1t1e: Difference between revisions

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 ==High Resolution Crystal Structure of the Intact Pro-Kumamolisin, a Sedolisin Type Proteinase (previously called Kumamolysin or KSCP)==
-<StructureSection load='1t1e' size='340' side='right' caption='[[1t1e]], [[Resolution|resolution]] 1.18&Aring;' scene=''>
+<StructureSection load='1t1e' size='340' side='right'caption='[[1t1e]], [[Resolution|resolution]] 1.18&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1t1e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_novosp._mn-32 Bacillus novosp. mn-32]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T1E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1t1e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._MN-32 Bacillus sp. MN-32]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T1E FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.18&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gt9|1gt9]], [[1gtg|1gtg]], [[1gtj|1gtj]], [[1gtl|1gtl]], [[1t1g|1t1g]], [[1t1i|1t1i]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KSCP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198803 Bacillus novosp. MN-32])</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=1t1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t1e OCA], [https://pdbe.org/1t1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t1e RCSB], [https://www.ebi.ac.uk/pdbsum/1t1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t1e ProSAT]</span></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=1t1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t1e OCA], [http://pdbe.org/1t1e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t1e RCSB], [http://www.ebi.ac.uk/pdbsum/1t1e PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8RR56_9BACI Q8RR56_9BACI]
 == 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/t1/1t1e_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t1/1t1e_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1t1e ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Kumamolisin, an extracellular proteinase derived from an acido/thermophilic Bacillus, belongs to the sedolisin family of endopeptidases characterized by a subtilisin-like fold and a Ser-Glu-Asp catalytic triad. In kumamolisin, the Asp82 carboxylate hydrogen bonds to Glu32-Trp129, which might act as a proton sink stabilizing the catalytic residues. The 1.2/1.3 A crystal structures of the Glu32--&gt;Ala and Trp129--&gt;Ala mutants show that both mutations affect the active-site conformation, causing a 95% activity decrease. In addition, the 1.2 A crystal structure of the Ser278--&gt;Ala mutant of pro-kumamolisin was determined. The prodomain exhibits a half-beta sandwich core docking to the catalytic domain similarly as the equivalent subtilisin prodomains in their catalytic-domain complexes. This pro-kumamolisin structure displays, for the first time, the uncleaved linker segment running across the active site and connecting the prodomain with the properly folded catalytic domain. The structure strongly points to an initial intramolecular activation cleavage in subtilases, as presumed for pro-subtilisin and pro-furin.
-.2 A crystal structure of the serine carboxyl proteinase pro-kumamolisin; structure of an intact pro-subtilase.,Comellas-Bigler M, Maskos K, Huber R, Oyama H, Oda K, Bode W Structure. 2004 Jul;12(7):1313-23. PMID:15242607<ref>PMID:15242607</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1t1e" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus novosp. mn-32]]
+[[Category: Bacillus sp. MN-32]]
-[[Category: Bode, W]]
+[[Category: Large Structures]]
-[[Category: Comellas-Bigler, M]]
+[[Category: Bode W]]
-[[Category: Huber, R]]
+[[Category: Comellas-Bigler M]]
-[[Category: Maskos, K]]
+[[Category: Huber R]]
-[[Category: Oda, K]]
+[[Category: Maskos K]]
-[[Category: Oyama, H]]
+[[Category: Oda K]]
-[[Category: Activation mechanism]]
+[[Category: Oyama H]]
-[[Category: Hydrolase]]
-[[Category: Proenzyme]]
-[[Category: Prosubtilase]]
-[[Category: Sedolisin]]
-[[Category: Serine-carboxyl proteinase]]