (2010).
Structural models for interactions between the 20S proteasome and its PAN/19S activators.
  J Biol Chem, 285, 13-17.
PDB codes: 3jrm 3jse 3jtl
20091677 E.Jankowska, M.Gaczynska, P.Osmulski, E.Sikorska, R.Rostankowski, S.Madabhushi, M.Tokmina-Lukaszewska, and F.Kasprzykowski (2010).
Potential allosteric modulators of the proteasome activity.
  Biopolymers, 93, 481-495.  
20238402 F.Bardag-Gorce (2010).
Effects of ethanol on the proteasome interacting proteins.
  World J Gastroenterol, 16, 1349-1357.  
20227375 K.Sadre-Bazzaz, F.G.Whitby, H.Robinson, T.Formosa, and C.P.Hill (2010).
Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening.
  Mol Cell, 37, 728-735.
PDB codes: 1vsy 3l5q
20427185 L.Bedford, S.Paine, P.W.Sheppard, R.J.Mayer, and J.Roelofs (2010).
Assembly, structure, and function of the 26S proteasome.
  Trends Cell Biol, 20, 391-401.  
20010787 M.Groettrup, C.J.Kirk, and M.Basler (2010).
Proteasomes in immune cells: more than peptide producers?
  Nat Rev Immunol, 10, 73-78.  
20541423 N.Gallastegui, and M.Groll (2010).
The 26S proteasome: assembly and function of a destructive machine.
  Trends Biochem Sci, 35, 634-642.  
19793765 S.R.Powell, and A.Divald (2010).
The ubiquitin-proteasome system in myocardial ischaemia and preconditioning.
  Cardiovasc Res, 85, 303-311.  
20360109 T.L.Religa, R.Sprangers, and L.E.Kay (2010).
Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR.
  Science, 328, 98.
PDB codes: 2ku1 2ku2
20930034 Y.Xie (2010).
Structure, Assembly and Homeostatic Regulation of the 26S Proteasome.
  J Mol Cell Biol, 2, 308-317.  
20019667 Y.Yu, D.M.Smith, H.M.Kim, V.Rodriguez, A.L.Goldberg, and Y.Cheng (2010).
Interactions of PAN's C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions.
  EMBO J, 29, 692-702.
PDB code: 3ipm
20005843 A.Peth, H.C.Besche, and A.L.Goldberg (2009).
Ubiquitinated proteins activate the proteasome by binding to Usp14/Ubp6, which causes 20S gate opening.
  Mol Cell, 36, 794-804.  
19489727 D.Finley (2009).
Recognition and processing of ubiquitin-protein conjugates by the proteasome.
  Annu Rev Biochem, 78, 477-513.  
19639565 G.Chen, Y.Luo, X.Wang, Z.Zhao, H.Liu, H.Zhang, and Z.Li (2009).
A relatively simple and economical protocol for proteomic analyses of human 20S proteasome: Compatible with both scaled-up and scaled-down purifications.
  Electrophoresis, 30, 2422-2430.  
19895750 J.E.Rodríguez, J.C.Schisler, C.Patterson, and M.S.Willis (2009).
Seek and destroy: the ubiquitin----proteasome system in cardiac disease.
  Curr Hypertens Rep, 11, 396-405.  
19277057 J.M.Belote, and L.Zhong (2009).
Duplicated proteasome subunit genes in Drosophila and their roles in spermatogenesis.
  Heredity, 103, 23-31.  
19145068 K.Tanaka (2009).
The proteasome: overview of structure and functions.
  Proc Jpn Acad Ser B Phys Biol Sci, 85, 12-36.  
19365565 L.Gustafsson, S.Aits, P.Onnerfjord, M.Trulsson, P.Storm, and C.Svanborg (2009).
Changes in proteasome structure and function caused by HAMLET in tumor cells.
  PLoS ONE, 4, e5229.  
19006106 M.Cuccioloni, F.Montecchia, M.Amici, M.Mozzicafreddo, A.M.Eleuteri, and M.Angeletti (2009).
Co-chaperonin GroES as a modulator of proteasomal activity.
