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| - | [[Image:1q5q.gif|left|200px]] | |
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| - | {{Structure
| + | ==The Rhodococcus 20S proteasome== |
| - | |PDB= 1q5q |SIZE=350|CAPTION= <scene name='initialview01'>1q5q</scene>, resolution 2.60Å
| + | <StructureSection load='1q5q' size='340' side='right'caption='[[1q5q]], [[Resolution|resolution]] 2.60Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND=
| + | <table><tr><td colspan='2'>[[1q5q]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q5Q FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> |
| - | |GENE= PRCA(1) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1833 Rhodococcus erythropolis]), PRCB(1) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1833 Rhodococcus erythropolis])
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q5q OCA], [https://pdbe.org/1q5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q5q RCSB], [https://www.ebi.ac.uk/pdbsum/1q5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q5q ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=[[1q5r|1Q5R]] | + | == Function == |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q5q OCA], [http://www.ebi.ac.uk/pdbsum/1q5q PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q5q RCSB]</span>
| + | [https://www.uniprot.org/uniprot/PSA1_RHOER PSA1_RHOER] Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The R.erythropolis proteasomes are able to cleave oligopeptides after Tyr, Phe and Leu, very poorly after Arg but not after Glu. Thus, displays chymotrypsin-like activity, low trypsin-like activity but no caspase-like activity.[HAMAP-Rule:MF_00289]<ref>PMID:7583123</ref> <ref>PMID:9000518</ref> |
| - | }}
| + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q5/1q5q_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1q5q ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | To understand the role of the pro-peptide in proteasome assembly, we have determined structures of the Rhodococcus proteasome and a mutant form that prevents the autocatalytic removal of its pro-peptides. The structures reveal that the pro-peptide acts as an assembly-promoting factor by linking its own beta-subunit to two adjacent alpha-subunits, thereby providing a molecular explanation for the observed kinetics of proteasome assembly. The Rhodococcus proteasome has been found to have a substantially smaller contact region between alpha-subunits compared to those regions in the proteasomes of Thermoplasma, yeast, and mammalian cells, suggesting that a smaller contact area between alpha-subunits is likely the structural basis for the Rhodococcus alpha-subunits not assembling into alpha-rings when expressed alone. Analysis of all available beta-subunit structures shows that the contact area between beta-subunits within a beta-ring is not sufficient for beta-ring self-assembly without the additional contact provided by the alpha-ring. This appears to be a fail-safe mechanism ensuring that the active sites on the beta-subunits are activated only after proteasome assembly is complete. |
| | | | |
| - | '''The Rhodococcus 20S proteasome'''
| + | Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly.,Kwon YD, Nagy I, Adams PD, Baumeister W, Jap BK J Mol Biol. 2004 Jan 2;335(1):233-45. PMID:14659753<ref>PMID:14659753</ref> |
| | | | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 1q5q" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Overview== | + | ==See Also== |
| - | To understand the role of the pro-peptide in proteasome assembly, we have determined structures of the Rhodococcus proteasome and a mutant form that prevents the autocatalytic removal of its pro-peptides. The structures reveal that the pro-peptide acts as an assembly-promoting factor by linking its own beta-subunit to two adjacent alpha-subunits, thereby providing a molecular explanation for the observed kinetics of proteasome assembly. The Rhodococcus proteasome has been found to have a substantially smaller contact region between alpha-subunits compared to those regions in the proteasomes of Thermoplasma, yeast, and mammalian cells, suggesting that a smaller contact area between alpha-subunits is likely the structural basis for the Rhodococcus alpha-subunits not assembling into alpha-rings when expressed alone. Analysis of all available beta-subunit structures shows that the contact area between beta-subunits within a beta-ring is not sufficient for beta-ring self-assembly without the additional contact provided by the alpha-ring. This appears to be a fail-safe mechanism ensuring that the active sites on the beta-subunits are activated only after proteasome assembly is complete.
| + | *[[Proteasome 3D structures|Proteasome 3D structures]] |
| - | | + | == References == |
| - | ==About this Structure== | + | <references/> |
| - | 1Q5Q is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q5Q OCA].
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==Reference==
| + | [[Category: Large Structures]] |
| - | Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly., Kwon YD, Nagy I, Adams PD, Baumeister W, Jap BK, J Mol Biol. 2004 Jan 2;335(1):233-45. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14659753 14659753]
| + | |
| - | [[Category: Proteasome endopeptidase complex]]
| + | |
| - | [[Category: Protein complex]] | + | |
| | [[Category: Rhodococcus erythropolis]] | | [[Category: Rhodococcus erythropolis]] |
| - | [[Category: Adams, P D.]] | + | [[Category: Adams PD]] |
| - | [[Category: Baumeister, W.]] | + | [[Category: Baumeister W]] |
| - | [[Category: Jap, B K.]] | + | [[Category: Jap BK]] |
| - | [[Category: Kwon, Y D.]] | + | [[Category: Kwon YD]] |
| - | [[Category: Nagy, I.]] | + | [[Category: Nagy I]] |
| - | [[Category: inter-subunit contact]]
| + | |
| - | [[Category: pro-peptide]]
| + | |
| - | [[Category: proteasome assembly]]
| + | |
| - | [[Category: rhodococcus erythropoli]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:09:08 2008''
| + | |
| Structural highlights
Function
PSA1_RHOER Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The R.erythropolis proteasomes are able to cleave oligopeptides after Tyr, Phe and Leu, very poorly after Arg but not after Glu. Thus, displays chymotrypsin-like activity, low trypsin-like activity but no caspase-like activity.[HAMAP-Rule:MF_00289][1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
To understand the role of the pro-peptide in proteasome assembly, we have determined structures of the Rhodococcus proteasome and a mutant form that prevents the autocatalytic removal of its pro-peptides. The structures reveal that the pro-peptide acts as an assembly-promoting factor by linking its own beta-subunit to two adjacent alpha-subunits, thereby providing a molecular explanation for the observed kinetics of proteasome assembly. The Rhodococcus proteasome has been found to have a substantially smaller contact region between alpha-subunits compared to those regions in the proteasomes of Thermoplasma, yeast, and mammalian cells, suggesting that a smaller contact area between alpha-subunits is likely the structural basis for the Rhodococcus alpha-subunits not assembling into alpha-rings when expressed alone. Analysis of all available beta-subunit structures shows that the contact area between beta-subunits within a beta-ring is not sufficient for beta-ring self-assembly without the additional contact provided by the alpha-ring. This appears to be a fail-safe mechanism ensuring that the active sites on the beta-subunits are activated only after proteasome assembly is complete.
Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly.,Kwon YD, Nagy I, Adams PD, Baumeister W, Jap BK J Mol Biol. 2004 Jan 2;335(1):233-45. PMID:14659753[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tamura T, Nagy I, Lupas A, Lottspeich F, Cejka Z, Schoofs G, Tanaka K, De Mot R, Baumeister W. The first characterization of a eubacterial proteasome: the 20S complex of Rhodococcus. Curr Biol. 1995 Jul 1;5(7):766-74. PMID:7583123
- ↑ Zuhl F, Tamura T, Dolenc I, Cejka Z, Nagy I, De Mot R, Baumeister W. Subunit topology of the Rhodococcus proteasome. FEBS Lett. 1997 Jan 2;400(1):83-90. PMID:9000518
- ↑ Kwon YD, Nagy I, Adams PD, Baumeister W, Jap BK. Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly. J Mol Biol. 2004 Jan 2;335(1):233-45. PMID:14659753
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