3bgo: Difference between revisions

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-[[Image:3bgo.png|left|200px]]
-<!--
+==Azide complex of Engineered Subtilisin SUBT_BACAM==
-The line below this paragraph, containing "STRUCTURE_3bgo", creates the "Structure Box" on the page.
+<StructureSection load='3bgo' size='340' side='right'caption='[[3bgo]], [[Resolution|resolution]] 1.80&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'>[[3bgo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BGO 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3bgo|  PDB=3bgo  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bgo OCA], [https://pdbe.org/3bgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bgo RCSB], [https://www.ebi.ac.uk/pdbsum/3bgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bgo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUBT_BACAM SUBT_BACAM] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides. Has a high substrate specificity to fibrin.<ref>PMID:12524032</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/bg/3bgo_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=3bgo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+An engineered variant of the protease subtilisin from Bacillus amyloliquefaciens, in which the D32A mutation renders the enzyme's activity dependent on the presence of certain small anions such as fluoride or azide, has been produced. This modified enzyme has applications as an azide or fluoride-triggered expression-purification tool. We report activity measurements showing that the enzyme is activated more than 3000-fold by azide and describe the 1.8 A resolution structure of an inactive form (by replacing the catalytic nucleophile Ser 221 with alanine) of the protease, in complex with azide and with a substrate that spans the active site. Both enzyme and substrate have been engineered to increase their stability and the affinity of their interaction. The substrate is based on a stabilized subtilisin prodomain, extended across the active site by the addition of four residues at its C-terminus. In the crystal structure, the substrate is well-ordered across the active site, and the azide anion is observed bound adjacent to Ala 32. The structures of the substrate complex in three different crystals (anion-free, fluoride-soaked, and azide-soaked) are compared. These structures provide extensive information for understanding subtilisin's substrate binding and catalytic mechanism, and for the development of biotechnology tools based on anion-activated proteolysis. The mechanism of anion-dependent proteolysis appears to be a slight modification of the accepted charge-relay mechanism for serine proteases.
-===Azide complex of Engineered Subtilisin SUBT_BACAM===
+Structure of a switchable subtilisin complexed with a substrate and with the activator azide.,Gallagher T, Ruan B, London M, Bryan MA, Bryan PN Biochemistry. 2009 Nov 3;48(43):10389-94. doi: 10.1021/bi900577n. PMID:19761257<ref>PMID:19761257</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-[[3bgo]] is a 2 chain structure of [[Subtilisin]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BGO OCA].
+<div class="pdbe-citations 3bgo" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Subtilisin]]
+*[[Subtilisin 3D structures|Subtilisin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus amyloliquefaciens]]
-[[Category: Subtilisin]]
+[[Category: Large Structures]]
-[[Category: Bryan, P N.]]
+[[Category: Bryan PN]]
-[[Category: Gallagher, D T.]]
+[[Category: Gallagher DT]]
-[[Category: Anion sensor]]
-[[Category: Azide switch]]
-[[Category: Calcium]]
-[[Category: Hydrolase]]
-[[Category: Metal-binding]]
-[[Category: Protease]]
-[[Category: Secreted]]
-[[Category: Serine protease]]
-[[Category: Sporulation]]
-[[Category: Zymogen]]