  J Mol Recognit, 22, 46-54.  
19688289 M.Matsushita, R.Matsudaira, K.Ikeda, M.Nawata, N.Tamura, and Y.Takasaki (2009).
Anti-proteasome activator 28alpha is a novel anti-cytoplasmic antibody in patients with systemic lupus erythematosus and Sjögren's syndrome.
  Mod Rheumatol, 19, 622-628.  
19342661 M.Ostankovitch, M.Altrich-Vanlith, V.Robila, and V.H.Engelhard (2009).
N-glycosylation enhances presentation of a MHC class I-restricted epitope from tyrosinase.
  J Immunol, 182, 4830-4835.  
19363223 N.Medalia, A.Beer, P.Zwickl, O.Mihalache, M.Beck, O.Medalia, and A.Navon (2009).
Architecture and molecular mechanism of PAN, the archaeal proteasome regulatory ATPase.
  J Biol Chem, 284, 22952-22960.  
19679091 P.A.Osmulski, M.Hochstrasser, and M.Gaczynska (2009).
A tetrahedral transition state at the active sites of the 20S proteasome is coupled to opening of the alpha-ring channel.
  Structure, 17, 1137-1147.  
19411624 P.Masson, D.Lundin, F.Söderbom, and P.Young (2009).
Characterization of a REG/PA28 proteasome activator homolog in Dictyostelium discoideum indicates that the ubiquitin- and ATP-independent REGgamma proteasome is an ancient nuclear protease.
  Eukaryot Cell, 8, 844-851.  
19165213 S.Murata, H.Yashiroda, and K.Tanaka (2009).
Molecular mechanisms of proteasome assembly.
  Nat Rev Mol Cell Biol, 10, 104-115.  
19412160 S.Park, J.Roelofs, W.Kim, J.Robert, M.Schmidt, S.P.Gygi, and D.Finley (2009).
Hexameric assembly of the proteasomal ATPases is templated through their C termini.
  Nature, 459, 866-870.  
  20047011 V.Milacic, and Q.P.Dou (2009).
The tumor proteasome as a novel target for gold(III) complexes: implications for breast cancer therapy.
  Coord Chem Rev, 253, 1649-1660.  
19435460 X.Li, and G.N.Demartino (2009).
Variably modulated gating of the 26S proteasome by ATP and polyubiquitin.
  Biochem J, 421, 397-404.  
19286367 Y.Cheng (2009).
Toward an atomic model of the 26S proteasome.
  Curr Opin Struct Biol, 19, 203-208.  
18713001 A.R.Kusmierczyk, and M.Hochstrasser (2008).
Some assembly required: dedicated chaperones in eukaryotic proteasome biogenesis.
  Biol Chem, 389, 1143-1151.  
17951257 E.Kario, B.Tirosh, H.L.Ploegh, and A.Navon (2008).
N-linked glycosylation does not impair proteasomal degradation but affects class I major histocompatibility complex presentation.
  J Biol Chem, 283, 244-254.  
18343811 G.Pratt, and M.Rechsteiner (2008).
Proteasomes cleave at multiple sites within polyglutamine tracts: activation by PA28gamma(K188E).
  J Biol Chem, 283, 12919-12925.  
18649350 G.S.Stein, J.R.Davie, J.R.Knowlton, and S.K.Zaidi (2008).
Nuclear microenvironments and cancer.
  J Cell Biochem, 104, 1949-1952.  
18471981 J.Rabl, D.M.Smith, Y.Yu, S.C.Chang, A.L.Goldberg, and Y.Cheng (2008).
Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases.
  Mol Cell, 30, 360-368.
PDB codes: 3c91 3c92
18208355 N.Breusing, and T.Grune (2008).
Regulation of proteasome-mediated protein degradation during oxidative stress and aging.
  Biol Chem, 389, 203-209.  
18534977 P.C.da Fonseca, and E.P.Morris (2008).
Structure of the Human 26S Proteasome: SUBUNIT RADIAL DISPLACEMENTS OPEN THE GATE INTO THE PROTEOLYTIC CORE.
  J Biol Chem, 283, 23305-23314.  
