5jxu - Revision history

OCA at 19:14, 20 September 2023

OCA — Wed, 20 Sep 2023 19:14:24 GMT

←Older revision		Revision as of 19:14, 20 September 2023
Line 1:		Line 1:

	==Structural basis for the catalytic activity of Thermomonospora curvata heme-containing DyP-type peroxidase.==		==Structural basis for the catalytic activity of Thermomonospora curvata heme-containing DyP-type peroxidase.==
-	<StructureSection load='5jxu' size='340' side='right' caption='[[5jxu]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5jxu' size='340' side='right'caption='[[5jxu]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jxu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_19995 Atcc 19995~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jxu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermomonospora_curvata Thermomonospora curvata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JXU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.751Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Tcur_2987 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=2020 ATCC 19995])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5jxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxu OCA], [~~http~~://pdbe.org/5jxu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jxu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jxu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxu 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=5jxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxu OCA], [https://pdbe.org/5jxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jxu RCSB], [https://www.ebi.ac.uk/pdbsum/5jxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D1A807_THECD D1A807_THECD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 19995~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Carlson, E A~~]]	+	[[Category: Thermomonospora curvata]]
-	[[Category: ~~Geisbrecht, B V~~]]	+	[[Category: Carlson EA]]
-	[[Category: ~~Li, P~~]]	+	[[Category: Geisbrecht BV]]
-	[[Category: ~~Ramyar, K X~~]]	+	[[Category: Li P]]
-	[[Category: ~~Heme-containing]]~~	+	[[Category: Ramyar KX]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 20:37, 24 January 2018

OCA — Wed, 24 Jan 2018 20:37:40 GMT

←Older revision		Revision as of 20:37, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5jxu' size='340' side='right' caption='[[5jxu]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5jxu' size='340' side='right' caption='[[5jxu]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jxu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jxu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19995 Atcc 19995]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JXU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tcur_2987 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2020 ATCC 19995])</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=5jxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxu OCA], [http://pdbe.org/5jxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jxu RCSB], [http://www.ebi.ac.uk/pdbsum/5jxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxu ProSAT]</span></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=5jxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxu OCA], [http://pdbe.org/5jxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jxu RCSB], [http://www.ebi.ac.uk/pdbsum/5jxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxu ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dye-decolorizing peroxidases (DyPs) are a family of heme peroxidases, in which a catalytic distal aspartate is involved in H2O2 activation to catalyze oxidations in acidic conditions. They have received much attention due to their potential applications in lignin compound degradation and biofuel production from biomass. However, the mode of oxidation in bacterial DyPs remains unknown. We have recently reported that the bacterial TcDyP from Thermomonospora curvata is among the most active DyPs and shows activity toward phenolic lignin model compounds (J. Biol. Chem.2015, 290, 23447). Based on the X-ray crystal structure solved at 1.75 A, sigmoidal steady-state kinetics with Reactive Blue 19 (RB19), and formation of compound II-like product in the absence of reducing substrates observed with stopped-flow spectroscopy and electron paramagnetic resonance (EPR), we hypothesized that the TcDyP catalyzes oxidation of large-size substrates via multiple surface-exposed protein radicals. Among 7 tryptophans and 3 tyrosines in TcDyP consisting of 376 residues for the matured protein, W263, W376, and Y332 were identified as surface-exposed protein radicals. Only the W263 was also characterized as one of surface-exposed oxidation sites. SDS-PAGE and size-exclusion chromatography demonstrated that W376 represents an off-pathway destination for electron transfer, resulting in the crosslinking of proteins in the absence of substrates. Mutation of W376 improved compound I stability and overall catalytic efficiency toward RB19. While Y332 is highly conserved across all four classes of DyPs, its catalytic function in A-class TcDyP is minimal possibly due to its extremely small solvent accessible areas. Identification of surface-exposed protein radicals and substrate oxidation sites is important for understanding DyP mechanism and modulating its catalytic functions for improved activity on phenolic lignin.
		+
		+	Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata.,Shrestha R, Chen X, Ramyar KX, Hayati Z, Carlson EA, Bossmann SH, Song L, Geisbrecht BV, Li P ACS Catal. 2016 Dec 2;6(12):8036-8047. doi: 10.1021/acscatal.6b01952. Epub 2016, Oct 12. PMID:29308294<ref>PMID:29308294</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jxu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 19995]]
	[[Category: Carlson, E A]]		[[Category: Carlson, E A]]
	[[Category: Geisbrecht, B V]]		[[Category: Geisbrecht, B V]]

OCA at 00:59, 20 October 2016

OCA — Thu, 20 Oct 2016 00:59:45 GMT

←Older revision		Revision as of 00:59, 20 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jxu is ~~ON HOLD until Paper Publication~~	+	==Structural basis for the catalytic activity of Thermomonospora curvata heme-containing DyP-type peroxidase.==
-		+	<StructureSection load='5jxu' size='340' side='right' caption='[[5jxu]], [[Resolution\|resolution]] 1.75Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jxu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JXU FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5jxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxu OCA], [http://pdbe.org/5jxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jxu RCSB], [http://www.ebi.ac.uk/pdbsum/5jxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxu ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carlson, E A]]
		+	[[Category: Geisbrecht, B V]]
		+	[[Category: Li, P]]
		+	[[Category: Ramyar, K X]]
		+	[[Category: Heme-containing]]
		+	[[Category: Oxidoreductase]]

OCA at 13:14, 20 June 2016

OCA — Mon, 20 Jun 2016 13:14:14 GMT

←Older revision		Revision as of 13:14, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jxu is ON HOLD	+	The entry 5jxu is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5jxu" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:01:05 GMT

Protected "5jxu" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:01, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jxu is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 14:01:04 GMT

New page: '''Unreleased structure''' The entry 5jxu is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5jxu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]