2zpr: Difference between revisions

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-[[Image:2zpr.png|left|200px]]
-<!--
+==Crystal structure of anionic trypsin isoform 2 from chum salmon==
-The line below this paragraph, containing "STRUCTURE_2zpr", creates the "Structure Box" on the page.
+<StructureSection load='2zpr' size='340' side='right'caption='[[2zpr]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2zpr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oncorhynchus_keta Oncorhynchus keta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZPR FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-{{STRUCTURE_2zpr|  PDB=2zpr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zpr OCA], [https://pdbe.org/2zpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zpr RCSB], [https://www.ebi.ac.uk/pdbsum/2zpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zpr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/B3Y8K5_ONCKE B3Y8K5_ONCKE]
+== 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/zp/2zpr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2zpr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Three anionic salmon trypsin isoforms (CST-1, CST-2 and CST-3) were isolated from the pyloric caeca of chum salmon (Oncorhynchus keta). The order of catalytic efficiency (K(m)/k(cat)) of the isoforms during BAPA hydrolysis was CST-2 &gt; CST-1 &gt; CST-3. In order to find a structural rationalization for the observed difference in catalytic efficiency, the X-ray crystallographic structures of the three isoforms were compared in detail. Some structural differences were observed in the C-terminal alpha-helix, interdomain loop and active-site region. From the results of the detailed comparison, it appears that the structural flexibility of the C-terminal alpha-helix, which interacts with the N-terminal domain, and the substrate-binding pocket in CST-3 are lower than those in CST-1 and CST-2. In addition, the conformation of the catalytic triad (His57, Asp102 and Ser195) differs among the three isoforms. The imidazole N atom of His57 in CST-1 and CST-2 forms a hydrogen bond to the hydroxyl O atom of Ser195, but the distance between the imidazole N atom of His57 and the hydroxyl O atom of Ser195 in CST-3 is too great (3.8 A) for the formation of a hydrogen bond. Thus, the nucleophilicity of the hydroxyl group of Ser195 in CST-3 is weaker than that in CST-1 or CST-2. Furthermore, the electrostatic potential of the substrate-binding pocket in CST-2 is markedly lower than those in CST-1 and CST-3 owing to the negative charges of Asp150, Asp153 and Glu221B that arise from the long-range effect. These results may explain the higher catalytic efficiency of CST-2 compared with CST-1 and CST-3.
-===Crystal structure of anionic trypsin isoform 2 from chum salmon===
+A structural comparison of three isoforms of anionic trypsin from chum salmon (Oncorhynchus keta).,Toyota E, Iyaguchi D, Sekizaki H, Tateyama M, Ng KK Acta Crystallogr D Biol Crystallogr. 2009 Jul;65(Pt 7):717-23. Epub 2009, Jun 20. PMID:19564692<ref>PMID:19564692</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19564692}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2zpr" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19564692 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_19564692}}
-==About this Structure==
-[[2zpr]] is a 2 chain structure of [[Trypsin]] with sequence from [http://en.wikipedia.org/wiki/Oncorhynchus_keta Oncorhynchus keta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZPR OCA].
 ==See Also==
-*[[Trypsin]]
+*[[Trypsin 3D structures|Trypsin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019564692</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Oncorhynchus keta]]
-[[Category: Iyaguchi, D.]]
+[[Category: Iyaguchi D]]
-[[Category: Toyota, E.]]
+[[Category: Toyota E]]
-[[Category: Hydrolase]]
-[[Category: Protease]]
-[[Category: Serine protease]]
-[[Category: Serine proteinase]]
-[[Category: Trypsin]]