1lee: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1lee.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM IN COMPLEX WITH INHIBITOR RS367==
-The line below this paragraph, containing "STRUCTURE_1lee", creates the "Structure Box" on the page.
+<StructureSection load='1lee' size='340' side='right'caption='[[1lee]], [[Resolution|resolution]] 1.90&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'>[[1lee]] 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=1LEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LEE 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R36:4-AMINO-N-{4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-1-ISOBUTYL-5-PHENYL-PENTYL}-BENZAMIDE'>R36</scene></td></tr>
-{{STRUCTURE_1lee|  PDB=1lee  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lee OCA], [https://pdbe.org/1lee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lee RCSB], [https://www.ebi.ac.uk/pdbsum/1lee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lee ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PLM2_PLAFX PLM2_PLAFX] During the asexual blood stage, participates in initial cleavage of native host hemoglobin (Hb) resulting in Hb denaturation (PubMed:11782538, PubMed:15574427, PubMed:8844673). May cleave preferentially denatured hemoglobin that has been cleaved by PMI (PubMed:8844673). Digestion of host Hb is an essential step which provides the parasite with amino acids for protein synthesis, and regulates osmolarity (Probable).<ref>PMID:11782538</ref> <ref>PMID:15574427</ref> <ref>PMID:8844673</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/le/1lee_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=1lee ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Plasmepsin II is one of the four catalytically active plasmepsins found in the food vacuole of Plasmodium falciparum. These enzymes initiate hemoglobin degradation by cleavage at the alpha-chain between Phe33 and Leu34. The crystal structures of Ser205 mutant plasmepsin II from P. falciparum in complex with two inhibitors have been refined at a resolution of 1.8 A in the space group I222 and to R factors of 19.9 and 19.5%. Each crystal contains one monomer in the asymmetric unit. Both inhibitors have a Phe-Leu core and incorporate tetrahedral transition-state mimetic hydroxypropylamine. The inhibitor rs367 possesses a 2,6-dimethylphenyloxyacetyl group at the P2 position and 3-aminobenzamide at the P2' position, while rs370 has the same P2 group but 4-aminobenzamide in the P2' position. These complexes reveal key conserved hydrogen bonds between the inhibitor and the binding-cavity residues, notably with the flap residues Val78 and Ser79, the catalytic dyad Asp34 and Asp214 and the residues Ser218 and Gly36 that are in proximity to the catalytic dyad. The structures also show unexpected conformational variability of the binding cavity of plasmepsin II and may reflect the mode of binding of the hemoglobin alpha-chain for cleavage.
-===CRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM IN COMPLEX WITH INHIBITOR RS367===
+Structures of Ser205 mutant plasmepsin II from Plasmodium falciparum at 1.8 A in complex with the inhibitors rs367 and rs370.,Asojo OA, Afonina E, Gulnik SV, Yu B, Erickson JW, Randad R, Medjahed D, Silva AM Acta Crystallogr D Biol Crystallogr. 2002 Dec;58(Pt 12):2001-8. Epub 2002, Nov 23. PMID:12454457<ref>PMID:12454457</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1lee" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12454457}}, adds the Publication Abstract to the page
+*[[Plasmepsin|Plasmepsin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12454457 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12454457}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[1lee]] 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=1LEE OCA].
-==Reference==
-<ref group="xtra">PMID:12454457</ref><ref group="xtra">PMID:12614616</ref><references group="xtra"/>
-[[Category: Plasmepsin II]]
-[[Category: Plasmodium falciparum]]
-[[Category: Afonina, E.]]
-[[Category: Asojo, O A.]]
-[[Category: Erickson, J W.]]
-[[Category: Gulnik, S V.]]
-[[Category: Mehadjed, D.]]
-[[Category: Randad, R.]]
-[[Category: Silva, A M.]]
-[[Category: Yu, B.]]
-[[Category: Aspartic protease]]
-[[Category: Hydrolase]]
-[[Category: Plasmepsin]]
 [[Category: Plasmodium falciparum]]
+[[Category: Afonina E]]
+[[Category: Asojo OA]]
+[[Category: Erickson JW]]
+[[Category: Gulnik SV]]
+[[Category: Mehadjed D]]
+[[Category: Randad R]]
+[[Category: Silva AM]]
+[[Category: Yu B]]