2gdr

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(New page: 200px<br /><applet load="2gdr" size="350" color="white" frame="true" align="right" spinBox="true" caption="2gdr, resolution 2.1&Aring;" /> '''Crystal structure of ...)
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[[Image:2gdr.gif|left|200px]]<br /><applet load="2gdr" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2gdr, resolution 2.1&Aring;" />
 
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'''Crystal structure of a bacterial glutathione transferase'''<br />
 
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==Overview==
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==Crystal structure of a bacterial glutathione transferase==
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Prokaryotic glutathione S-transferases are as diverse as their eukaryotic, counterparts but are much less well characterized. BphK from Burkholderia, xenovorans LB400 consumes two GSH molecules to reductively dehalogenate, chlorinated 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (HOPDAs), inhibitory, polychlorinated biphenyl metabolites. Crystallographic structures of two, ternary complexes of BphK were solved to a resolution of 2.1A. In the, BphK-GSH-HOPDA complex, GSH and HOPDA molecules occupy the G- and, H-subsites, respectively. The thiol nucleophile of the GSH molecule is, positioned for SN2 attack at carbon 3 of the bound HOPDA. The respective, sulfur atoms of conserved Cys-10 and the bound GSH are within 3.0A, consistent with product release and the formation of a mixed disulfide, intermediate. In the BphK-(GSH)2 complex, a GSH molecule occupies each of, the two subsites. The three sulfur atoms of the two GSH molecules and, Cys-10 are aligned suitably for a disulfide exchange reaction that would, regenerate the resting enzyme and yield disulfide-linked GSH molecules. A, second conserved residue, His-106, is adjacent to the thiols of Cys-10 and, the GSH bound to the G-subsite and thus may stabilize a transition state, in the disulfide exchange reaction. Overall, the structures support and, elaborate a proposed dehalogenation mechanism for BphK and provide insight, into the plasticity of the H-subsite.
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<StructureSection load='2gdr' size='340' side='right'caption='[[2gdr]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2gdr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GDR FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gdr OCA], [https://pdbe.org/2gdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gdr RCSB], [https://www.ebi.ac.uk/pdbsum/2gdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gdr ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q59721_PARXL Q59721_PARXL]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/2gdr_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2gdr ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Prokaryotic glutathione S-transferases are as diverse as their eukaryotic counterparts but are much less well characterized. BphK from Burkholderia xenovorans LB400 consumes two GSH molecules to reductively dehalogenate chlorinated 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (HOPDAs), inhibitory polychlorinated biphenyl metabolites. Crystallographic structures of two ternary complexes of BphK were solved to a resolution of 2.1A. In the BphK-GSH-HOPDA complex, GSH and HOPDA molecules occupy the G- and H-subsites, respectively. The thiol nucleophile of the GSH molecule is positioned for SN2 attack at carbon 3 of the bound HOPDA. The respective sulfur atoms of conserved Cys-10 and the bound GSH are within 3.0A, consistent with product release and the formation of a mixed disulfide intermediate. In the BphK-(GSH)2 complex, a GSH molecule occupies each of the two subsites. The three sulfur atoms of the two GSH molecules and Cys-10 are aligned suitably for a disulfide exchange reaction that would regenerate the resting enzyme and yield disulfide-linked GSH molecules. A second conserved residue, His-106, is adjacent to the thiols of Cys-10 and the GSH bound to the G-subsite and thus may stabilize a transition state in the disulfide exchange reaction. Overall, the structures support and elaborate a proposed dehalogenation mechanism for BphK and provide insight into the plasticity of the H-subsite.
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==About this Structure==
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Structures of ternary complexes of BphK, a bacterial glutathione S-transferase that reductively dechlorinates polychlorinated biphenyl metabolites.,Tocheva EI, Fortin PD, Eltis LD, Murphy ME J Biol Chem. 2006 Oct 13;281(41):30933-40. Epub 2006 Aug 17. PMID:16920719<ref>PMID:16920719</ref>
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2GDR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans] with <scene name='pdbligand=GTT:'>GTT</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glutathione_transferase Glutathione transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.18 2.5.1.18] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GDR OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structures of ternary complexes of BphK, a bacterial glutathione S-transferase that reductively dechlorinates polychlorinated biphenyl metabolites., Tocheva EI, Fortin PD, Eltis LD, Murphy ME, J Biol Chem. 2006 Oct 13;281(41):30933-40. Epub 2006 Aug 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16920719 16920719]
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</div>
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[[Category: Burkholderia xenovorans]]
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<div class="pdbe-citations 2gdr" style="background-color:#fffaf0;"></div>
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[[Category: Glutathione transferase]]
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[[Category: Single protein]]
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[[Category: Eltis, L.D.]]
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[[Category: Fortin, P.D.]]
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[[Category: Murphy, M.E.P.]]
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[[Category: Tocheva, E.I.]]
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[[Category: GTT]]
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[[Category: c-term domain is alpha helical]]
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[[Category: each monomer contains two domains]]
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[[Category: n-term domain is mixed beta sheets and alpha helices]]
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[[Category: protein homodimer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 19:57:17 2008''
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==See Also==
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*[[Glutathione S-transferase 3D structures|Glutathione S-transferase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Paraburkholderia xenovorans LB400]]
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[[Category: Eltis LD]]
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[[Category: Fortin PD]]
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[[Category: Murphy MEP]]
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[[Category: Tocheva EI]]

Current revision

Crystal structure of a bacterial glutathione transferase

PDB ID 2gdr

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