6el4: Difference between revisions

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-'''Unreleased structure'''
-The entry 6el4 is ON HOLD  until Paper Publication
+==Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with veratryl alcohol==
+<StructureSection load='6el4' size='340' side='right'caption='[[6el4]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6el4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrae Agrae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EL4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EL4 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=VOH:Veratryl+alcohol'>VOH</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2yor|2yor]], [[2yp1|2yp1]], [[5oxu|5oxu]], [[5oxt|5oxt]], [[5oy1|5oy1]], [[5oy2|5oy2]], [[6ekw|6ekw]], [[6ekx|6ekx]], [[6eky|6eky]], [[6ekz|6ekz]], [[6el0|6el0]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APO1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5400 AGRAE])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unspecific_peroxygenase Unspecific peroxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.2.1 1.11.2.1] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6el4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6el4 OCA], [http://pdbe.org/6el4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6el4 RCSB], [http://www.ebi.ac.uk/pdbsum/6el4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6el4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/APO1_AGRAE APO1_AGRAE]] Aromatic peroxidase that oxidizes aryl alcohols into the corresponding aldehydes and then into the corresponding benzoic acids. Oxidizes toluene and naphthalene. Catalyzes the regioselective peroxide-dependent hydroxylation of propranolol and diclofenac to 5-hydroxypropranolol and 4'-hydroxydiclofenac. Catalyzes the regioselective peroxide-dependent hydroxylation of naphthalene to 1-naphthol or 2-naphthol via a naphthalene 1,2-oxide intermediate. Catalyzes the regioselective peroxide-dependent oxidation of pyridine to pyridine N-oxide. Halogenates monochlorodimedone and phenol. Oxidizes the sulfer-containing heterocycle dibenzothiophene to yield ring-hydroxylation products and to a lesser extent sulfoxidation products.<ref>PMID:15294788</ref> <ref>PMID:16253244</ref> <ref>PMID:17410351</ref> <ref>PMID:19022254</ref> <ref>PMID:19039585</ref> <ref>PMID:18815784</ref> <ref>PMID:19394224</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Because of their minimal requirements, substrate promiscuity and product selectivity, fungal peroxygenases are now considered to be the jewel in the crown of C-H oxyfunctionalization biocatalysts. In this work, the crystal structure of the first laboratory-evolved peroxygenase expressed by yeast was determined at a resolution of 1.5 A. Notable differences were detected between the evolved and native peroxygenase from Agrocybe aegerita, including the presence of a full N-terminus and a broader heme access channel due to the mutations that accumulated through directed evolution. Further mutagenesis and soaking experiments with a palette of peroxygenative and peroxidative substrates suggested dynamic trafficking through the heme channel as the main driving force for the exceptional substrate promiscuity of peroxygenase. Accordingly, this study provides the first structural evidence at an atomic level regarding the mode of substrate binding for this versatile biocatalyst, which is discussed within a biological and chemical context.
-Authors:
+Structural Insights into the Substrate Promiscuity of a Laboratory-Evolved Peroxygenase.,Ramirez-Escudero M, Molina-Espeja P, Gomez de Santos P, Hofrichter M, Sanz-Aparicio J, Alcalde M ACS Chem Biol. 2018 Nov 16. doi: 10.1021/acschembio.8b00500. PMID:30376293<ref>PMID:30376293</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6el4" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Agrae]]
+[[Category: Large Structures]]
+[[Category: Unspecific peroxygenase]]
+[[Category: Ramirez-Escudero, M]]
+[[Category: Sanz-Aparicio, J]]
+[[Category: 4-dimethoxybenzyl alcohol]]
+[[Category: Agrocybe aegerita]]
+[[Category: Directed evolution]]
+[[Category: Heme-thiolate peroxidase]]
+[[Category: Oxidoreductase]]
+[[Category: Padai]]
+[[Category: Upo]]
+[[Category: Veratryl alcohol]]