17880010 S.Meiners, A.Ludwig, V.Stangl, and K.Stangl (2008).
Proteasome inhibitors: poisons and remedies.
  Med Res Rev, 28, 309-327.  
18256291 V.Baldin, M.Militello, Y.Thomas, C.Doucet, W.Fic, S.Boireau, I.Jariel-Encontre, M.Piechaczyk, E.Bertrand, J.Tazi, and O.Coux (2008).
A Novel Role for PA28{gamma}-Proteasome in Nuclear Speckle Organization and SR Protein Trafficking.
  Mol Biol Cell, 19, 1706-1716.  
18685789 Y.Zhou, L.Fang, D.Du, W.Zhou, X.Feng, J.Chen, Z.Zhang, and Z.Chen (2008).
Proteome identification of binding-partners interacting with cell polarity protein Par3 in Jurkat cells.
  Acta Biochim Biophys Sin (Shanghai), 40, 729-739.  
17911101 A.J.Marques, C.Glanemann, P.C.Ramos, and R.J.Dohmen (2007).
The C-terminal extension of the beta7 subunit and activator complexes stabilize nascent 20 S proteasomes and promote their maturation.
  J Biol Chem, 282, 34869-34876.  
17612489 A.Martin, T.A.Baker, and R.T.Sauer (2007).
Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease.
  Mol Cell, 27, 41-52.  
17803938 D.M.Smith, S.C.Chang, S.Park, D.Finley, Y.Cheng, and A.L.Goldberg (2007).
Docking of the proteasomal ATPases' carboxyl termini in the 20S proteasome's alpha ring opens the gate for substrate entry.
  Mol Cell, 27, 731-744.  
17696779 L.Borissenko, and M.Groll (2007).
Diversity of proteasomal missions: fine tuning of the immune response.
  Biol Chem, 388, 947-955.  
17466621 M.Kristiansen, P.Deriziotis, D.E.Dimcheff, G.S.Jackson, H.Ovaa, H.Naumann, A.R.Clarke, F.W.van Leeuwen, V.Menéndez-Benito, N.P.Dantuma, J.L.Portis, J.Collinge, and S.J.Tabrizi (2007).
Disease-associated prion protein oligomers inhibit the 26S proteasome.
  Mol Cell, 26, 175-188.  
17390294 O.Drews, C.Zong, and P.Ping (2007).
Exploring proteasome complexes by proteomic approaches.
  Proteomics, 7, 1047-1058.  
17103119 P.Voss, and T.Grune (2007).
The nuclear proteasome and the degradation of oxidatively damaged proteins.
  Amino Acids, 32, 527-534.  
17143051 R.M.Vabulas (2007).
Proteasome function and protein biosynthesis.
  Curr Opin Clin Nutr Metab Care, 10, 24-31.  
17762877 R.Sprangers, A.Velyvis, and L.E.Kay (2007).
Solution NMR of supramolecular complexes: providing new insights into function.
  Nat Methods, 4, 697-703.  
17237764 R.Sprangers, and L.E.Kay (2007).
Quantitative dynamics and binding studies of the 20S proteasome by NMR.
  Nature, 445, 618-622.  
17941820 X.Wang, C.Guerrero, P.Kaiser, and L.Huang (2007).
Proteomics of proteasome complexes and ubiquitinated proteins.
  Expert Rev Proteomics, 4, 649-665.  
16973439 A.Stanhill, C.M.Haynes, Y.Zhang, G.Min, M.C.Steele, J.Kalinina, E.Martinez, C.M.Pickart, X.P.Kong, and D.Ron (2006).
An arsenite-inducible 19S regulatory particle-associated protein adapts proteasomes to proteotoxicity.
  Mol Cell, 23, 875-885.  
16713559 E.Lorentzen, and E.Conti (2006).
The exosome and the proteasome: nano-compartments for degradation.
  Cell, 125, 651-654.  
16468985 G.Lin, G.Hu, C.Tsu, Y.Z.Kunes, H.Li, L.Dick, T.Parsons, P.Li, Z.Chen, P.Zwickl, N.Weich, and C.Nathan (2006).
Mycobacterium tuberculosis prcBA genes encode a gated proteasome with broad oligopeptide specificity.
