7o9l - Revision history

OCA at 12:47, 1 February 2024

2024-02-01T12:47:50Z

←Older revision		Revision as of 12:47, 1 February 2024
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	==Dictyostelium discoideum dye decolorizing peroxidase DyPA in complex with cyanide.==		==Dictyostelium discoideum dye decolorizing peroxidase DyPA in complex with cyanide.==
-	<StructureSection load='7o9l' size='340' side='right'caption='[[7o9l]]' scene=''>	+	<StructureSection load='7o9l' size='340' side='right'caption='[[7o9l]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O9L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7o9l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O9L FirstGlance]. <br>
-	</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=7o9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o9l OCA], [https://pdbe.org/7o9l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o9l RCSB], [https://www.ebi.ac.uk/pdbsum/7o9l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o9l ProSAT]</span></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]] 1.85Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=7o9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o9l OCA], [https://pdbe.org/7o9l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o9l RCSB], [https://www.ebi.ac.uk/pdbsum/7o9l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o9l ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q556V8_DICDI Q556V8_DICDI]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A novel cytoplasmic dye-decolorizing peroxidase from Dictyostelium discoideum was investigated that oxidizes anthraquinone dyes, lignin model compounds, and general peroxidase substrates such as ABTS efficiently. Unlike related enzymes, an aspartate residue replaces the first glycine of the conserved GXXDG motif in Dictyostelium DyPA. In solution, Dictyostelium DyPA exists as a stable dimer with the side chain of Asp146 contributing to the stabilization of the dimer interface by extending the hydrogen bond network connecting two monomers. To gain mechanistic insights, we solved the Dictyostelium DyPA structures in the absence of substrate as well as in the presence of potassium cyanide and veratryl alcohol to 1.7, 1.85, and 1.6 A resolution, respectively. The active site of Dictyostelium DyPA has a hexa-coordinated heme iron with a histidine residue at the proximal axial position and either an activated oxygen or CN(-) molecule at the distal axial position. Asp149 is in an optimal conformation to accept a proton from H2O2 during the formation of compound I. Two potential distal solvent channels and a conserved shallow pocket leading to the heme molecule were found in Dictyostelium DyPA. Further, we identified two substrate-binding pockets per monomer in Dictyostelium DyPA at the dimer interface. Long-range electron transfer pathways associated with a hydrogen-bonding network that connects the substrate-binding sites with the heme moiety are described.
		+
		+	Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum.,Rai A, Klare JP, Reinke PYA, Englmaier F, Fohrer J, Fedorov R, Taft MH, Chizhov I, Curth U, Plettenburg O, Manstein DJ Int J Mol Sci. 2021 Jun 10;22(12). pii: ijms22126265. doi: 10.3390/ijms22126265. PMID:34200865<ref>PMID:34200865</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7o9l" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dictyostelium discoideum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fedorov R]]		[[Category: Fedorov R]]
	[[Category: Manstein DJ]]		[[Category: Manstein DJ]]
	[[Category: Rai A]]		[[Category: Rai A]]

OCA at 09:55, 14 July 2021

2021-07-14T09:55:45Z

←Older revision		Revision as of 09:55, 14 July 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7o9l ~~is ON HOLD until Paper Publication~~	+	==Dictyostelium discoideum dye decolorizing peroxidase DyPA in complex with cyanide.==
-		+	<StructureSection load='7o9l' size='340' side='right'caption='[[7o9l]]' scene=''>
-	~~Authors~~: ~~Rai~~, A., ~~Fedorov~~, R., ~~Manstein~~, D.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O9L FirstGlance]. <br>
-	~~Description: Dictyostelium discoideum dye decolorizing peroxidase DyPA in complex with cyanide.~~	+	</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=7o9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o9l OCA], [https://pdbe.org/7o9l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o9l RCSB], [https://www.ebi.ac.uk/pdbsum/7o9l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o9l ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Manstein, D.J~~]]	+	__TOC__
-	[[Category: ~~Fedorov, R~~]]	+	</StructureSection>
-	[[Category: Rai, A]]	+	[[Category: Large Structures]]
		+	[[Category: Fedorov R]]
		+	[[Category: Manstein DJ]]
		+	[[Category: Rai A]]

OCA at 09:02, 19 May 2021

2021-05-19T09:02:44Z

←Older revision		Revision as of 09:02, 19 May 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7o9l is ON HOLD	+	The entry 7o9l is ON HOLD until Paper Publication

	Authors: Rai, A., Fedorov, R., Manstein, D.J.		Authors: Rai, A., Fedorov, R., Manstein, D.J.

OCA: Protected "7o9l" [edit=sysop:move=sysop]

2021-04-28T04:25:32Z

Protected "7o9l" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:25, 28 April 2021

OCA: New page: '''Unreleased structure''' The entry 7o9l is ON HOLD Authors: Rai, A., Fedorov, R., Manstein, D.J. Description: Dictyostelium discoideum dye decolorizing peroxidase DyPA in complex wit...

2021-04-28T04:25:32Z

New page: '''Unreleased structure''' The entry 7o9l is ON HOLD Authors: Rai, A., Fedorov, R., Manstein, D.J. Description: Dictyostelium discoideum dye decolorizing peroxidase DyPA in complex wit...

New page

'''Unreleased structure'''

The entry 7o9l is ON HOLD

Authors: Rai, A., Fedorov, R., Manstein, D.J.

Description: Dictyostelium discoideum dye decolorizing peroxidase DyPA in complex with cyanide.
[[Category: Unreleased Structures]]
[[Category: Manstein, D.J]]
[[Category: Fedorov, R]]
[[Category: Rai, A]]