1dq2: Difference between revisions

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OCA

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 ==Unlocked metal-free concanavalin A==
-<StructureSection load='1dq2' size='340' side='right' caption='[[1dq2]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+<StructureSection load='1dq2' size='340' side='right'caption='[[1dq2]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dq2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DQ2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dq2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQ2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</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]] 2.05&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dq0|1dq0]], [[1dq1|1dq1]], [[1dq4|1dq4]], [[1dq5|1dq5]], [[1dq6|1dq6]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></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=1dq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dq2 OCA], [http://pdbe.org/1dq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1dq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dq2 ProSAT]</span></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=1dq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dq2 OCA], [https://pdbe.org/1dq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dq2 RCSB], [https://www.ebi.ac.uk/pdbsum/1dq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dq2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CONA_CANBR CONA_CANBR]] Glucose/D-mannose specific lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from hamster and rat. Induces lymphocyte proliferation and IFNG production. Shows toxicity against the aquatic snail B.glabrata at concentrations higher than 20 ug/ml.<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:8891754</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref> <ref>PMID:19765980</ref>
+[https://www.uniprot.org/uniprot/CONA_CANBR CONA_CANBR] Glucose/D-mannose specific lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from hamster and rat. Induces lymphocyte proliferation and IFNG production. Shows toxicity against the aquatic snail B.glabrata at concentrations higher than 20 ug/ml.<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:8891754</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref> <ref>PMID:19765980</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/dq/1dq2_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dq/1dq2_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 20: @@
 </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=1dq2 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The reversible binding of manganese and calcium to concanavalin A determines the carbohydrate binding of the lectin by inducing large conformational changes. These changes are governed by the isomerization of a non-proline peptide bond, Ala-207-Asp-208, positioned in a beta-strand in between the calcium binding site S2 and the carbohydrate specificity-determining loop. The replacement of calcium by manganese allowed us to investigate the structures of the carbohydrate binding, locked state and the inactive, unlocked state of concanavalin A, both with and without metal ions bound. Crystals of unlocked metal-free concanavalin A convert to the locked form with the binding of two Mn(2+) ions. Removal of these ions from the crystals traps metal-free concanavalin A in its locked state, a minority species in solution. The ligation of a metal ion in S2 to unlocked concanavalin A causes bending of the beta-strand foregoing the S2 ligand residues Asp-10 and Tyr-12. This bending disrupts conventional beta-sheet hydrogen bonding and forces the Thr-11 side chain against the Ala-207-Asp-208 peptide bond. The steric strain exerted by Thr-11 is presumed to drive the trans-to-cis isomerization. Upon isomerization, Asp-208 flips into its carbohydrate binding position, and the conformation of the carbohydrate specificity determining loop changes dramatically.
-The structural features of concanavalin A governing non-proline peptide isomerization.,Bouckaert J, Dewallef Y, Poortmans F, Wyns L, Loris R J Biol Chem. 2000 Jun 30;275(26):19778-87. PMID:10748006<ref>PMID:10748006</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1dq2" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Concanavalin A|Concanavalin A]]
+*[[Concanavalin 3D structures|Concanavalin 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 28: @@
 </StructureSection>
 [[Category: Canavalia ensiformis]]
-[[Category: Bouckaert, J]]
+[[Category: Large Structures]]
-[[Category: Dewallef, Y]]
+[[Category: Bouckaert J]]
-[[Category: Loris, R]]
+[[Category: Dewallef Y]]
-[[Category: Poortmans, F]]
+[[Category: Loris R]]
-[[Category: Wyns, L]]
+[[Category: Poortmans F]]
-[[Category: Concanavalin some]]
+[[Category: Wyns L]]
-[[Category: Demetallized]]
-[[Category: Lectin]]
-[[Category: Metal-free]]
-[[Category: Sugar binding protein]]
-[[Category: Unlocked]]