7o9j - Revision history

OCA at 12:47, 1 February 2024

OCA — Thu, 01 Feb 2024 12:47:49 GMT

←Older revision		Revision as of 12:47, 1 February 2024
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	==Crystal structure of DyP-type peroxidase from Dictyostelium discoideum in complex with an activated form of oxygen==		==Crystal structure of DyP-type peroxidase from Dictyostelium discoideum in complex with an activated form of oxygen==
-	<StructureSection load='7o9j' size='340' side='right'caption='[[7o9j]]' scene=''>	+	<StructureSection load='7o9j' size='340' side='right'caption='[[7o9j]], [[Resolution\|resolution]] 1.70Å' 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=7O9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7o9j]] 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=7O9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O9J 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=7o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o9j OCA], [https://pdbe.org/7o9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o9j RCSB], [https://www.ebi.ac.uk/pdbsum/7o9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o9j 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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=7o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o9j OCA], [https://pdbe.org/7o9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o9j RCSB], [https://www.ebi.ac.uk/pdbsum/7o9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o9j 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 7o9j" 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

OCA — Wed, 14 Jul 2021 09:55:44 GMT

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

-	~~The entry 7o9j is ON HOLD until Paper Publication~~	+	==Crystal structure of DyP-type peroxidase from Dictyostelium discoideum in complex with an activated form of oxygen==
-		+	<StructureSection load='7o9j' size='340' side='right'caption='[[7o9j]]' 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=7O9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O9J FirstGlance]. <br>
-	~~Description:~~ Crystal structure of DyP-type peroxidase from Dictyostelium discoideum in complex with an activated form of oxygen	+	</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=7o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o9j OCA], [https://pdbe.org/7o9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o9j RCSB], [https://www.ebi.ac.uk/pdbsum/7o9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o9j 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 02:31, 2 July 2021

OCA — Fri, 02 Jul 2021 02:31:49 GMT

←Older revision		Revision as of 02:31, 2 July 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7o9j is ON HOLD	+	The entry 7o9j is ON HOLD until Paper Publication

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

OCA at 11:11, 9 June 2021

OCA — Wed, 09 Jun 2021 11:11:53 GMT

←Older revision		Revision as of 11:11, 9 June 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7o9j is ON HOLD ~~until Paper Publication~~	+	The entry 7o9j is ON HOLD

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

-	Description: Crystal structure of DyP-type peroxidase from Dictyostelium discoideum	+	Description: Crystal structure of DyP-type peroxidase from Dictyostelium discoideum in complex with an activated form of oxygen
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Manstein, D.J]]		[[Category: Manstein, D.J]]
	[[Category: Fedorov, R]]		[[Category: Fedorov, R]]
	[[Category: Rai, A]]		[[Category: Rai, A]]

OCA at 09:02, 19 May 2021

OCA — Wed, 19 May 2021 09:02:41 GMT

←Older revision		Revision as of 09:02, 19 May 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7o9j is ON HOLD	+	The entry 7o9j is ON HOLD until Paper Publication

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

OCA: Protected "7o9j" [edit=sysop:move=sysop]

OCA — Wed, 28 Apr 2021 04:25:25 GMT

Protected "7o9j" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:25, 28 April 2021

OCA: New page: '''Unreleased structure''' The entry 7o9j is ON HOLD Authors: Rai, A., Fedorov, R., Manstein, D.J. Description: Crystal structure of DyP-type peroxidase from Dictyostelium discoideum [...

OCA — Wed, 28 Apr 2021 04:25:24 GMT

New page: '''Unreleased structure''' The entry 7o9j is ON HOLD Authors: Rai, A., Fedorov, R., Manstein, D.J. Description: Crystal structure of DyP-type peroxidase from Dictyostelium discoideum [...

New page

'''Unreleased structure'''

The entry 7o9j is ON HOLD

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

Description: Crystal structure of DyP-type peroxidase from Dictyostelium discoideum
[[Category: Unreleased Structures]]
[[Category: Manstein, D.J]]
[[Category: Fedorov, R]]
[[Category: Rai, A]]