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5chq

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==Dehaloperoxidase B in complex with substrate p-nitrophenol==
==Dehaloperoxidase B in complex with substrate p-nitrophenol==
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<StructureSection load='5chq' size='340' side='right' caption='[[5chq]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
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<StructureSection load='5chq' size='340' side='right'caption='[[5chq]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5chq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CHQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CHQ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5chq]] 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=5CHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CHQ FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NPO:P-NITROPHENOL'>NPO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.87&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5chr|5chr]]</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NPO:P-NITROPHENOL'>NPO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<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=5chq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chq OCA], [http://pdbe.org/5chq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5chq RCSB], [http://www.ebi.ac.uk/pdbsum/5chq PDBsum]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5chq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chq OCA], [https://pdbe.org/5chq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5chq RCSB], [https://www.ebi.ac.uk/pdbsum/5chq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5chq 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/Q9NAV7_9ANNE Q9NAV7_9ANNE]
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The marine hemoglobin dehaloperoxidase (DHP) from Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of nitrophenols, an unprecedented nonmicrobial degradation pathway for nitrophenols by a hemoglobin. Using 4-nitrophenol (4-NP) as a representative substrate, the major monooxygenated product was 4-nitrocatechol (4-NC). Isotope labeling studies confirmed that the O atom incorporated was derived exclusively from H2O2, indicative of a peroxygenase mechanism for 4-NP oxidation. Accordingly, X-ray crystal structures of 4-NP (1.87 A) and 4-NC (1.98 A) bound to DHP revealed a binding site in close proximity to the heme cofactor. Peroxygenase activity could be initiated from either the ferric or oxyferrous states with equivalent substrate conversion and product distribution. The 4-NC product was itself a peroxidase substrate for DHP, leading to the secondary products 5-nitrobenzene-triol and hydroxy-5-nitro-1,2-benzoquinone. DHP was able to react with 2,4-dinitrophenol (2,4-DNP) but was unreactive against 2,4,6-trinitrophenol (2,4,6-TNP). pH dependence studies demonstrated increased reactivity at lower pH for both 4-NP and 2,4-DNP, suggestive of a pH effect that precludes the reaction with 2,4,6-TNP at or near physiological conditions. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the mechanism of 4-NP oxidation. The results demonstrate that there may be a much larger number of nonmicrobial enzymes that are underrepresented when it comes to understanding the degradation of persistent organic pollutants such as nitrophenols in the environment.
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Nonmicrobial Nitrophenol Degradation via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin from Amphitrite ornata.,McCombs NL, D'Antonio J, Barrios DA, Carey LM, Ghiladi RA Biochemistry. 2016 May 3;55(17):2465-78. doi: 10.1021/acs.biochem.6b00143. Epub, 2016 Apr 22. PMID:27070125<ref>PMID:27070125</ref>
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==See Also==
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*[[Dehaloperoxidase 3D structures|Dehaloperoxidase 3D structures]]
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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 5chq" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Carey, L]]
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[[Category: Amphitrite ornata]]
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[[Category: Ghiladi, R]]
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[[Category: Large Structures]]
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[[Category: Oxidoreductase]]
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[[Category: Carey L]]
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[[Category: Substrate]]
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[[Category: Ghiladi R]]

Current revision

Dehaloperoxidase B in complex with substrate p-nitrophenol

PDB ID 5chq

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