1z5h: Difference between revisions

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OCA

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 ==Crystal structures of the Tricorn interacting Factor F3 from Thermoplasma acidophilum==
-<StructureSection load='1z5h' size='340' side='right' caption='[[1z5h]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='1z5h' size='340' side='right'caption='[[1z5h]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1z5h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z5H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1z5h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z5H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1z5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5h OCA], [http://pdbe.org/1z5h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z5h RCSB], [http://www.ebi.ac.uk/pdbsum/1z5h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5h ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1z5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5h OCA], [https://pdbe.org/1z5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z5h RCSB], [https://www.ebi.ac.uk/pdbsum/1z5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5h ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRF3_THEAC TRF3_THEAC]] Proteases F1, F2 and F3 degrade oligopeptides produced by Tricorn (themselves probably produced by the proteasome), yielding free amino acids.
+[https://www.uniprot.org/uniprot/TRF3_THEAC TRF3_THEAC] Proteases F1, F2 and F3 degrade oligopeptides produced by Tricorn (themselves probably produced by the proteasome), yielding free amino acids.
 == 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/z5/1z5h_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z5/1z5h_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 20: @@
 </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=1z5h ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The tricorn interacting factor F3 is an 89 kDa zinc aminopeptidase from the archaeon Thermoplasma acidophilum. Together with the tricorn interacting factors F1 and F2, F3 degrades the tricorn protease products and thus completes the proteasomal degradation pathway by generating free amino acids. Here, we present the crystal structures of F3 in three different conformations at 2.3 A resolution. The zinc aminopeptidase is composed of four domains: an N-terminal saddle-like beta-structure domain; a thermolysin-like catalytic domain; a small barrel-like beta-structure domain; and an alpha-helical C-terminal domain, the latter forming a deep cavity at the active site. Three crystal forms provide snapshots of the molecular dynamics of F3 where the C-terminal domain can adapt to form an open, an intermediate and a nearly closed cavity, respectively. With the conserved Zn(2+)-binding motifs HEXXH and NEXFA as well as the N-terminal substrate-anchoring glutamate residues, F3 together with the leukotriene A4 hydrolase, represents a novel gluzincin subfamily of aminoproteases. We discuss the functional implications of these structures with respect to the underlying catalytic mechanism, substrate recognition and processing, and possible component interactions.
-Crystal structures of the tricorn interacting factor F3 from Thermoplasma acidophilum, a zinc aminopeptidase in three different conformations.,Kyrieleis OJ, Goettig P, Kiefersauer R, Huber R, Brandstetter H J Mol Biol. 2005 Jun 17;349(4):787-800. Epub 2005 Apr 26. PMID:15893768<ref>PMID:15893768</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1z5h" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Brandstetter, H]]
+[[Category: Large Structures]]
-[[Category: Goettig, P]]
+[[Category: Thermoplasma acidophilum]]
-[[Category: Huber, R]]
+[[Category: Brandstetter H]]
-[[Category: Kiefersauer, R]]
+[[Category: Goettig P]]
-[[Category: Kyrieleis, O J.P]]
+[[Category: Huber R]]
-[[Category: Gluzicin]]
+[[Category: Kiefersauer R]]
-[[Category: Hydrolase]]
+[[Category: Kyrieleis OJP]]
-[[Category: Superhelix]]
-[[Category: Tricorn protease]]
-[[Category: Zinc aminopeptidase]]