  Mol Microbiol, 59, 1405-1416.  
16604260 J.C.Wu, Z.Q.Liang, and Z.H.Qin (2006).
Quality control system of the endoplasmic reticulum and related diseases.
  Acta Biochim Biophys Sin (Shanghai), 38, 219-226.  
16952374 J.Iwanczyk, K.Sadre-Bazzaz, K.Ferrell, E.Kondrashkina, T.Formosa, C.P.Hill, and J.Ortega (2006).
Structure of the Blm10-20 S proteasome complex by cryo-electron microscopy. Insights into the mechanism of activation of mature yeast proteasomes.
  J Mol Biol, 363, 648-659.  
16858705 K.Schulze, A.Mulder, A.Tinazli, and R.Tampé (2006).
Controlling the activity of the 20S proteasome complex by synthetic gatekeepers.
  Angew Chem Int Ed Engl, 45, 5702-5705.  
16802355 M.Brychcy, U.Kuckelkorn, G.Hausdorf, K.Egerer, P.M.Kloetzel, G.R.Burmester, and E.Feist (2006).
Anti-20S proteasome autoantibodies inhibit proteasome stimulation by proteasome activator PA28.
  Arthritis Rheum, 54, 2175-2183.  
16445356 M.Gaczynska, K.Rodriguez, S.Madabhushi, and P.A.Osmulski (2006).
Highbrow proteasome in high-throughput technology.
  Expert Rev Proteomics, 3, 115-127.  
16487055 T.C.Squier (2006).
Redox modulation of cellular metabolism through targeted degradation of signaling proteins by the proteasome.
  Antioxid Redox Signal, 8, 217-228.  
16987959 T.Shibatani, E.J.Carlson, F.Larabee, A.L.McCormack, K.Früh, and W.R.Skach (2006).
Global organization and function of mammalian cytosolic proteasome pools: Implications for PA28 and 19S regulatory complexes.
  Mol Biol Cell, 17, 4962-4971.  
16877706 T.V.Rotanova, I.Botos, E.E.Melnikov, F.Rasulova, A.Gustchina, M.R.Maurizi, and A.Wlodawer (2006).
Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains.
  Protein Sci, 15, 1815-1828.  
  17166407 X.F.Yang, D.Mirkovic, S.Zhang, Q.E.Zhang, Y.Yan, Z.Xiong, F.Yang, I.H.Chen, L.Li, and H.Wang (2006).
Processing sites are different in the generation of HLA-A2.1-restricted, T cell reactive tumor antigen epitopes and viral epitopes.
  Int J Immunopathol Pharmacol, 19, 853-870.  
15701650 A.Gribun, M.S.Kimber, R.Ching, R.Sprangers, K.M.Fiebig, and W.A.Houry (2005).
The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation.
  J Biol Chem, 280, 16185-16196.
PDB code: 1y7o
16337593 D.M.Smith, G.Kafri, Y.Cheng, D.Ng, T.Walz, and A.L.Goldberg (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.  
16184768 D.M.Taylor, E.Kabashi, J.N.Agar, S.Minotti, and H.D.Durham (2005).
Proteasome activity or expression is not altered by activation of the heat shock transcription factor Hsf1 in cultured fibroblasts or myoblasts.
  Cell Stress Chaperones, 10, 230-241.  
15771591 E.S.Trombetta, and I.Mellman (2005).
Cell biology of antigen processing in vitro and in vivo.
  Annu Rev Immunol, 23, 975.  
15665121 F.Luciani, C.Keşmir, M.Mishto, M.Or-Guil, and R.J.de Boer (2005).
A mathematical model of protein degradation by the proteasome.
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15678420 M.Groll, M.Bochtler, H.Brandstetter, T.Clausen, and R.Huber (2005).
Molecular machines for protein degradation.
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15653075 M.Rechsteiner, and C.P.Hill (2005).
Mobilizing the proteolytic machine: cell biological roles of proteasome activators and inhibitors.
