2wbf: Difference between revisions

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-==CRYSTAL STRUCTURE ANALYSIS OF SERA5E FROM PLASMODIUM FALCIPARUM WITH LOOP 690-700 ORDERED==
-<StructureSection load='2wbf' size='340' side='right' caption='[[2wbf]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+==Crystal Structure Analysis of SERA5E from plasmodium falciparum with loop 690-700 ordered==
+<StructureSection load='2wbf' size='340' side='right'caption='[[2wbf]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wbf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WBF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wbf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WBF 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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</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]] 1.6&#8491;</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=2wbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wbf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2wbf RCSB], [http://www.ebi.ac.uk/pdbsum/2wbf PDBsum]</span></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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</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=2wbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wbf OCA], [https://pdbe.org/2wbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wbf RCSB], [https://www.ebi.ac.uk/pdbsum/2wbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wbf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SERA_PLAFD SERA_PLAFD]] It may function at the red blood cell membrane, perhaps as a component that influences the invasion process.
+[https://www.uniprot.org/uniprot/SERA5_PLAF7 SERA5_PLAF7] Plays an essential role during the asexual blood stage development by controlling the kinetics of merozoite egress from host erythrocytes (PubMed:25599609, PubMed:28683142). Specifically, prevents premature rupture of the parasitophorous vacuole and host erythrocyte membranes (PubMed:28683142).<ref>PMID:25599609</ref> <ref>PMID:28683142</ref>   May prevent merozoite phagocytosis by host monocytes via interaction with host VTN at the merozoite surface (By similarity). Plays a role in parasite growth (By similarity).[UniProtKB:P69193]  Protease activity is controversial (PubMed:25599609). Has been shown in a number of studies to have protease activity towards a synthetic peptide in vitro (PubMed:13679369, PubMed:24769454, PubMed:29716996). Has also been shown to lack protease activity towards a synthetic peptide in vitro (PubMed:25599609).<ref>PMID:13679369</ref> <ref>PMID:24769454</ref> <ref>PMID:25599609</ref> <ref>PMID:29716996</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/wb/2wbf_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wb/2wbf_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <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/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=2wbf ConSurf].
 <div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The sera genes of the malaria-causing parasite Plasmodium encode a family of unique proteins that are maximally expressed at the time of egress of parasites from infected red blood cells. These multi-domain proteins are unique, containing a central papain-like cysteine-protease fragment enclosed between the disulfide-linked N- and C-terminal domains. However, the central fragment of several members of this family, including serine repeat antigen 5 (SERA5), contains a serine (S596) in place of the active-site cysteine. Here we report the crystal structure of the central protease-like domain of Plasmodium falciparum SERA5, revealing a number of anomalies in addition to the putative nucleophilic serine: (1) the structure of the putative active site is not conducive to binding substrate in the canonical cysteine-protease manner; (2) the side chain of D594 restricts access of substrate to the putative active site; and (3) the S(2) specificity pocket is occupied by the side chain of Y735, reducing this site to a small depression on the protein surface. Attempts to determine the structure in complex with known inhibitors were not successful. Thus, despite having revealed its structure, the function of the catalytic domain of SERA5 remains an enigma.
+Structural insights into the protease-like antigen Plasmodium falciparum SERA5 and its noncanonical active-site serine.,Hodder AN, Malby RL, Clarke OB, Fairlie WD, Colman PM, Crabb BS, Smith BJ J Mol Biol. 2009 Sep 11;392(1):154-65. Epub 2009 Jul 8. PMID:19591843<ref>PMID:19591843</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2wbf" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Plasmodium falciparum]]
-[[Category: Clarke, O B]]
+[[Category: Clarke OB]]
-[[Category: Colman, P M]]
+[[Category: Colman PM]]
-[[Category: Malby, R L]]
+[[Category: Malby RL]]
-[[Category: Smith, B J]]
+[[Category: Smith BJ]]
-[[Category: Cathepsin]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Malaria]]
-[[Category: Plasmodium]]
-[[Category: Protease]]
-[[Category: Sera]]
-[[Category: Serine repeat antigen]]
-[[Category: Thiol protease]]
-[[Category: Vacuole]]