4uzi

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of AauDyP Complexed with Imidazole

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4uzi"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4uzi is ON HOLD  until Paper Publication
+==Crystal Structure of AauDyP Complexed with Imidazole==
+<StructureSection load='4uzi' size='340' side='right'caption='[[4uzi]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</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'>[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>
+== 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;">
+== 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.
-Authors: Strittmatter, E., Liers, C., Ullrich, R., Hofrichter, M., Piontek, K., Plattner, D.A., ,
+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<ref>PMID:25542606</ref>
-Description: Crystal Structure of AauDyP Complexed with Imidazole
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4uzi" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Auricularia auricula-judae]]
+[[Category: Large Structures]]
+[[Category: Hofrichter M]]
+[[Category: Liers C]]
+[[Category: Piontek K]]
+[[Category: Plattner DA]]
+[[Category: Strittmatter E]]
+[[Category: Ullrich R]]

4uzi

From Proteopedia

Current revision

Crystal Structure of AauDyP Complexed with Imidazole

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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