1y0r: Difference between revisions

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-[[Image:1y0r.gif|left|200px]]
- {{Structure
+==Crystal structure of the tetrahedral aminopeptidase from P. horikoshii==
-|PDB= 1y0r |SIZE=350|CAPTION= <scene name='initialview01'>1y0r</scene>, resolution 1.75&Aring;
+<StructureSection load='1y0r' size='340' side='right'caption='[[1y0r]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=ARS:ARSENIC'>ARS</scene>
+<table><tr><td colspan='2'>[[1y0r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y0R FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARS:ARSENIC'>ARS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-}}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1y0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y0r OCA], [https://pdbe.org/1y0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y0r RCSB], [https://www.ebi.ac.uk/pdbsum/1y0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y0r ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TET_PYRHO TET_PYRHO] Functions as an aminopeptidase, with a clear preference for leucine as the N-terminal amino acid. However, can also cleave moderately long polypeptide substrates of various compositions in a fairly unspecific manner. Has neither carboxypeptidase nor endoproteolytic activities, and it is devoid of N-terminal deblocking activity. Is involved in protein degradation, performing degradation of oligopeptides produced by the proteasome into single amino acids.<ref>PMID:15375159</ref> <ref>PMID:15713475</ref> <ref>PMID:15736957</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/y0/1y0r_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=1y0r ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of the tetrahedral aminopeptidase from P. horikoshii'''
+==See Also==
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
+== References ==
-==Overview==
+<references/>
-Protein degradation is an essential and strictly controlled process with proteasome and functionally related proteases representing its central part. Tricorn protease (TRI) has been shown to act downstream of the proteasome, degrading produced peptides. Recently, a novel large prokaryotic aminopeptidase oligomeric complex, named TET, has been identified. This complex degrades peptides of different length in organisms where TRI is not present. We determined the crystal structure of TET from the thermophilic archaeon Pyrococcus horikoshii at 1.6 A resolution in native form and in complex with the inhibitor amastatin. We demonstrate that, beside the novel tetrahedral oligomerisation pattern, TET possesses a unique mechanism of substrate attraction and orientation. TET sequentially degrades peptides produced by the proteasome to single amino acids. Furthermore, we reconstituted in vitro the minimal protein degradation system from initial unfolding of labelled protein substrates, up to release of free amino acids. We propose that TET and TRI act as functional analogues in different organisms, with TET being more widely distributed. Thus, TET and TRI represent two evolutionarily diverged pathways of peptide degradation in prokaryotes.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Y0R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y0R OCA].
-==Reference==
-Crystal structure of TET protease reveals complementary protein degradation pathways in prokaryotes., Borissenko L, Groll M, J Mol Biol. 2005 Mar 11;346(5):1207-19. Epub 2005 Jan 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15713475 15713475]
 [[Category: Pyrococcus horikoshii]]
-[[Category: Single protein]]
+[[Category: Borissenko L]]
-[[Category: Borissenko, L.]]
+[[Category: Groll M]]
-[[Category: Groll, M.]]
-[[Category: ARS]]
-[[Category: ZN]]
-[[Category: aminopeptidase domain]]
-[[Category: pdz domain]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:17:00 2008''