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16201867 M.Schmidt, J.Hanna, S.Elsasser, and D.Finley (2005).
Proteasome-associated proteins: regulation of a proteolytic machine.
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15778719 M.Schmidt, W.Haas, B.Crosas, P.G.Santamaria, S.P.Gygi, T.Walz, and D.Finley (2005).
The HEAT repeat protein Blm10 regulates the yeast proteasome by capping the core particle.
  Nat Struct Mol Biol, 12, 294-303.  
16115876 S.G.Kang, M.N.Dimitrova, J.Ortega, A.Ginsburg, and M.R.Maurizi (2005).
Human mitochondrial ClpP is a stable heptamer that assembles into a tetradecamer in the presence of ClpX.
  J Biol Chem, 280, 35424-35432.  
16181327 T.A.Groothuis, A.C.Griekspoor, J.J.Neijssen, C.A.Herberts, and J.J.Neefjes (2005).
MHC class I alleles and their exploration of the antigen-processing machinery.
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15831487 Y.Park, Y.P.Hwang, J.S.Lee, S.H.Seo, S.K.Yoon, and J.B.Yoon (2005).
Proteasomal ATPase-associated factor 1 negatively regulates proteasome activity by interacting with proteasomal ATPases.
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14990998 C.M.Pickart, and R.E.Cohen (2004).
Proteasomes and their kin: proteases in the machine age.
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15122206 J.Adams (2004).
The proteasome: a suitable antineoplastic target.
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15319444 J.E.Whittier, Y.Xiong, M.C.Rechsteiner, and T.C.Squier (2004).
Hsp90 enhances degradation of oxidized calmodulin by the 20 S proteasome.
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15224091 P.M.Kloetzel (2004).
Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII.
  Nat Immunol, 5, 661-669.  
14734113 P.M.Kloetzel, and F.Ossendorp (2004).
Proteasome and peptidase function in MHC-class-I-mediated antigen presentation.
  Curr Opin Immunol, 16, 76-81.  
15068806 P.Venkatraman, R.Wetzel, M.Tanaka, N.Nukina, and A.L.Goldberg (2004).
Eukaryotic proteasomes cannot digest polyglutamine sequences and release them during degradation of polyglutamine-containing proteins.
  Mol Cell, 14, 95.  
15270077 R.Beedholm, B.F.Clark, and S.I.Rattan (2004).
Mild heat stress stimulates 20S proteasome and its 11S activator in human fibroblasts undergoing aging in vitro.
  Cell Stress Chaperones, 9, 49-57.  
15454077 R.T.Sauer, D.N.Bolon, B.M.Burton, R.E.Burton, J.M.Flynn, R.A.Grant, G.L.Hersch, S.A.Joshi, J.A.Kenniston, I.Levchenko, S.B.Neher, E.S.Oakes, S.M.Siddiqui, D.A.Wah, and T.A.Baker (2004).
Sculpting the proteome with AAA(+) proteases and disassembly machines.
  Cell, 119, 9.  
15064753 S.A.Joshi, G.L.Hersch, T.A.Baker, and R.T.Sauer (2004).
Communication between ClpX and ClpP during substrate processing and degradation.
  Nat Struct Mol Biol, 11, 404-411.  
15175655 S.Hutschenreiter, A.Tinazli, K.Model, and R.Tampé (2004).
Two-substrate association with the 20S proteasome at single-molecule level.
  EMBO J, 23, 2488-2497.  
12407112 A.C.Vertegaal, H.B.Kuiperij, A.Houweling, M.Verlaan, A.J.van der Eb, and A.Zantema (2003).
Differential expression of tapasin and immunoproteasome subunits in adenovirus type 5- versus type 12-transformed cells.
  J Biol Chem, 278, 139-146.  
12941688 A.Förster, F.G.Whitby, and C.P.Hill (2003).
The pore of activated 20S proteasomes has an ordered 7-fold symmetric conformation.
  EMBO J, 22, 4356-4364.  
12815064 A.F.Kisselev, M.Garcia-Calvo, H.S.Overkleeft, E.Peterson, M.W.Pennington, H.L.Ploegh, N.A.Thornberry, and A.L.Goldberg (2003).
