2yfl

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[[Image:2yfl.jpg|left|200px]]
 
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==Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran==
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The line below this paragraph, containing "STRUCTURE_2yfl", creates the "Structure Box" on the page.
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<StructureSection load='2yfl' size='340' side='right'caption='[[2yfl]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2yfl]] is a 12 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=2YFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YFL 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]] 2.6&#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=DC4:2-CHLORODIBENZOFURAN'>DC4</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
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{{STRUCTURE_2yfl| PDB=2yfl | SCENE= }}
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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=2yfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yfl OCA], [https://pdbe.org/2yfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yfl RCSB], [https://www.ebi.ac.uk/pdbsum/2yfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yfl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/BPHA_PARXL BPHA_PARXL]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE(LB400)) is a Rieske-type oxygenase that catalyzes the stereospecific oxygenation of many heterocyclic aromatics including dibenzofuran. In a previous work, we evolved BphAE(LB400) and obtained BphAE(RR41). This variant metabolizes dibenzofuran and 2-chlorodibenzofuran more efficiently than BphAE(LB400). However, the regiospecificity of BphAE(RR41) toward these substrates differs. Dibenzofuran is metabolized principally through a lateral dioxygenation whereas 2-chlorodibenzofuran is metabolized principally through an angular dioxygenation. In order to explain this difference, we examined the crystal structures of both substrate-bound forms of BphAE(RR41) obtained under anaerobic conditions. This structure analysis, in combination with biochemical data for a Ser283Gly mutant provided evidences that the substrate is compelled to move after oxygen-binding in BphAE(RR41):dibenzofuran. In BphAE(RR41):2-chlorodibenzofuran, the chlorine atom is close to the side chain of Ser283. This contact is missing in the BphAE(RR41):dibenzofuran, and strong enough in the BphAE(RR41):2-chlorodibenzofuran to help prevent substrate movement during the catalytic reaction.
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===Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran===
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Structural insights into the metabolism of 2-chlorodibenzofuran by an evolved biphenyl dioxygenase.,Kumar P, Mohammadi M, Dhindwal S, Pham TT, Bolin JT, Sylvestre M Biochem Biophys Res Commun. 2012 Apr 22. PMID:22546558<ref>PMID:22546558</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2yfl" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 22546558 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_22546558}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[2yfl]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YFL OCA].
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[[Category: Paraburkholderia xenovorans LB400]]
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[[Category: Bolin JT]]
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==Reference==
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[[Category: Kumar P]]
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<ref group="xtra">PMID:022546558</ref><references group="xtra"/>
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[[Category: Biphenyl 2,3-dioxygenase]]
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[[Category: Burkholderia xenovorans]]
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[[Category: Bolin, J T.]]
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[[Category: Kumar, P.]]
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[[Category: Bpdo]]
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[[Category: Degradation]]
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[[Category: Oxidoreductase]]
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Current revision

Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran

PDB ID 2yfl

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