2yfl: Difference between revisions

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-[[Image:2yfl.jpg|left|200px]]
-<!--
+==Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran==
-The line below this paragraph, containing "STRUCTURE_2yfl", creates the "Structure Box" on the page.
+<StructureSection load='2yfl' size='340' side='right'caption='[[2yfl]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<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>
-{{STRUCTURE_2yfl|  PDB=2yfl  |  SCENE=  }}
+<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>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BPHA_PARXL BPHA_PARXL]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2yfl" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22546558}}, adds the Publication Abstract to the page
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22546558 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22546558}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[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].
+[[Category: Paraburkholderia xenovorans LB400]]
+[[Category: Bolin JT]]
-==Reference==
+[[Category: Kumar P]]
-<ref group="xtra">PMID:022546558</ref><references group="xtra"/>
-[[Category: Biphenyl 2,3-dioxygenase]]
-[[Category: Burkholderia xenovorans]]
-[[Category: Bolin, J T.]]
-[[Category: Kumar, P.]]
-[[Category: Bpdo]]
-[[Category: Degradation]]
-[[Category: Oxidoreductase]]