2drd: Difference between revisions

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-[[Image:2drd.gif|left|200px]]<br /><applet load="2drd" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2drd, resolution 3.10&Aring;" />
-'''Crystal structure of a multidrug transporter reveal a functionally rotating mechanism'''<br />
-==Overview==
+==Crystal structure of a multidrug transporter reveal a functionally rotating mechanism==
-AcrB is a principal multidrug efflux transporter in Escherichia coli that, cooperates with an outer-membrane channel, TolC, and a membrane-fusion, protein, AcrA. Here we describe crystal structures of AcrB with and, without substrates. The AcrB-drug complex consists of three protomers, each of which has a different conformation corresponding to one of the, three functional states of the transport cycle. Bound substrate was found, in the periplasmic domain of one of the three protomers. The voluminous, binding pocket is aromatic and allows multi-site binding. The structures, indicate that drugs are exported by a three-step functionally rotating, mechanism in which substrates undergo ordered binding change.
+<StructureSection load='2drd' size='340' side='right'caption='[[2drd]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2drd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The November 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Multidrug Resistance Transporters''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_11 10.2210/rcsb_pdb/mom_2007_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DRD FirstGlance]. <br>
-DRD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MIY:'>MIY</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRD OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MIY:(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE'>MIY</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2drd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2drd OCA], [https://pdbe.org/2drd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2drd RCSB], [https://www.ebi.ac.uk/pdbsum/2drd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2drd ProSAT]</span></td></tr>
-Crystal structures of a multidrug transporter reveal a functionally rotating mechanism., Murakami S, Nakashima R, Yamashita E, Matsumoto T, Yamaguchi A, Nature. 2006 Sep 14;443(7108):173-9. Epub 2006 Aug 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16915237 16915237]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ACRB_ECOLI ACRB_ECOLI] AcrAB is a drug efflux protein with a broad substrate specificity.<ref>PMID:16915237</ref> <ref>PMID:16946072</ref> <ref>PMID:17194213</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/dr/2drd_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=2drd ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Matsumoto, T.]]
+[[Category: Multidrug Resistance Transporters]]
-[[Category: Murakami, S.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Nakashima, R.]]
+[[Category: Matsumoto T]]
-[[Category: Yamashita, E.]]
+[[Category: Murakami S]]
-[[Category: MIY]]
+[[Category: Nakashima R]]
-[[Category: antiporter]]
+[[Category: Yamashita E]]
-[[Category: drug resistance]]
-[[Category: exporter]]
-[[Category: membrane protein]]
-[[Category: membrane transporter]]
-[[Category: multidrug efflux]]
-[[Category: transporter]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 17:22:08 2008''