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PDBsum entry 1yau
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Hydrolase/hydrolase activator PDB id
1yau

 

 

 

 

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Contents
Protein chains
(+ 1 more) 222 a.a. *
(+ 1 more) 203 a.a. *
(+ 1 more) 218 a.a. *
Ligands
SO4 ×25
GOL ×7
Waters ×1571
* Residue conservation analysis
PDB id:
1yau
Name: Hydrolase/hydrolase activator
Title: Structure of archeabacterial 20s proteasome- pa26 complex
Structure: Proteasome alpha subunit. Chain: a, b, c, d, e, f, g. Synonym: multicatalytic endopeptidase complex alpha subunit. Engineered: yes. Mutation: yes. Proteasome beta subunit. Chain: h, i, j, k, l, m, n. Synonym: multicatalytic endopeptidase complex beta subunit. Engineered: yes.
Source: Thermoplasma acidophilum. Organism_taxid: 2303. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Trypanosoma brucei. Organism_taxid: 5691.
Biol. unit: 42mer (from PDB file)
Resolution:
2.40Å     R-factor:   0.180     R-free:   0.233
Authors: A.Forster,E.I.Masters,F.G.Whitby,H.Robinson,C.P.Hill
Key ref:
A.Förster et al. (2005). The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. Mol Cell, 18, 589-599. PubMed id: 15916965 DOI: 10.1016/j.molcel.2005.04.016
Date:
17-Dec-04     Release date:   26-Jul-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P25156  (PSA_THEAC) -  Proteasome subunit alpha from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
Seq:
Struc: 		233 a.a.
222 a.a.
Protein chains
Pfam   ArchSchema ?
P28061  (PSB_THEAC) -  Proteasome subunit beta from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
Seq:
Struc: 		211 a.a.
203 a.a.
Protein chains
Pfam   ArchSchema ?
Q9U8G2  (Q9U8G2_9TRYP) -  Proteasome activator protein PA26 (Fragment) from Trypanosoma brucei
Seq:
Struc: 		231 a.a.
218 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N: E.C.3.4.25.1  - proteasome endopeptidase complex.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cleavage at peptide bonds with very broad specificity.

 

 
DOI no: 10.1016/j.molcel.2005.04.016 Mol Cell 18:589-599 (2005)
PubMed id: 15916965  
 
 
The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions.
A.Förster, E.I.Masters, F.G.Whitby, H.Robinson, C.P.Hill.
 
