2zpr: Difference between revisions
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< | ==Crystal structure of anionic trypsin isoform 2 from chum salmon== | ||
<StructureSection load='2zpr' size='340' side='right'caption='[[2zpr]], [[Resolution|resolution]] 1.75Å' scene=''> | |||
You may | == Structural highlights == | ||
<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 | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</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> | ||
<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 > CST-1 > 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. | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2zpr" style="background-color:#fffaf0;"></div> | |||
== | |||
==See Also== | ==See Also== | ||
*[[Trypsin]] | *[[Trypsin 3D structures|Trypsin 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Oncorhynchus keta]] | [[Category: Oncorhynchus keta]] | ||
[[Category: Iyaguchi | [[Category: Iyaguchi D]] | ||
[[Category: Toyota | [[Category: Toyota E]] | ||
Latest revision as of 11:42, 30 October 2024
Crystal structure of anionic trypsin isoform 2 from chum salmonCrystal structure of anionic trypsin isoform 2 from chum salmon
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThree 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 > CST-1 > 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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