6yrc - Revision history

OCA at 07:40, 1 May 2024

2024-05-01T07:40:11Z

←Older revision		Revision as of 07:40, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='6yrc' size='340' side='right'caption='[[6yrc]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='6yrc' size='340' side='right'caption='[[6yrc]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yrc]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptomyces_lividans_1326 Streptomyces lividans 1326]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YRC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YRC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yrc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lividans_1326 Streptomyces lividans 1326]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YRC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YRC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7PE:2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL'>7PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.99Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAMN05428941_7146 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1200984 Streptomyces lividans 1326])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7PE:2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL'>7PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6yrc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yrc OCA], [~~http~~://pdbe.org/6yrc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yrc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yrc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yrc 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=6yrc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yrc OCA], [https://pdbe.org/6yrc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yrc RCSB], [https://www.ebi.ac.uk/pdbsum/6yrc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yrc ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A1H2DDB9_9ACTN A0A1H2DDB9_9ACTN]
-	Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (Fe(IV) =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the Fe(III) and Fe(IV) =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.	+
-		+
-	Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe(IV) =O Formation.,Lucic M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR Angew Chem Int Ed Engl. 2020 Nov 23;59(48):~~21656-21662. doi:, 10.1002~~/~~anie.202008622. Epub 2020 Sep 23. PMID:32780931<ref>PMID:32780931<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6yrc" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Streptomyces lividans 1326]]		[[Category: Streptomyces lividans 1326]]
-	[[Category: Dworkowski~~, F S.N~~]]	+	[[Category: Dworkowski FSN]]
-	[[Category: Hough~~, M A~~]]	+	[[Category: Hough MA]]
-	[[Category: Lucic, M]]	+	[[Category: Lucic M]]
-	[[Category: Worrall~~, J A.R]]~~	+	[[Category: Worrall JAR]]
-	~~[[Category: Dye-decolourising]]~~	+
-	~~[[Category: Ferric]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Peroxidase]]~~	+
-	~~[[Category: Spectroscopically-validated~~]]	+

OCA at 05:51, 20 January 2021

2021-01-20T05:51:11Z

←Older revision		Revision as of 05:51, 20 January 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6yrc is ~~ON HOLD until Paper~~ Publication	+	==Spectroscopically-validated structure of DtpB from Streptomyces lividans in the ferric state==
		+	<StructureSection load='6yrc' size='340' side='right'caption='[[6yrc]], [[Resolution\|resolution]] 1.99Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6yrc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_lividans_1326 Streptomyces lividans 1326]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YRC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YRC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7PE:2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL'>7PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAMN05428941_7146 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1200984 Streptomyces lividans 1326])</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=6yrc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yrc OCA], [http://pdbe.org/6yrc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yrc RCSB], [http://www.ebi.ac.uk/pdbsum/6yrc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yrc ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (Fe(IV) =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the Fe(III) and Fe(IV) =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.

-	~~Authors: Lucic~~, M., ~~Dworkowski~~, ~~F.S.N.~~, ~~Worrall~~, J.A~~.R.~~, Hough, M.A.	+	Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe(IV) =O Formation.,Lucic M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR Angew Chem Int Ed Engl. 2020 Nov 23;59(48):21656-21662. doi:, 10.1002/anie.202008622. Epub 2020 Sep 23. PMID:32780931<ref>PMID:32780931</ref>

-	~~Description: Spectroscopically-validated structure~~ of ~~DtpB from Streptomyces lividans in~~ the ~~ferric state~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Dworkowski, F.S.N~~]]	+	<div class="pdbe-citations 6yrc" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Hough~~, M.A]]	+	== References ==
-	[[Category: ~~Worrall~~, J.A.R]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Streptomyces lividans 1326]]
		+	[[Category: Dworkowski, F S.N]]
		+	[[Category: Hough, M A]]
	[[Category: Lucic, M]]		[[Category: Lucic, M]]
		+	[[Category: Worrall, J A.R]]
		+	[[Category: Dye-decolourising]]
		+	[[Category: Ferric]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Peroxidase]]
		+	[[Category: Spectroscopically-validated]]

OCA at 04:38, 6 May 2020

2020-05-06T04:38:03Z

←Older revision		Revision as of 04:38, 6 May 2020
Line 5:		Line 5:
	Authors: Lucic, M., Dworkowski, F.S.N., Worrall, J.A.R., Hough, M.A.		Authors: Lucic, M., Dworkowski, F.S.N., Worrall, J.A.R., Hough, M.A.

-	Description: ~~SFX~~ structure of ~~dye-type peroxidase~~ DtpB in the ferric state	+	Description: Spectroscopically-validated structure of DtpB from Streptomyces lividans in the ferric state
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Worrall, J.A.R]]
	[[Category: Dworkowski, F.S.N]]		[[Category: Dworkowski, F.S.N]]
-	[[Category: Lucic, M]]
	[[Category: Hough, M.A]]		[[Category: Hough, M.A]]
		+	[[Category: Worrall, J.A.R]]
		+	[[Category: Lucic, M]]

OCA: Protected "6yrc" [edit=sysop:move=sysop]

2020-04-29T05:26:47Z

Protected "6yrc" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:26, 29 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yrc is ON HOLD until Paper Publication Authors: Lucic, M., Dworkowski, F.S.N., Worrall, J.A.R., Hough, M.A. Description: SFX structure of dye-type...

2020-04-29T05:26:45Z

New page: '''Unreleased structure''' The entry 6yrc is ON HOLD until Paper Publication Authors: Lucic, M., Dworkowski, F.S.N., Worrall, J.A.R., Hough, M.A. Description: SFX structure of dye-type...

New page

'''Unreleased structure'''

The entry 6yrc is ON HOLD until Paper Publication

Authors: Lucic, M., Dworkowski, F.S.N., Worrall, J.A.R., Hough, M.A.

Description: SFX structure of dye-type peroxidase DtpB in the ferric state
[[Category: Unreleased Structures]]
[[Category: Worrall, J.A.R]]
[[Category: Dworkowski, F.S.N]]
[[Category: Lucic, M]]
[[Category: Hough, M.A]]