2fgr: Difference between revisions

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OCA

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-[[Image:2fgr.gif|left|200px]]<br /><applet load="2fgr" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2fgr, resolution 1.500&Aring;" />
-'''High resolution Xray structure of Omp32'''<br />
-==Overview==
+==High resolution Xray structure of Omp32==
-The porin Omp32 is the major outer membrane protein of the bacterium, Delftia acidovorans. The crystal structures of the strongly, anion-selective porin alone and in complex with the substrate malate were, solved at 1.5 and 1.45 A resolution, respectively, and revealed a, malate-binding motif adjacent to the channel constriction zone. Binding is, mediated by interaction with a cluster of two arginine residues and two, threonines. This binding site is specific for Omp32 and reflects the, physiological adaptation of the organism to organic acids. Structural, studies are combined with a 7-ns unbiased molecular dynamics simulation of, the trimeric channel in a model membrane. Molecular dynamics trajectories, show how malate ions are efficiently captured from the surrounding bulk, solution by the electrostatic potential of the channel, translocated to, the binding site region, and immobilized in the constriction zone. In, accordance with these results, conductance measurements with Omp32, inserted in planar lipid membranes revealed binding of malate. The, anion-selective channel Omp32 is the first reported example of a porin, with a 16-stranded beta-barrel and proven substrate specificity. This, finding suggests a new view on the correlation of porin structure with, substrate binding in specific channels.
+<StructureSection load='2fgr' size='340' side='right'caption='[[2fgr]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2fgr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Delftia_acidovorans Delftia acidovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FGR 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]] 1.5&#8491;</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=SO4:SULFATE+ION'>SO4</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=2fgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fgr OCA], [https://pdbe.org/2fgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fgr RCSB], [https://www.ebi.ac.uk/pdbsum/2fgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fgr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OMP32_DELAC OMP32_DELAC]
+== 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/fg/2fgr_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=2fgr ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-FGR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Delftia_acidovorans Delftia acidovorans] with CA and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FGR OCA].
+*[[Porin 3D structures|Porin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32., Zachariae U, Kluhspies T, De S, Engelhardt H, Zeth K, J Biol Chem. 2006 Mar 17;281(11):7413-20. Epub 2006 Jan 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16434398 16434398]
 [[Category: Delftia acidovorans]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Engelhardt, H.]]
+[[Category: Engelhardt H]]
-[[Category: Zachariae, U.]]
+[[Category: Zachariae U]]
-[[Category: Zeth, K.]]
+[[Category: Zeth K]]
-[[Category: CA]]
-[[Category: SO4]]
-[[Category: omp32 porin outer membrane protein]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:32:50 2007''