6r9v - Revision history

OCA at 12:17, 24 January 2024

OCA — Wed, 24 Jan 2024 12:17:54 GMT

←Older revision		Revision as of 12:17, 24 January 2024
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	<StructureSection load='6r9v' size='340' side='right'caption='[[6r9v]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6r9v' size='340' side='right'caption='[[6r9v]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r9v]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pediococcus_acidilactici_dsm_20284~~ Pediococcus acidilactici ~~dsm~~ 20284]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r9v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pediococcus_acidilactici_DSM_20284 Pediococcus acidilactici DSM 20284]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R9V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 2Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lctO, HMPREF0623_0568 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=862514 Pediococcus acidilactici DSM 20284])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=6r9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9v OCA], [~~http~~://pdbe.org/6r9v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r9v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r9v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9v 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=6r9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9v OCA], [https://pdbe.org/6r9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r9v RCSB], [https://www.ebi.ac.uk/pdbsum/6r9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E0NE46_PEDAC E0NE46_PEDAC]
	<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: Pediococcus acidilactici ~~dsm~~ 20284]]	+	[[Category: Pediococcus acidilactici DSM 20284]]
-	[[Category: Ashok, Y]]	+	[[Category: Ashok Y]]
-	[[Category: Lehtio, L]]	+	[[Category: Lehtio L]]
-	[[Category: Maksimainen~~, M M]]~~	+	[[Category: Maksimainen MM]]
-	~~[[Category: Alpha hydroxyacid]]~~	+
-	~~[[Category: Fmn]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 07:15, 4 March 2020

OCA — Wed, 04 Mar 2020 07:15:37 GMT

←Older revision		Revision as of 07:15, 4 March 2020
Line 3:		Line 3:
	<StructureSection load='6r9v' size='340' side='right'caption='[[6r9v]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6r9v' size='340' side='right'caption='[[6r9v]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r9v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r9v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pediococcus_acidilactici_dsm_20284 Pediococcus acidilactici dsm 20284]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R9V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lctO, HMPREF0623_0568 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=862514 Pediococcus acidilactici DSM 20284])</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=6r9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9v OCA], [http://pdbe.org/6r9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r9v RCSB], [http://www.ebi.ac.uk/pdbsum/6r9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9v 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=6r9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9v OCA], [http://pdbe.org/6r9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r9v RCSB], [http://www.ebi.ac.uk/pdbsum/6r9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9v ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lactate oxidases belong to a group of FMN-dependent enzymes and they catalyze a conversion of lactate to pyruvate with a release of hydrogen peroxide. Hydrogen peroxide is also utilized as a read out in biosensors to quantitate lactate levels in biological samples. Aerococcus viridans lactate oxidase is the best characterized lactate oxidase and our knowledge of lactate oxidases relies largely to studies conducted with that particular enzyme. Pediococcus acidilactici lactate oxidase is also commercially available for e.g. lactate measurements, but this enzyme has not been characterized in detail before. Here we report structural characterization of the recombinant enzyme and its co-factor dependent oligomerization. The crystal structures revealed two distinct conformations in the loop closing the active site, consistent with previous biochemical studies implicating the role of loop in catalysis. Despite the structural conservation of active site residues, we were not able to detect either oxidase or monooxygenase activity when L-lactate was used as a substrate. Pediococcus acidilactici lactate oxidase is therefore an example of a misannotation of an FMN-dependent enzyme, which catalyzes likely a so far unknown oxidation reaction.
		+
		+	FMN-dependent oligomerization of putative lactate oxidase from Pediococcus acidilactici.,Ashok Y, Maksimainen MM, Kallio T, Kilpelainen P, Lehtio L PLoS One. 2020 Feb 24;15(2):e0223870. doi: 10.1371/journal.pone.0223870., eCollection 2020. PMID:32092083<ref>PMID:32092083</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6r9v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pediococcus acidilactici dsm 20284]]
	[[Category: Ashok, Y]]		[[Category: Ashok, Y]]
	[[Category: Lehtio, L]]		[[Category: Lehtio, L]]

OCA at 04:22, 13 February 2020

OCA — Thu, 13 Feb 2020 04:22:27 GMT

←Older revision		Revision as of 04:22, 13 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6r9v ~~is ON HOLD~~	+	==Crystal structure of Pediococcus acidilactici lactate oxidase A94G mutant==
-		+	<StructureSection load='6r9v' size='340' side='right'caption='[[6r9v]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6r9v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R9V FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=6r9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9v OCA], [http://pdbe.org/6r9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r9v RCSB], [http://www.ebi.ac.uk/pdbsum/6r9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9v ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ashok, Y]]
		+	[[Category: Lehtio, L]]
		+	[[Category: Maksimainen, M M]]
		+	[[Category: Alpha hydroxyacid]]
		+	[[Category: Fmn]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Tim barrel]]

OCA: Protected "6r9v" [edit=sysop:move=sysop]

OCA — Wed, 10 Apr 2019 05:47:33 GMT

Protected "6r9v" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:47, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6r9v is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Apr 2019 05:47:32 GMT

New page: '''Unreleased structure''' The entry 6r9v is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6r9v is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]