The caspase-like sites of proteasomes, their substrate specificity, new inhibitors and substrates, and allosteric interactions with the trypsin-like sites.
  J Biol Chem, 278, 35869-35877.  
12581666 A.Matouschek (2003).
Protein unfolding--an important process in vivo?
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12600991 C.C.Wang, Z.Bozdech, C.L.Liu, A.Shipway, B.J.Backes, J.L.Harris, and M.Bogyo (2003).
Biochemical analysis of the 20 S proteasome of Trypanosoma brucei.
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12606569 C.Hirsch, D.Blom, and H.L.Ploegh (2003).
A role for N-glycanase in the cytosolic turnover of glycoproteins.
  EMBO J, 22, 1036-1046.  
12481023 C.W.Liu, M.J.Corboy, G.N.DeMartino, and P.J.Thomas (2003).
Endoproteolytic activity of the proteasome.
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12948749 J.A.Maupin-Furlow, S.J.Kaczowka, C.J.Reuter, K.Zuobi-Hasona, and M.A.Gil (2003).
Archaeal proteasomes: potential in metabolic engineering.
  Metab Eng, 5, 151-163.  
12595534 J.Weber, A.Muharemagic, S.Wilke-Mounts, and A.E.Senior (2003).
F1F0-ATP synthase. Binding of delta subunit to a 22-residue peptide mimicking the N-terminal region of alpha subunit.
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12672453 M.Groll, and R.Huber (2003).
Substrate access and processing by the 20S proteasome core particle.
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14675543 M.Groll, and T.Clausen (2003).
Molecular shredders: how proteasomes fulfill their role.
  Curr Opin Struct Biol, 13, 665-673.  
14602444 M.P.Barrett, R.J.Burchmore, A.Stich, J.O.Lazzari, A.C.Frasch, J.J.Cazzulo, and S.Krishna (2003).
The trypanosomiases.
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14522242 P.A.Szweda, M.Camouse, K.C.Lundberg, T.D.Oberley, and L.I.Szweda (2003).
Aging, lipofuscin formation, and free radical-mediated inhibition of cellular proteolytic systems.
  Ageing Res Rev, 2, 383-405.  
12674498 R.Stohwasser, H.G.Holzhütter, U.Lehmann, P.Henklein, and P.M.Kloetzel (2003).
Hepatitis B virus HBx peptide 116-138 and proteasome activator PA28 compete for binding to the proteasome alpha4/MC6 subunit.
  Biol Chem, 384, 39-49.  
12377129 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Sequence and structural differences between enzyme and nonenzyme homologs.
  Structure, 10, 1435-1451.  
11927581 A.F.Kisselev, D.Kaganovich, and A.L.Goldberg (2002).
Binding of hydrophobic peptides to several non-catalytic sites promotes peptide hydrolysis by all active sites of 20 S proteasomes. Evidence for peptide-induced channel opening in the alpha-rings.
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12270919 A.V.Kajava (2002).
What curves alpha-solenoids? Evidence for an alpha-helical toroid structure of Rpn1 and Rpn2 proteins of the 26 S proteasome.
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12080075 C.Lee, S.Prakash, and A.Matouschek (2002).
Concurrent translocation of multiple polypeptide chains through the proteasomal degradation channel.
  J Biol Chem, 277, 34760-34765.  
11988752 D.Finley (2002).
Ubiquitin chained and crosslinked.
  Nat Cell Biol, 4, E121-E123.  
12200039 G.Carrard, A.L.Bulteau, I.Petropoulos, and B.Friguet (2002).
Impairment of proteasome structure and function in aging.
  Int J Biochem Cell Biol, 34, 1461-1474.  
12011053 I.S.Seong, M.S.Kang, M.K.Choi, J.W.Lee, O.J.Koh, J.Wang, S.H.Eom, and C.H.Chung (2002).
The C-terminal tails of HslU ATPase act as a molecular switch for activation of HslV peptidase.
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12234933 J.Ortega, H.S.Lee, M.R.Maurizi, and A.C.Steven (2002).
