2yfl: Difference between revisions
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==Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran== | ==Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran== | ||
<StructureSection load='2yfl' size='340' side='right' caption='[[2yfl]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='2yfl' size='340' side='right'caption='[[2yfl]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2yfl]] is a 12 chain structure with sequence from [ | <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> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> | ||
<tr id=' | <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> | ||
< | <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> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/BPHA_PARXL BPHA_PARXL] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 18: | Line 18: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2yfl" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Dioxygenase|Dioxygenase]] | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Paraburkholderia xenovorans LB400]] | ||
[[Category: Bolin | [[Category: Bolin JT]] | ||
[[Category: Kumar | [[Category: Kumar P]] | ||
Latest revision as of 13:51, 20 December 2023
Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuranCrystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran
Structural highlights
FunctionPublication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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