6onr: Difference between revisions
New page: '''Unreleased structure''' The entry 6onr is ON HOLD Authors: Ghiladi, R.A., de Serrano, V.S., Malewschik, T. Description: Dehaloperoxidase B in complex with substrate 4-methyl-cresol ... |
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==Dehaloperoxidase B in complex with substrate 4-methyl-cresol== | |||
<StructureSection load='6onr' size='340' side='right'caption='[[6onr]], [[Resolution|resolution]] 1.35Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6onr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ONR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ONR FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=N0D:2,4-dimethylphenol'>N0D</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6onr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6onr OCA], [https://pdbe.org/6onr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6onr RCSB], [https://www.ebi.ac.uk/pdbsum/6onr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6onr ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The multifunctional catalytic hemoglobin dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of EPA Priority Pollutants (4-Me-o-cresol, 4-Cl-m-cresol and pentachlorophenol) and EPA Toxic Substances Control Act compounds (o-, m-, p-cresol and 4-Cl-o-cresol). Biochemical assays (HPLC/LC-MS) indicated formation of multiple oxidation products, including the corresponding catechol, 2-methylbenzoquinone (2-MeBq), and oligomers with varying degrees of oxidation and/or dehalogenation. Using 4-Br-o-cresol as a representative substrate, labeling studies with (18)O confirmed that the O-atom incorporated into the catechol was derived exclusively from H2O2, whereas the O-atom incorporated into 2-MeBq was from H2O, consistent with this single substrate being oxidized by both peroxygenase and peroxidase mechanisms, respectively. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the peroxygenase mechanism leading to catechol formation, and for Compounds I and ES in the peroxidase mechanism that yields the 2-MeBq product. The X-ray crystal structures of DHP bound with 4-F-o-cresol (1.42A; PDB 6ONG), 4-Cl-o-cresol (1.50A; PDB 6ONK), 4-Br-o-cresol (1.70A; PDB 6ONX), 4-NO2-o-cresol (1.80A; PDB 6ONZ), o-cresol (1.60A; PDB 6OO1), p-cresol (2.10A; PDB 6OO6), 4-Me-o-cresol (1.35A; PDB 6ONR) and pentachlorophenol (1.80A; PDB 6OO8) revealed substrate binding sites in the distal pocket in close proximity to the heme cofactor, consistent with both oxidation mechanisms. The findings establish cresols as a new class of substrate for DHP, demonstrate that multiple oxidation mechanisms may exist for a given substrate, and provide further evidence that different substituents can serve as functional switches between the different activities performed by dehaloperoxidase. More broadly, the results demonstrate the complexities of marine pollution where both microbial and non-microbial systems may play significant roles in the biotransformations of EPA-classified pollutants, and further reinforces that heterocyclic compounds of anthropogenic origin should be considered as environmental stressors of infaunal organisms. | |||
The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants.,Malewschik T, de Serrano V, McGuire AH, Ghiladi RA Arch Biochem Biophys. 2019 Sep 30;673:108079. doi: 10.1016/j.abb.2019.108079., Epub 2019 Aug 21. PMID:31445024<ref>PMID:31445024</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Ghiladi | <div class="pdbe-citations 6onr" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
*[[Dehaloperoxidase 3D structures|Dehaloperoxidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Amphitrite ornata]] | |||
[[Category: Large Structures]] | |||
[[Category: Ghiladi RA]] | |||
[[Category: Malewschik T]] | |||
[[Category: De Serrano VS]] | |||
Latest revision as of 10:13, 11 October 2023
Dehaloperoxidase B in complex with substrate 4-methyl-cresolDehaloperoxidase B in complex with substrate 4-methyl-cresol
Structural highlights
FunctionPublication Abstract from PubMedThe multifunctional catalytic hemoglobin dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of EPA Priority Pollutants (4-Me-o-cresol, 4-Cl-m-cresol and pentachlorophenol) and EPA Toxic Substances Control Act compounds (o-, m-, p-cresol and 4-Cl-o-cresol). Biochemical assays (HPLC/LC-MS) indicated formation of multiple oxidation products, including the corresponding catechol, 2-methylbenzoquinone (2-MeBq), and oligomers with varying degrees of oxidation and/or dehalogenation. Using 4-Br-o-cresol as a representative substrate, labeling studies with (18)O confirmed that the O-atom incorporated into the catechol was derived exclusively from H2O2, whereas the O-atom incorporated into 2-MeBq was from H2O, consistent with this single substrate being oxidized by both peroxygenase and peroxidase mechanisms, respectively. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the peroxygenase mechanism leading to catechol formation, and for Compounds I and ES in the peroxidase mechanism that yields the 2-MeBq product. The X-ray crystal structures of DHP bound with 4-F-o-cresol (1.42A; PDB 6ONG), 4-Cl-o-cresol (1.50A; PDB 6ONK), 4-Br-o-cresol (1.70A; PDB 6ONX), 4-NO2-o-cresol (1.80A; PDB 6ONZ), o-cresol (1.60A; PDB 6OO1), p-cresol (2.10A; PDB 6OO6), 4-Me-o-cresol (1.35A; PDB 6ONR) and pentachlorophenol (1.80A; PDB 6OO8) revealed substrate binding sites in the distal pocket in close proximity to the heme cofactor, consistent with both oxidation mechanisms. The findings establish cresols as a new class of substrate for DHP, demonstrate that multiple oxidation mechanisms may exist for a given substrate, and provide further evidence that different substituents can serve as functional switches between the different activities performed by dehaloperoxidase. More broadly, the results demonstrate the complexities of marine pollution where both microbial and non-microbial systems may play significant roles in the biotransformations of EPA-classified pollutants, and further reinforces that heterocyclic compounds of anthropogenic origin should be considered as environmental stressors of infaunal organisms. The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants.,Malewschik T, de Serrano V, McGuire AH, Ghiladi RA Arch Biochem Biophys. 2019 Sep 30;673:108079. doi: 10.1016/j.abb.2019.108079., Epub 2019 Aug 21. PMID:31445024[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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