1dq6: Difference between revisions

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

OCA

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-[[Image:1dq6.jpg|left|200px]]<br /><applet load="1dq6" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1dq6, resolution 1.9&Aring;" />
-'''Manganese;Manganese concanavalin A at pH 7.0'''<br />
-==Overview==
+==Manganese;Manganese concanavalin A at pH 7.0==
-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.
+<StructureSection load='1dq6' size='340' side='right'caption='[[1dq6]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dq6]] is a 1 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=1DQ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQ6 FirstGlance]. <br>
+</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=MN:MANGANESE+(II)+ION'>MN</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=1dq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dq6 OCA], [https://pdbe.org/1dq6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dq6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dq6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dq6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CONA_CANEN CONA_CANEN] D-mannose specific lectin.
+== 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/1dq6_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=1dq6 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-DQ6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DQ6 OCA].
+*[[Concanavalin 3D structures|Concanavalin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10748006 10748006]
 [[Category: Canavalia ensiformis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bouckaert, J.]]
+[[Category: Bouckaert J]]
-[[Category: Dewallef, Y.]]
+[[Category: Dewallef Y]]
-[[Category: Loris, R.]]
+[[Category: Loris R]]
-[[Category: Poortmans, F.]]
+[[Category: Poortmans F]]
-[[Category: Wyns, L.]]
+[[Category: Wyns L]]
-[[Category: MN]]
-[[Category: binuclear]]
-[[Category: concanavalin a]]
-[[Category: lectin]]
-[[Category: manganese]]
-[[Category: metal binding]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:29:39 2007''