  ABSTRACT  
 
Proteasomes are cylindrical structures that function in multiple cellular processes by degrading a wide variety of cytosolic and nuclear proteins. Substrate access and product release from the enclosed catalytic chamber occurs through axial pores that are opened by activator complexes. Here, we report high-resolution structures of wild-type and mutant archaeal proteasomes bound to the activator PA26. These structures support the proposal that an ordered open conformation is required for proteolysis and that its formation can be triggered by outward displacement of surrounding residues. The structures and associated biochemical assays reveal the mechanism of binding, which involves an interaction between the PA26 C terminus and a conserved lysine. Surprisingly, biochemical observations implicate an equivalent interaction for the unrelated ATP-dependent activators PAN and PA700.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Pore Conformation 		Figure 5.
Figure 5. PA26-Proteasome Interaction
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 18, 589-599) copyright 2005.  
  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.  
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.  
21129723 A.K.Agarwal, C.Xing, G.N.DeMartino, D.Mizrachi, M.D.Hernandez, A.B.Sousa, L.Martínez de Villarreal, H.G.dos Santos, and A.Garg (2010).
PSMB8 encoding the β5i proteasome subunit is mutated in joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy syndrome.
  Am J Hum Genet, 87, 866-872.  
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.  
20203624 F.Striebel, M.Hunkeler, H.Summer, and E.Weber-Ban (2010).
The mycobacterial Mpa-proteasome unfolds and degrades pupylated substrates by engaging Pup's N-terminus.
  EMBO J, 29, 1262-1271.  
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
20541423 N.Gallastegui, and M.Groll (2010).
The 26S proteasome: assembly and function of a destructive machine.
  Trends Biochem Sci, 35, 634-642.  
20479273 R.Kulikov, J.Letienne, M.Kaur, S.R.Grossman, J.Arts, and C.Blattner (2010).
Mdm2 facilitates the association of p53 with the proteasome.
  Proc Natl Acad Sci U S A, 107, 10038-10043.  
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
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
19489727 D.Finley (2009).
Recognition and processing of ubiquitin-protein conjugates by the proteasome.
  Annu Rev Biochem, 78, 477-513.  
19223165 D.Russel, K.Lasker, J.Phillips, D.Schneidman-Duhovny, J.A.Velázquez-Muriel, and A.Sali (2009).
The structural dynamics of macromolecular processes.
  Curr Opin Cell Biol, 21, 97.  
19653995 F.Förster, K.Lasker, F.Beck, S.Nickell, A.Sali, and W.Baumeister (2009).
An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome.
  Biochem Biophys Res Commun, 388, 228-233.  
19412159 J.Roelofs, S.Park, W.Haas, G.Tian, F.E.McAllister, Y.Huo, B.H.Lee, F.Zhang, Y.Shi, S.P.Gygi, and D.Finley (2009).
Chaperone-mediated pathway of proteasome regulatory particle assembly.
  Nature, 459, 861-865.  
19145068 K.Tanaka (2009).
The proteasome: overview of structure and functions.
  Proc Jpn Acad Ser B Phys Biol Sci, 85, 12-36.  
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.  
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.  
19581588 S.Nickell, F.Beck, S.H.Scheres, A.Korinek, F.Förster, K.Lasker, O.Mihalache, N.Sun, I.Nagy, A.Sali, J.M.Plitzko, J.M.Carazo, M.Mann, and W.Baumeister (2009).
Insights into the molecular architecture of the 26S proteasome.
  Proc Natl Acad Sci U S A, 106, 11943-11947.  
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.  
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.  
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
18511945 R.Rosenzweig, P.A.Osmulski, M.Gaczynska, and M.H.Glickman (2008).
The central unit within the 19S regulatory particle of the proteasome.
  Nat Struct Mol Biol, 15, 573-580.  
18796432 T.G.Gillette, B.Kumar, D.Thompson, C.A.Slaughter, and G.N.Demartino (2008).
Differential Roles of the COOH Termini of AAA Subunits of PA700 (19 S Regulator) in Asymmetric Assembly and Activation of the 26 S Proteasome.
  J Biol Chem, 283, 31813-31822.  
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.  
18026118 M.F.Kleijnen, J.Roelofs, S.Park, N.A.Hathaway, M.Glickman, R.W.King, and D.Finley (2007).
Stability of the proteasome can be regulated allosterically through engagement of its proteolytic active sites.
  Nat Struct Mol Biol, 14, 1180-1188.  
17237764 R.Sprangers, and L.E.Kay (2007).
Quantitative dynamics and binding studies of the 20S proteasome by NMR.
  Nature, 445, 618-622.  
17889660 Y.Saeki, and K.Tanaka (2007).
Unlocking the proteasome door.
  Mol Cell, 27, 865-867.  
17018291 C.W.Liu, X.Li, D.Thompson, K.Wooding, T.L.Chang, Z.Tang, H.Yu, P.J.Thomas, and G.N.DeMartino (2006).
ATP binding and ATP hydrolysis play distinct roles in the function of 26S proteasome.
  Mol Cell, 24, 39-50.  
16595883 D.Nandi, P.Tahiliani, A.Kumar, and D.Chandu (2006).
The ubiquitin-proteasome system.
  J Biosci, 31, 137-155.  
16468986 G.Hu, G.Lin, M.Wang, L.Dick, R.M.Xu, C.Nathan, and H.Li (2006).
Structure of the Mycobacterium tuberculosis proteasome and mechanism of inhibition by a peptidyl boronate.
  Mol Microbiol, 59, 1417-1428.
PDB codes: 2fhg 2fhh
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.  
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.  
16445356 M.Gaczynska, K.Rodriguez, S.Madabhushi, and P.A.Osmulski (2006).
Highbrow proteasome in high-throughput technology.
  Expert Rev Proteomics, 3, 115-127.  
17082771 M.J.Pearce, P.Arora, R.A.Festa, S.M.Butler-Wu, R.S.Gokhale, and K.H.Darwin (2006).
Identification of substrates of the Mycobacterium tuberculosis proteasome.
  EMBO J, 25, 5423-5432.  
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.  
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.  
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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