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PDBsum entry 1j2q
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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1j2q

 

 

 

 

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Contents
Protein chains
(+ 1 more) 237 a.a. *
(+ 1 more) 202 a.a. *
Ligands
CIB ×7
Waters ×105
* Residue conservation analysis
PDB id:
1j2q
Name: Hydrolase
Title: 20s proteasome in complex with calpain-inhibitor i from archaeoglobus fulgidus
Structure: Proteasome alpha subunit. Chain: a, b, c, d, e, f, g. Engineered: yes. Proteasome beta subunit. Chain: h, i, j, k, l, m, n. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Heptamer (from PDB file)
Resolution:
2.83Å     R-factor:   0.241     R-free:   0.279
Authors: M.Groll,H.Brandstetter,H.Bartunik,G.Bourenkow,R.Huber
Key ref:
M.Groll et al. (2003). Investigations on the maturation and regulation of archaebacterial proteasomes. J Mol Biol, 327, 75-83. PubMed id: 12614609 DOI: 10.1016/S0022-2836(03)00080-9
Date:
08-Jan-03     Release date:   18-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O29760  (PSA_ARCFU) -  Proteasome subunit alpha from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		246 a.a.
237 a.a.
Protein chains
Pfam   ArchSchema ?
Q9P996  (PSB_ARCFU) -  Proteasome subunit beta from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		213 a.a.
202 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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/S0022-2836(03)00080-9 J Mol Biol 327:75-83 (2003)
PubMed id: 12614609  
 
 
Investigations on the maturation and regulation of archaebacterial proteasomes.
M.Groll, H.Brandstetter, H.Bartunik, G.Bourenkow, R.Huber.
 
  ABSTRACT  
 
The 20S proteasome (core particle, CP) is a multifunctional protease complex and composed of four heptameric subunit rings arranged in a hollow, barrel-shaped structure. Here, we report the crystal structure of the CP from Archaeoglobus fulgidus at 2.25A resolution. The analysis of the structure of early and late assembly intermediates of this CP gives new insights in the maturation of archaebacterial CPs and indicates similarities to assembly intermediates observed in eukaryotes. We also show a striking difference in mechanism and regulation of substrate access between eukaryotic and archaebacterial 20S proteasomes. While eukaryotic CPs are auto-inhibited by the N-terminal tails of the outer alpha-ring by imposing topological closure with a characteristic sequence motif (YDR-motif) and show regulatory gating this segment is disordered in the CP and differently structured in the alpha(7)-sub-complex of A.fulgidus leaving a pore leading into the particle with a diameter of 13A. Mutagenesis and functional studies indicate the absence of regulatory gating in the archaeal 20S proteasome.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo view of the overlay of the C^a tracings of the a-subunit from the a-ring (yellow) and the a-subunit from the CP (blue). 		Figure 5.
Figure 5. (a) and (b) Ribbon drawing of the a-ring from A. fulgidus in top and side view, respectively. The N-terminal segments are shown in red and the remaining part is shown in blue. (c) Stereo drawing of the open channel with a 7-fold averaged 2F[O] -F[C] map showing the YDR element. Contacts among residues of the YDR element in adjacent subunits are shown in black. The carboxylate group of Asp9 forms a hydrogen bond with the hydroxyl group of Tyr8 in the neighbouring a-subunit and adopts a major part for the open axial channel. (d) Stereo drawing of the closed channel of the a-ring from S. cerevisiae. Contacts among residues of the YDR element in the a3 and a4 subunit, which maintain the regulatory gate in eukaryotes, are shown in black sticks, whereas the N-terminal segments are coloured in red.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 75-83) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22183254 J.Maupin-Furlow (2012).
Proteasomes and protein conjugation across domains of life.
  Nat Rev Microbiol, 10, 100-111.  
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.  
20541423 N.Gallastegui, and M.Groll (2010).
The 26S proteasome: assembly and function of a destructive machine.
  Trends Biochem Sci, 35, 634-642.  
19376868 M.A.Humbard, G.Zhou, and J.A.Maupin-Furlow (2009).
The N-terminal penultimate residue of 20S proteasome alpha1 influences its N(alpha) acetylation and protein levels as well as growth rate and stress responses of Haloferax volcanii.
  J Bacteriol, 191, 3794-3803.  
19109822 M.Groll, R.Huber, and L.Moroder (2009).
The persisting challenge of selective and specific proteasome inhibition.
  J Pept Sci, 15, 58-66.  
19580545 S.Liao, Q.Shang, X.Zhang, J.Zhang, C.Xu, and X.Tu (2009).
Pup, a prokaryotic ubiquitin-like protein, is an intrinsically disordered protein.
  Biochem J, 422, 207-215.  
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
  18931431 K.Felderer, M.Groves, J.Diez, E.Pohl, and S.Witt (2008).
Crystallization and preliminary X-ray analysis of the Thermoplasma acidophilum 20S proteasome in complex with protein substrates.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 899-902.  
18786393 P.C.Ramos, and R.J.Dohmen (2008).
PACemakers of proteasome core particle assembly.
  Structure, 16, 1296-1304.  
17696779 L.Borissenko, and M.Groll (2007).
Diversity of proteasomal missions: fine tuning of the immune response.
  Biol Chem, 388, 947-955.  
17114253 L.S.Madding, J.K.Michel, K.R.Shockley, S.B.Conners, K.L.Epting, M.R.Johnson, and R.M.Kelly (2007).
Role of the beta1 subunit in the function and stability of the 20S proteasome in the hyperthermophilic archaeon Pyrococcus furiosus.
  J Bacteriol, 189, 583-590.  
17430901 M.Sharon, S.Witt, E.Glasmacher, W.Baumeister, and C.V.Robinson (2007).
Mass spectrometry reveals the missing links in the assembly pathway of the bacterial 20 S proteasome.
  J Biol Chem, 282, 18448-18457.  
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
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.  
16843899 S.Witt, Y.D.Kwon, M.Sharon, K.Felderer, M.Beuttler, C.V.Robinson, W.Baumeister, and B.K.Jap (2006).
Proteasome assembly triggers a switch required for active-site maturation.
  Structure, 14, 1179-1188.
PDB code: 2h6j
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.  
15937278 H.Cheng, and N.V.Grishin (2005).
DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.
  Protein Sci, 14, 1902-1910.  
15678420 M.Groll, M.Bochtler, H.Brandstetter, T.Clausen, and R.Huber (2005).
Molecular machines for protein degradation.
  Chembiochem, 6, 222-256.  
15944226 S.Heink, D.Ludwig, P.M.Kloetzel, and E.Krüger (2005).
IFN-gamma-induced immune adaptation of the proteasome system is an accelerated and transient response.
  Proc Natl Acad Sci U S A, 102, 9241-9246.  
15368577 M.Kaiser, M.Groll, C.Siciliano, I.Assfalg-Machleidt, E.Weyher, J.Kohno, A.G.Milbradt, C.Renner, R.Huber, and L.Moroder (2004).
Binding mode of TMC-95A analogues to eukaryotic 20S proteasome.
  Chembiochem, 5, 1256-1266.  
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.  
15361411 S.Mullapudi, L.Pullan, O.T.Bishop, H.Khalil, J.K.Stoops, R.Beckmann, P.M.Kloetzel, E.Krüger, and P.A.Penczek (2004).
Rearrangement of the 16S precursor subunits is essential for the formation of the active 20S proteasome.
  Biophys J, 87, 4098-4105.  
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.  
14675543 M.Groll, and T.Clausen (2003).
Molecular shredders: how proteasomes fulfill their role.
  Curr Opin Struct Biol, 13, 665-673.  
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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