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| | ==Crystal Structure of AauDyP Complexed with Imidazole== | | ==Crystal Structure of AauDyP Complexed with Imidazole== |
| - | <StructureSection load='4uzi' size='340' side='right' caption='[[4uzi]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='4uzi' size='340' side='right'caption='[[4uzi]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4uzi]] is a 2 chain structure with sequence from [http://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=4UZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UZI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4uzi]] is a 2 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=4UZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UZI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXD:OXALIC+ACID'>OXD</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dye_decolorizing_peroxidase Dye decolorizing peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.19 1.11.1.19] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXD:OXALIC+ACID'>OXD</scene></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=4uzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uzi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4uzi RCSB], [http://www.ebi.ac.uk/pdbsum/4uzi PDBsum]</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=4uzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uzi OCA], [https://pdbe.org/4uzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uzi RCSB], [https://www.ebi.ac.uk/pdbsum/4uzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uzi ProSAT]</span></td></tr> |
| | </table> | | </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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4uzi" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Auricularia auricula-judae]] | | [[Category: Auricularia auricula-judae]] |
| - | [[Category: Dye decolorizing peroxidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Hofrichter, M]] | + | [[Category: Hofrichter M]] |
| - | [[Category: Liers, C]] | + | [[Category: Liers C]] |
| - | [[Category: Piontek, K]] | + | [[Category: Piontek K]] |
| - | [[Category: Plattner, D A]] | + | [[Category: Plattner DA]] |
| - | [[Category: Strittmatter, E]] | + | [[Category: Strittmatter E]] |
| - | [[Category: Ullrich, R]] | + | [[Category: Ullrich R]] |
| - | [[Category: Dyp-type peroxidase]]
| + | |
| - | [[Category: Glycoprotein]]
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| - | [[Category: Heme]]
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| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Peroxidase]]
| + | |
| Structural highlights
4uzi is a 2 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 2.1Å |
| Ligands: | , , , , , , , , , , , |
| 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]
Publication Abstract from PubMed
Dye-decolorizing peroxidases (DyPs) such as AauDyPI from the fungus Auricularia auricula-judae are able to oxidize substrates of different kinds and sizes. A crystal structure of an AauDyPI-imidazole complex gives insight into the binding patterns of organic molecules within the heme cavity of a DyP. Several small N-containing heterocyclic aromatics are shown to bind in the AauDyPI heme cavity, hinting to susceptibility of DyPs to azole-based inhibitors similar to cytochromes P450. Imidazole is confirmed as a competitive inhibitor with regard to peroxide binding. In contrast, bulky substrates such as anthraquinone dyes are converted at the enzyme surface. In the crystal structure a substrate analog, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), binds to a tyrosine-rich hollow harboring Y25, Y147, and Y337. Spin trapping with a nitric oxide donor uncovers Y229 as an additional tyrosine-based radical center in AauDyPI. Multi-frequency EPR spectroscopy further reveals the presence of at least one intermediate tryptophanyl radical center in activated AauDyPI with W377 as the most likely candidate.
The toolbox of Auricularia auricula-judae dye-decolorizing peroxidase - Identification of three new potential substrate-interaction sites.,Strittmatter E, Serrer K, Liers C, Ullrich R, Hofrichter M, Piontek K, Schleicher E, Plattner DA Arch Biochem Biophys. 2014 Dec 23. pii: S0003-9861(14)00432-9. doi:, 10.1016/j.abb.2014.12.016. PMID:25542606[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
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:http://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:http://dx.doi.org/10.1016/j.abb.2014.12.016
- ↑ 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:http://dx.doi.org/10.1016/j.abb.2014.12.016
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