5ikg: Difference between revisions

Latest revision as of 13:58, 30 August 2023

Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase

Structural highlights

5ikg is a 1 chain structure with sequence from Auricularia auricula-judae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:	HEM
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DYP_AURAJ Manganese-independent peroxidase that is able to convert a large number of compounds, but its physiological substrate is not known. In addition to classic peroxidase substrates (e.g. 2,6-dimethoxyphenol), oxidizes dyes such as Reactive Blue 5 and Reactive Black 5.^[1] ^[2] ^[3] ^[4] ^[5]

References

↑ Liers C, Bobeth C, Pecyna M, Ullrich R, Hofrichter M. DyP-like peroxidases of the jelly fungus Auricularia auricula-judae oxidize nonphenolic lignin model compounds and high-redox potential dyes. Appl Microbiol Biotechnol. 2010 Feb;85(6):1869-79. PMID:19756587 doi:10.1007/s00253-009-2173-7
↑ Liers C, Pecyna MJ, Kellner H, Worrich A, Zorn H, Steffen KT, Hofrichter M, Ullrich R. Substrate oxidation by dye-decolorizing peroxidases (DyPs) from wood litter-degrading agaricomycetes compared to other fungal and plant heme-peroxidases. Appl Microbiol Biotechnol. 2013 Jul;97(13):5839-49. PMID:23111597 doi:10.1007/s00253-012-4521-2
↑ Linde D, Coscolín C, Liers C, Hofrichter M, Martínez AT, Ruiz-Dueñas FJ. Heterologous expression and physicochemical characterization of a fungal dye-decolorizing peroxidase from Auricularia auricula-judae. Protein Expr Purif. 2014 Nov;103:28-37. PMID:25153532 doi:10.1016/j.pep.2014.08.007
↑ Linde D, Pogni R, Canellas M, Lucas F, Guallar V, Baratto MC, Sinicropi A, Saez-Jimenez V, Coscolin C, Romero A, Medrano FJ, Ruiz-Duenas FJ, Martinez AT. Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study. Biochem J. 2015 Mar 1;466(2):253-62. doi: 10.1042/BJ20141211. PMID:25495127 doi:https://dx.doi.org/10.1042/BJ20141211
↑ Strittmatter E, Serrer K, Liers C, Ullrich R, Hofrichter M, Piontek K, Schleicher E, Plattner DA. The toolbox of Auricularia auricula-judae dye-decolorizing peroxidase - Identification of three new potential substrate-interaction sites. Arch Biochem Biophys. 2014 Dec 23. pii: S0003-9861(14)00432-9. doi:, 10.1016/j.abb.2014.12.016. PMID:25542606 doi:https://dx.doi.org/10.1016/j.abb.2014.12.016

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OCA

[1] Liers C, Bobeth C, Pecyna M, Ullrich R, Hofrichter M. DyP-like peroxidases of the jelly fungus Auricularia auricula-judae oxidize nonphenolic lignin model compounds and high-redox potential dyes. Appl Microbiol Biotechnol. 2010 Feb;85(6):1869-79. PMID:19756587 doi:10.1007/s00253-009-2173-7

[2] Liers C, Pecyna MJ, Kellner H, Worrich A, Zorn H, Steffen KT, Hofrichter M, Ullrich R. Substrate oxidation by dye-decolorizing peroxidases (DyPs) from wood litter-degrading agaricomycetes compared to other fungal and plant heme-peroxidases. Appl Microbiol Biotechnol. 2013 Jul;97(13):5839-49. PMID:23111597 doi:10.1007/s00253-012-4521-2

[3] Linde D, Coscolín C, Liers C, Hofrichter M, Martínez AT, Ruiz-Dueñas FJ. Heterologous expression and physicochemical characterization of a fungal dye-decolorizing peroxidase from Auricularia auricula-judae. Protein Expr Purif. 2014 Nov;103:28-37. PMID:25153532 doi:10.1016/j.pep.2014.08.007

[4] Linde D, Pogni R, Canellas M, Lucas F, Guallar V, Baratto MC, Sinicropi A, Saez-Jimenez V, Coscolin C, Romero A, Medrano FJ, Ruiz-Duenas FJ, Martinez AT. Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study. Biochem J. 2015 Mar 1;466(2):253-62. doi: 10.1042/BJ20141211. PMID:25495127 doi:https://dx.doi.org/10.1042/BJ20141211

[5] Strittmatter E, Serrer K, Liers C, Ullrich R, Hofrichter M, Piontek K, Schleicher E, Plattner DA. The toolbox of Auricularia auricula-judae dye-decolorizing peroxidase - Identification of three new potential substrate-interaction sites. Arch Biochem Biophys. 2014 Dec 23. pii: S0003-9861(14)00432-9. doi:, 10.1016/j.abb.2014.12.016. PMID:25542606 doi:https://dx.doi.org/10.1016/j.abb.2014.12.016

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5ikg is ON HOLD
+==Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase==
+<StructureSection load='5ikg' size='340' side='right'caption='[[5ikg]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
-Authors: Antonio Romero, Irene Davo-Siguero, Angel Tomas Martinez
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5ikg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Auricularia_auricula-judae Auricularia auricula-judae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IKG FirstGlance]. <br>
-Description: Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<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>
-[[Category: Antonio Romero, Irene Davo-Siguero, Angel Tomas Martinez]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ikg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ikg OCA], [https://pdbe.org/5ikg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ikg RCSB], [https://www.ebi.ac.uk/pdbsum/5ikg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ikg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DYP_AURAJ DYP_AURAJ] Manganese-independent peroxidase that is able to convert a large number of compounds, but its physiological substrate is not known. In addition to classic peroxidase substrates (e.g. 2,6-dimethoxyphenol), oxidizes dyes such as Reactive Blue 5 and Reactive Black 5.<ref>PMID:19756587</ref> <ref>PMID:23111597</ref> <ref>PMID:25153532</ref> <ref>PMID:25495127</ref> <ref>PMID:25542606</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Auricularia auricula-judae]]
+[[Category: Large Structures]]
+[[Category: Davo-Siguero I]]
+[[Category: Martinez AT]]
+[[Category: Romero A]]

5ikg: Difference between revisions

Latest revision as of 13:58, 30 August 2023

Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase

Structural highlights

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References

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