6ubz - Revision history

OCA at 07:48, 11 October 2023

OCA — Wed, 11 Oct 2023 07:48:52 GMT

←Older revision		Revision as of 07:48, 11 October 2023
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	<StructureSection load='6ubz' size='340' side='right'caption='[[6ubz]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='6ubz' size='340' side='right'caption='[[6ubz]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ubz]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseudoalteromonas_luteoviolacea_dsm_6061~~ Pseudoalteromonas luteoviolacea ~~dsm~~ 6061]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UBZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6UBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ubz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoalteromonas_luteoviolacea_DSM_6061 Pseudoalteromonas luteoviolacea DSM 6061]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UBZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GLY:GLYCINE'>GLY</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]] 1.83Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N475_19905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1365250 Pseudoalteromonas luteoviolacea DSM 6061])</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=6ubz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ubz OCA], [https://pdbe.org/6ubz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ubz RCSB], [https://www.ebi.ac.uk/pdbsum/6ubz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ubz 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=6ubz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ubz OCA], [~~http~~://pdbe.org/6ubz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ubz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ubz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ubz ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A161XU12_9GAMM A0A161XU12_9GAMM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pseudoalteromonas luteoviolacea ~~dsm~~ 6061]]	+	[[Category: Pseudoalteromonas luteoviolacea DSM 6061]]
-	[[Category: Yukl~~, E T]]~~	+	[[Category: Yukl ET]]
-	~~[[Category: Oxidase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Tryotiophylquinone~~]]	+

OCA at 09:45, 30 October 2019

OCA — Wed, 30 Oct 2019 09:45:05 GMT

←Older revision		Revision as of 09:45, 30 October 2019
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	<StructureSection load='6ubz' size='340' side='right'caption='[[6ubz]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='6ubz' size='340' side='right'caption='[[6ubz]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ubz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ubz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudoalteromonas_luteoviolacea_dsm_6061 Pseudoalteromonas luteoviolacea dsm 6061]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UBZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N475_19905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1365250 Pseudoalteromonas luteoviolacea DSM 6061])</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=6ubz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ubz OCA], [http://pdbe.org/6ubz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ubz RCSB], [http://www.ebi.ac.uk/pdbsum/6ubz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ubz 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=6ubz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ubz OCA], [http://pdbe.org/6ubz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ubz RCSB], [http://www.ebi.ac.uk/pdbsum/6ubz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ubz ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PlGoxA from Pseudoalteromonas luteoviolacea is a glycine oxidase that utilizes a protein-derived cysteine tryptophylquinone (CTQ) cofactor. A notable feature of its catalytic mechanism is that it forms a stable product-reduced CTQ adduct that is not hydrolyzed in the absence of O2 Asp-678 resides near the quinone moiety of PlGoxA, and an Asp is structurally conserved in this position in all tryptophylquinone enzymes. In those other enzymes, mutation of that Asp results in no or negligible CTQ formation. In this study, mutation of Asp-678 in PlGoxA did not abolish CTQ formation. This allowed for the first time, studying the role of this residue in catalysis. D678A and D678N substitutions yielded enzyme variants with CTQ, which did not react with glycine, although glycine was present in the crystal structures in the active site. D678E PlGoxA was active, but exhibited a much slower k cat This mutation altered the kinetic mechanism of the reductive half-reaction such that one could observe a previously undetected reactive intermediate, an initial substrate-oxidized CTQ adduct, which converted to the product-reduced CTQ adduct. These results indicate that Asp-678 is involved in the initial deprotonation of the amino group of glycine, enabling nucleophilic attack of CTQ, as well as the deprotonation of the substrate-oxidized CTQ adduct, which is coupled to CTQ reduction. The structures also suggest that Asp-678 is acting as a proton relay that directs these protons to a water channel that connects the active sites on the subunits of this homotetrameric enzyme.
		+
		+	Kinetic and structural evidence that Asp-678 plays multiple roles in catalysis by the quinoprotein glycine oxidase.,Mamounis KJ, Avalos D, Yukl ET, Davidson VL J Biol Chem. 2019 Oct 15. pii: RA119.011255. doi: 10.1074/jbc.RA119.011255. PMID:31615898<ref>PMID:31615898</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ubz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pseudoalteromonas luteoviolacea dsm 6061]]
	[[Category: Yukl, E T]]		[[Category: Yukl, E T]]
	[[Category: Oxidase]]		[[Category: Oxidase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Tryotiophylquinone]]		[[Category: Tryotiophylquinone]]

OCA at 07:06, 23 October 2019

OCA — Wed, 23 Oct 2019 07:06:19 GMT

←Older revision		Revision as of 07:06, 23 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6ubz is ON HOLD~~	+	==Crystal structure of D678A GoxA bound to glycine at pH 5.5==
-		+	<StructureSection load='6ubz' size='340' side='right'caption='[[6ubz]], [[Resolution\|resolution]] 1.83Å' scene=''>
-	~~Authors: Yukl, E.T.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ubz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UBZ FirstGlance]. <br>
-	~~Description:~~ Crystal structure of D678A GoxA bound to glycine at pH 5.5	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene></td></tr>
-	[[Category: Yukl, E.T]]	+	<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=6ubz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ubz OCA], [http://pdbe.org/6ubz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ubz RCSB], [http://www.ebi.ac.uk/pdbsum/6ubz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ubz ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Yukl, E T]]
		+	[[Category: Oxidase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Tryotiophylquinone]]

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

OCA — Wed, 02 Oct 2019 08:33:45 GMT

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

←Older revision

Revision as of 08:33, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6ubz is ON HOLD Authors: Yukl, E.T. Description: Crystal structure of D678A GoxA bound to glycine at pH 5.5 Category: Unreleased Structures [[C...

OCA — Wed, 02 Oct 2019 08:33:44 GMT

New page: '''Unreleased structure''' The entry 6ubz is ON HOLD Authors: Yukl, E.T. Description: Crystal structure of D678A GoxA bound to glycine at pH 5.5 Category: Unreleased Structures [[C...

New page

'''Unreleased structure'''

The entry 6ubz is ON HOLD

Authors: Yukl, E.T.

Description: Crystal structure of D678A GoxA bound to glycine at pH 5.5
[[Category: Unreleased Structures]]
[[Category: Yukl, E.T]]