6vmv - Revision history

OCA at 08:15, 11 October 2023

2023-10-11T08:15:18Z

← Older revision		Revision as of 08:15, 11 October 2023
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	<StructureSection load='6vmv' size='340' side='right'caption='[[6vmv]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6vmv' size='340' side='right'caption='[[6vmv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6vmv]] 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=6VMV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VMV FirstGlance]. <br>		<table><tr><td colspan='2'>[[6vmv]] 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=6VMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VMV FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~TGH~~:'>~~TGH~~</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TGH:6-{[(S)-carboxy(hydroxy)methyl]amino}-7-hydroxy-L-tryptophan'>TGH</scene></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class="sblockDat">[[3byw\|3byw]]</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=6vmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vmv OCA], [https://pdbe.org/6vmv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vmv RCSB], [https://www.ebi.ac.uk/pdbsum/6vmv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vmv ProSAT]</span></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~~://proteopedia.org/fgij/fg.htm?mol=6vmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vmv OCA], [~~http~~://pdbe.org/6vmv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vmv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vmv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vmv 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: Ctq]]~~
	~~[[Category: Oxidoreductase~~]]

OCA at 07:21, 15 April 2020

2020-04-15T07:21:12Z

← Older revision		Revision as of 07:21, 15 April 2020
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	<StructureSection load='6vmv' size='340' side='right'caption='[[6vmv]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6vmv' size='340' side='right'caption='[[6vmv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6vmv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VMV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VMV FirstGlance]. <br>		<table><tr><td colspan='2'>[[6vmv]] 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=6VMV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VMV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TGH:'>TGH</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TGH:'>TGH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3byw\|3byw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3byw\|3byw]]</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://proteopedia.org/fgij/fg.htm?mol=6vmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vmv OCA], [http://pdbe.org/6vmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vmv RCSB], [http://www.ebi.ac.uk/pdbsum/6vmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vmv ProSAT]</span></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=6vmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vmv OCA], [http://pdbe.org/6vmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vmv RCSB], [http://www.ebi.ac.uk/pdbsum/6vmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vmv ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The quinoprotein glycine oxidase from the marine bacterium Pseudoalteromonas luteoviolacea (PlGoxA) uses a protein-derived cysteine tryptophylquinone (CTQ) cofactor to catalyze conversion of glycine to glyoxylate and ammonia. This homotetremeric enzyme exhibits strong cooperativity towards glycine binding. It is a good model for studying enzyme kinetics and cooperativity, specifically for being able to separate those aspects of protein function through directed mutagenesis. Variant proteins were generated with mutations in four active-site residues, Phe-316, His-583, Tyr-766 and His-767. Structures for glycine-soaked crystals were obtained for each. Different mutations had differential effects on kcat and K0.5 for catalysis, K0.5 for substrate binding, and the Hill coefficients describing the steady-state kinetics or substrate binding. Phe-316 and Tyr-766 variants retained catalytic activity, albeit with altered kinetics and cooperativity. Substitutions of His-583 revealed that it is essential for glycine binding and the structure of H583C PlGoxA had no active-site glycine present in glycine-soaked crystals. The structure of H767A PlGoxA revealed a previously undetected reaction intermediate, a carbinolamine product-reduced CTQ adduct, and exhibited only negligible activity. The results of these experiments, as well as those with the native enzyme and previous variants enabled construction of a detailed mechanism for the reductive half-reaction of glycine oxidation. This proposed mechanism includes three discrete reaction intermediates that are covalently bound to CTQ during the reaction, two of which have now been structurally characterized by X-ray crystallography.

			Roles of active site residues in catalysis, substrate binding, cooperativity and the reaction mechanism of the quinoprotein glycine oxidase.,Mamounis KJ, Yukl ET, Davidson VL J Biol Chem. 2020 Mar 31. pii: RA120.013198. doi: 10.1074/jbc.RA120.013198. PMID:32234764<ref>PMID:32234764</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6vmv" 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: Ctq]]		[[Category: Ctq]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 06:58, 8 April 2020

2020-04-08T06:58:38Z

← Older revision		Revision as of 06:58, 8 April 2020
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	~~'''Unreleased structure'''~~

	~~The entry 6vmv is ON HOLD until Paper Publication~~		==Crystal structure of the H767A mutant of GoxA soaked with glycine==
			<StructureSection load='6vmv' size='340' side='right'caption='[[6vmv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	~~Authors: Yukl, E.T.~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[6vmv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VMV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VMV FirstGlance]. <br>
	~~Description:~~ Crystal structure of the H767A mutant of GoxA soaked with glycine		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=TGH:'>TGH</scene></td></tr>
	[[Category: Yukl, E.T]]		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3byw\|3byw]]</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=6vmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vmv OCA], [http://pdbe.org/6vmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vmv RCSB], [http://www.ebi.ac.uk/pdbsum/6vmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vmv ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Yukl, E T]]
			[[Category: Ctq]]
			[[Category: Oxidoreductase]]

OCA at 05:17, 19 February 2020

2020-02-19T05:17:14Z

← Older revision		Revision as of 05:17, 19 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6vmv is ON HOLD		The entry 6vmv is ON HOLD until Paper Publication

	Authors: Yukl, E.T.		Authors: Yukl, E.T.

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

2020-02-05T06:19:03Z

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

← Older revision	Revision as of 06:19, 5 February 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6vmv is ON HOLD Authors: Yukl, E.T. Description: Crystal structure of the H767A mutant of GoxA soaked with glycine [[Category: Unreleased Structure...

2020-02-05T06:19:02Z

New page: '''Unreleased structure''' The entry 6vmv is ON HOLD Authors: Yukl, E.T. Description: Crystal structure of the H767A mutant of GoxA soaked with glycine [[Category: Unreleased Structure...

New page

'''Unreleased structure'''

The entry 6vmv is ON HOLD

Authors: Yukl, E.T.

Description: Crystal structure of the H767A mutant of GoxA soaked with glycine
[[Category: Unreleased Structures]]
[[Category: Yukl, E.T]]