7anv - Revision history

OCA at 12:12, 1 February 2024

OCA — Thu, 01 Feb 2024 12:12:48 GMT

←Older revision		Revision as of 12:12, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7anv' size='340' side='right'caption='[[7anv]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='7anv' size='340' side='right'caption='[[7anv]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7anv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7anv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geotrichum_candidum Geotrichum candidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.65Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7anv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anv OCA], [https://pdbe.org/7anv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anv RCSB], [https://www.ebi.ac.uk/pdbsum/7anv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anv ProSAT]</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=7anv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anv OCA], [https://pdbe.org/7anv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anv RCSB], [https://www.ebi.ac.uk/pdbsum/7anv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anv ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geotrichum candidum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fraaije~~, M W~~]]	+	[[Category: Fraaije MW]]
-	[[Category: Rozeboom~~, H J]]~~	+	[[Category: Rozeboom HJ]]
-	~~[[Category: D-type dyp]]~~	+
-	~~[[Category: Dye decolorizing peroxidase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 14:55, 17 June 2021

OCA — Thu, 17 Jun 2021 14:55:37 GMT

←Older revision		Revision as of 14:55, 17 June 2021
Line 3:		Line 3:
	<StructureSection load='7anv' size='340' side='right'caption='[[7anv]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='7anv' size='340' side='right'caption='[[7anv]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7anv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7ANV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7anv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7anv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anv OCA], [~~http~~://pdbe.org/7anv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7anv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7anv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7anv ProSAT]</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=7anv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anv OCA], [https://pdbe.org/7anv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anv RCSB], [https://www.ebi.ac.uk/pdbsum/7anv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:03, 20 January 2021

OCA — Wed, 20 Jan 2021 06:03:56 GMT

←Older revision		Revision as of 06:03, 20 January 2021
Line 1:		Line 1:

	==Mutational and structural analysis of an ancestral D-type dye decolorizing peroxidase==		==Mutational and structural analysis of an ancestral D-type dye decolorizing peroxidase==
-	<StructureSection load='7anv' size='340' side='right'caption='[[7anv]]' scene=''>	+	<StructureSection load='7anv' size='340' side='right'caption='[[7anv]], [[Resolution\|resolution]] 1.65Å' 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=7ANV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7ANV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7anv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7ANV FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7anv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anv OCA], [http://pdbe.org/7anv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7anv RCSB], [http://www.ebi.ac.uk/pdbsum/7anv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7anv ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7anv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anv OCA], [http://pdbe.org/7anv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7anv RCSB], [http://www.ebi.ac.uk/pdbsum/7anv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7anv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dye-decolorizing peroxidases (DyPs) constitute a superfamily of heme-containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A-C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D-type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D-type DyP ancestor, AncDyPD-b1. Expression of AncDyPD-b1 in Escherichia coli results in large amounts of a heme-containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV-Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady-state kinetics and the crystal structure, reveal fine pH-dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long-range electron transfer process. DATABASE: Structural data are available in the PDB database under the accession number 7ANV.
		+
		+	Mutational and structural analysis of an ancestral fungal dye-decolorizing peroxidase.,Zitare UA, Habib MH, Rozeboom H, Mascotti ML, Todorovic S, Fraaije MW FEBS J. 2020 Dec 23. doi: 10.1111/febs.15687. PMID:33369202<ref>PMID:33369202</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7anv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fraaije MW]]	+	[[Category: Fraaije, M W]]
-	[[Category: Rozeboom HJ]]	+	[[Category: Rozeboom, H J]]
		+	[[Category: D-type dyp]]
		+	[[Category: Dye decolorizing peroxidase]]
		+	[[Category: Oxidoreductase]]

OCA at 06:47, 30 December 2020

OCA — Wed, 30 Dec 2020 06:47:32 GMT

←Older revision		Revision as of 06:47, 30 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7anv is ON HOLD until Paper Publication~~	+	==Mutational and structural analysis of an ancestral D-type dye decolorizing peroxidase==
-		+	<StructureSection load='7anv' size='340' side='right'caption='[[7anv]]' scene=''>
-	~~Authors: Rozeboom, H.J., Fraaije, M.W.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7ANV FirstGlance]. <br>
-	~~Description:~~ Mutational and structural analysis of an ancestral D-type dye decolorizing peroxidase	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7anv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anv OCA], [http://pdbe.org/7anv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7anv RCSB], [http://www.ebi.ac.uk/pdbsum/7anv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7anv ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Rozeboom~~, H.J]]	+	__TOC__
-	[[Category: Fraaije~~, M.W~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Fraaije MW]]
		+	[[Category: Rozeboom HJ]]

OCA at 18:55, 28 October 2020

OCA — Wed, 28 Oct 2020 18:55:26 GMT

←Older revision		Revision as of 18:55, 28 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Rozeboom, H.J., Fraaije, M.W.		Authors: Rozeboom, H.J., Fraaije, M.W.

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

OCA — Wed, 21 Oct 2020 06:38:00 GMT

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

←Older revision

Revision as of 06:38, 21 October 2020

OCA: New page: '''Unreleased structure''' The entry 7anv is ON HOLD Authors: Rozeboom, H.J., Fraaije, M.W. Description: Mutational and structural analysis of an ancestral D-type dye decolorizing pero...

OCA — Wed, 21 Oct 2020 06:37:58 GMT

New page: '''Unreleased structure''' The entry 7anv is ON HOLD Authors: Rozeboom, H.J., Fraaije, M.W. Description: Mutational and structural analysis of an ancestral D-type dye decolorizing pero...

New page

'''Unreleased structure'''

The entry 7anv is ON HOLD

Authors: Rozeboom, H.J., Fraaije, M.W.

Description: Mutational and structural analysis of an ancestral D-type dye decolorizing peroxidase
[[Category: Unreleased Structures]]
[[Category: Rozeboom, H.J]]
[[Category: Fraaije, M.W]]