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 [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia 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 [http:// | <table><tr><td colspan='2'>[[2yfl]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia 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 [http://proteopedia.org/fgij/fg.htm?mol=2YFL FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | </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> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xsh|2xsh]], [[2xrx|2xrx]], [[2xso|2xso]], [[2xr8|2xr8]], [[2yfj|2yfj]], [[2yfi|2yfi]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xsh|2xsh]], [[2xrx|2xrx]], [[2xso|2xso]], [[2xr8|2xr8]], [[2yfj|2yfj]], [[2yfi|2yfi]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl_2,3-dioxygenase Biphenyl 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.18 1.14.12.18] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl_2,3-dioxygenase Biphenyl 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.18 1.14.12.18] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2yfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yfl OCA], [http://pdbe.org/2yfl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yfl RCSB], [http://www.ebi.ac.uk/pdbsum/2yfl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yfl ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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==See Also== | ==See Also== | ||
*[[Dioxygenase|Dioxygenase]] | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Biphenyl 2,3-dioxygenase]] | [[Category: Biphenyl 2,3-dioxygenase]] | ||
[[Category: Burkholderia cepacia lb400]] | [[Category: Burkholderia cepacia lb400]] | ||
[[Category: Large Structures]] | |||
[[Category: Bolin, J T]] | [[Category: Bolin, J T]] | ||
[[Category: Kumar, P]] | [[Category: Kumar, P]] |
Revision as of 15:48, 22 July 2020
Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuranCrystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran
Structural highlights
Function[BPHE_BURXL] The beta subunit may be responsible for the substrate specificity of the enzyme. Publication 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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