Alternating translocation of protein substrates from both ends of ClpXP protease.
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12045098 M.Klemba, and D.E.Goldberg (2002).
Biological roles of proteases in parasitic protozoa.
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12033938 P.A.Osmulski, and M.Gaczynska (2002).
Nanoenzymology of the 20S proteasome: proteasomal actions are controlled by the allosteric transition.
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12032076 P.Cascio, M.Call, B.M.Petre, T.Walz, and A.L.Goldberg (2002).
Properties of the hybrid form of the 26S proteasome containing both 19S and PA28 complexes.
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12237893 R.Gavioli, S.Vertuani, and M.G.Masucci (2002).
Proteasome inhibitors reconstitute the presentation of cytotoxic T-cell epitopes in Epstein-Barr virus-associated tumors.
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11779829 R.Jansen, D.Greenbaum, and M.Gerstein (2002).
Relating whole-genome expression data with protein-protein interactions.
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12032294 R.Ramachandran, C.Hartmann, H.K.Song, R.Huber, and M.Bochtler (2002).
Functional interactions of HslV (ClpQ) with the ATPase HslU (ClpY).
  Proc Natl Acad Sci U S A, 99, 7396-7401.  
12093752 V.Ustrell, L.Hoffman, G.Pratt, and M.Rechsteiner (2002).
PA200, a nuclear proteasome activator involved in DNA repair.
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11854272 Z.Li, C.B.Zou, Y.Yao, M.A.Hoyt, S.McDonough, Z.B.Mackey, P.Coffino, and C.C.Wang (2002).
An easily dissociated 26 S proteasome catalyzes an essential ubiquitin-mediated protein degradation pathway in Trypanosoma brucei.
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11514224 A.F.Kisselev, and A.L.Goldberg (2001).
Proteasome inhibitors: from research tools to drug candidates.
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11779508 A.Navon, and A.L.Goldberg (2001).
Proteins are unfolded on the surface of the ATPase ring before transport into the proteasome.
  Mol Cell, 8, 1339-1349.  
11602750 J.Hemelaar, F.Bex, B.Booth, V.Cerundolo, A.McMichael, and S.Daenke (2001).
Human T-cell leukemia virus type 1 Tax protein binds to assembled nuclear proteasomes and enhances their proteolytic activity.
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11755392 J.L.Harris, P.B.Alper, J.Li, M.Rechsteiner, and B.J.Backes (2001).
Substrate specificity of the human proteasome.
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11295500 J.Li, and M.Rechsteiner (2001).
Molecular dissection of the 11S REG (PA28) proteasome activators.
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11432824 J.Li, X.Gao, J.Ortega, T.Nazif, L.Joss, M.Bogyo, A.C.Steven, and M.Rechsteiner (2001).
Lysine 188 substitutions convert the pattern of proteasome activation by REGgamma to that of REGs alpha and beta.
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11410931 J.Myung, K.B.Kim, and C.M.Crews (2001).
The ubiquitin-proteasome pathway and proteasome inhibitors.
  Med Res Rev, 21, 245-273.  
11709174 J.Wang, J.J.Song, I.S.Seong, M.C.Franklin, S.Kamtekar, S.H.Eom, and C.H.Chung (2001).
Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU.
  Structure, 9, 1107-1116.
PDB codes: 1hqy 1ht1 1ht2
12540272 M.Hofmann, A.K.Nussbaum, N.P.Emmerich, L.Stoltze, and H.Schild (2001).
Mechanisms of MHC class I-restricted antigen presentation.
  Expert Opin Ther Targets, 5, 379-393.  
11387208 R.Farrás, A.Ferrando, J.Jásik, T.Kleinow, L.Okrész, A.Tiburcio, K.Salchert, C.del Pozo, J.Schell, and C.Koncz (2001).
SKP1-SnRK protein kinase interactions mediate proteasomal binding of a plant SCF ubiquitin ligase.
  EMBO J, 20, 2742-2756.  
11248031 Y.Xie, and A.Varshavsky (2001).
RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit.
  Proc Natl Acad Sci U S A, 98, 3056-3061.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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