2vid: Difference between revisions

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-[[Image:2vid.png|left|200px]]
-<!--
+==Serine protease SplB from Staphylococcus aureus at 1.8A resolution==
-The line below this paragraph, containing "STRUCTURE_2vid", creates the "Structure Box" on the page.
+<StructureSection load='2vid' size='340' side='right'caption='[[2vid]], [[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'>[[2vid]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VID 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vid OCA], [https://pdbe.org/2vid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vid RCSB], [https://www.ebi.ac.uk/pdbsum/2vid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vid ProSAT]</span></td></tr>
-{{STRUCTURE_2vid|  PDB=2vid  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SPLB_STAA8 SPLB_STAA8] Serine protease that cleaves specifically after the sequence Trp-Glu-Leu-Gln.<ref>PMID:18448121</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/vi/2vid_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/main_output.php?pdb_ID=2vid ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Proteases are of significant importance for the virulence of Staphylococcus aureus. Nevertheless, their subset, the serine protease-like proteins, remains poorly characterized. Here presented is an investigation of SplB protease catalytic activity revealing that the enzyme possesses exquisite specificity and only cleaves efficiently after the sequence Trp-Glu-Leu-Gln. To understand the molecular basis for such selectivity, we solved the three-dimensional structure of SplB to 1.8 A. Modeling of substrate binding to the protease demonstrated that selectivity relies in part on a canonical specificity pockets-based mechanism. Significantly, the conformation of residues that ordinarily form the oxyanion hole, an essential structural element of the catalytic machinery of serine proteases, is not canonical in the SplB structure. We postulate that within SplB, the oxyanion hole is only formed upon docking of a substrate containing the consensus sequence motif. It is suggested that this unusual activation mechanism is used in parallel with classical determinants to further limit enzyme specificity. Finally, to guide future development, we attempt to point at likely physiological substrates and thus the role of SplB in staphylococcal physiology.
-===SERINE PROTEASE SPLB FROM STAPHYLOCOCCUS AUREUS AT 1.8A RESOLUTION===
+Enzymatic activity of the Staphylococcus aureus SplB serine protease is induced by substrates containing the sequence Trp-Glu-Leu-Gln.,Dubin G, Stec-Niemczyk J, Kisielewska M, Pustelny K, Popowicz GM, Bista M, Kantyka T, Boulware KT, Stennicke HR, Czarna A, Phopaisarn M, Daugherty PS, Thogersen IB, Enghild JJ, Thornberry N, Dubin A, Potempa J J Mol Biol. 2008 May 30;379(2):343-56. Epub 2008 Apr 3. PMID:18448121<ref>PMID:18448121</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_18448121}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vid" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18448121 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18448121}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2vid]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VID OCA].
-==Reference==
-<ref group="xtra">PMID:18448121</ref><ref group="xtra">PMID:16516230</ref><references group="xtra"/>
-[[Category: Staphylococcus aureus]]
-[[Category: Bista, M.]]
-[[Category: Boulware, K T.]]
-[[Category: Czarna, A.]]
-[[Category: Daugherty, P S.]]
-[[Category: Dubin, A.]]
-[[Category: Dubin, G.]]
-[[Category: Enghild, J J.]]
-[[Category: Kantyka, T.]]
-[[Category: Kisielewska, M.]]
-[[Category: Phopaisarn, M.]]
-[[Category: Popowicz, G M.]]
-[[Category: Potempa, J.]]
-[[Category: Pustelny, K.]]
-[[Category: Stec-Niemczyk, J.]]
-[[Category: Stennicke, H R.]]
-[[Category: Thogersen, I B.]]
-[[Category: Thornberry, N.]]
-[[Category: Hydrolase]]
-[[Category: Protease]]
-[[Category: Serine protease]]
 [[Category: Staphylococcus aureus]]
+[[Category: Bista M]]
+[[Category: Boulware KT]]
+[[Category: Czarna A]]
+[[Category: Daugherty PS]]
+[[Category: Dubin A]]
+[[Category: Dubin G]]
+[[Category: Enghild JJ]]
+[[Category: Kantyka T]]
+[[Category: Kisielewska M]]
+[[Category: Phopaisarn M]]
+[[Category: Popowicz GM]]
+[[Category: Potempa J]]
+[[Category: Pustelny K]]
+[[Category: Stec-Niemczyk J]]
+[[Category: Stennicke HR]]
+[[Category: Thogersen IB]]
+[[Category: Thornberry N]]