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7qyz

From Proteopedia

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<StructureSection load='7qyz' size='340' side='right'caption='[[7qyz]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
<StructureSection load='7qyz' size='340' side='right'caption='[[7qyz]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[7qyz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QYZ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7qyz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QYZ FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
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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]] 2.452&#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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=7qyz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qyz OCA], [https://pdbe.org/7qyz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qyz RCSB], [https://www.ebi.ac.uk/pdbsum/7qyz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qyz ProSAT]</span></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=7qyz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qyz OCA], [https://pdbe.org/7qyz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qyz RCSB], [https://www.ebi.ac.uk/pdbsum/7qyz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qyz ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q88HV5_PSEPK Q88HV5_PSEPK]
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DyP-type peroxidases (DyPs) are microbial enzymes that catalyze the oxidation of a wide range of substrates, including synthetic dyes, lignin-derived compounds, and metals, such as Mn(2+) and Fe(2+), and have enormous biotechnological potential in biorefineries. However, many questions on the molecular basis of enzyme function and stability remain unanswered. In this work, high-resolution structures of PpDyP wild-type and two engineered variants (6E10 and 29E4) generated by directed evolution were obtained. The X-ray crystal structures revealed the typical ferredoxin-like folds, with three heme access pathways, two tunnels, and one cavity, limited by three long loops including catalytic residues. Variant 6E10 displays significantly increased loops' flexibility that favors function over stability: despite the considerably higher catalytic efficiency, this variant shows poorer protein stability compared to wild-type and 29E4 variants. Constant-pH MD simulations revealed a more positively charged microenvironment near the heme pocket of variant 6E10, particularly in the neutral to alkaline pH range. This microenvironment affects enzyme activity by modulating the pK a of essential residues in the heme vicinity and should account for variant 6E10 improved activity at pH 7-8 compared to the wild-type and 29E4 that show optimal enzymatic activity close to pH 4. Our findings shed light on the structure-function relationships of DyPs at the molecular level, including their pH-dependent conformational plasticity. These are essential for understanding and engineering the catalytic properties of DyPs for future biotechnological applications.
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Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase.,Borges PT, Silva D, Silva TFD, Brissos V, Canellas M, Lucas MF, Masgrau L, Melo EP, Machuqueiro M, Frazao C, Martins LO Comput Struct Biotechnol J. 2022 Jul 21;20:3899-3910. doi:, 10.1016/j.csbj.2022.07.032. eCollection 2022. PMID:35950185<ref>PMID:35950185</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 7qyz" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Borges, P T]]
 
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[[Category: Frazao, C]]
 
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[[Category: Martins, L O]]
 
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[[Category: Silva, D]]
 
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[[Category: Directed evolution]]
 
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[[Category: Dyp]]
 
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[[Category: Heme]]
 
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[[Category: Oxidoreductase]]
 
[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
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[[Category: Borges PT]]
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[[Category: Frazao C]]
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[[Category: Martins LO]]
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[[Category: Silva D]]

Current revision

Crystal structure of a DyP-type peroxidase 6E10 variant from Pseudomonas putida

PDB ID 7qyz

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