4feg - Revision history

OCA at 15:23, 14 March 2024

2024-03-14T15:23:08Z

←Older revision		Revision as of 15:23, 14 March 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [https://pdbe.org/4feg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [https://www.ebi.ac.uk/pdbsum/4feg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4feg 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=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [https://pdbe.org/4feg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [https://www.ebi.ac.uk/pdbsum/4feg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4feg ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Thiamin diphosphate, the vitamin B1 coenzyme, plays critical roles in fundamental metabolic pathways that require acyl carbanion equivalents. Studies on chemical models and enzymes had suggested that these carbanions are resonance-stabilized as enamines. A crystal structure of this intermediate in pyruvate oxidase at 1.1 A resolution now challenges this paradigm by revealing that the enamine does not accumulate. Instead, the intermediate samples between the ketone and the carbanion both interlocked in a tautomeric equilibrium. Formation of the keto tautomer is associated with a loss of aromaticity of the cofactor. The alternate confinement of electrons to neighboring atoms rather than pi-conjugation seems to be of importance for the enzyme-catalyzed, redox-coupled acyl transfer to phosphate, which requires a dramatic inversion of polarity of the reacting substrate carbon in two subsequent catalytic steps. The ability to oscillate between a nucleophilic (carbanion) and an electrophilic (ketone) substrate center highlights a hitherto unrecognized versatility of the thiamin cofactor. It remains to be studied whether formation of the keto tautomer is a general feature of all thiamin enzymes, as it could provide for stable storage of the carbanion state, or whether this feature represents a specific trait of thiamin oxidases. In addition, the protonation state of the two-electron reduced flavin cofactor can be fully assigned, demonstrating the power of high-resolution cryocrystallography for elucidation of enzymatic mechanisms.
-
-	Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin.,Meyer D, Neumann P, Koers E, Sjuts H, Ludtke S, Sheldrick GM, Ficner R, Tittmann K Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10867-72. Epub 2012 Jun 22. PMID:22730460<ref>PMID:22730460</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4feg" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:13, 15 November 2023

2023-11-15T09:13:47Z

←Older revision		Revision as of 09:13, 15 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4feg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum_JDM1 Lactiplantibacillus plantarum JDM1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FEG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4feg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum_JDM1 Lactiplantibacillus plantarum JDM1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FEG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TDM:2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TDM</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]] 1.09Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TDM:2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TDM</scene></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=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [https://pdbe.org/4feg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [https://www.ebi.ac.uk/pdbsum/4feg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4feg 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=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [https://pdbe.org/4feg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [https://www.ebi.ac.uk/pdbsum/4feg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4feg ProSAT]</span></td></tr>
	</table>		</table>

OCA at 04:51, 7 October 2022

2022-10-07T04:51:56Z

←Older revision		Revision as of 04:51, 7 October 2022
Line 1:		Line 1:

	==High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal A==		==High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal A==
-	<StructureSection load='4feg' size='340' side='right' caption='[[4feg]], [[Resolution\|resolution]] 1.09Å' scene=''>	+	<StructureSection load='4feg' size='340' side='right'caption='[[4feg]], [[Resolution\|resolution]] 1.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4feg]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lacpj Lacpj~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4FEG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4feg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum_JDM1 Lactiplantibacillus plantarum JDM1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FEG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TDM:2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TDM</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TDM:2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TDM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pow\|1pow]], [[1pox\|1pox]], [[2ez4\|2ez4]], [[2ezt\|2ezt]], [[2ez8\|2ez8]], [[2ez9\|2ez9]], [[2ezu\|2ezu]], [[4fee\|4fee]]</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=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [https://pdbe.org/4feg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [https://www.ebi.ac.uk/pdbsum/4feg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4feg ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pox5, JDM1_2870 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644042 LACPJ])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_oxidase Pyruvate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.3.3 1.2.3.3] </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=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [~~http~~://pdbe.org/4feg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4feg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4feg ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lacpj~~]]	+	[[Category: Lactiplantibacillus plantarum JDM1]]
-	[[Category: ~~Pyruvate oxidase~~]]	+	[[Category: Large Structures]]
-	[[Category: Ficner, R]]	+	[[Category: Ficner R]]
-	[[Category: Koers, E]]	+	[[Category: Koers E]]
-	[[Category: Luedtke, S]]	+	[[Category: Luedtke S]]
-	[[Category: Meyer, D]]	+	[[Category: Meyer D]]
-	[[Category: Neumann, P]]	+	[[Category: Neumann P]]
-	[[Category: Sheldrick~~, G M~~]]	+	[[Category: Sheldrick GM]]
-	[[Category: Sjuts, H]]	+	[[Category: Sjuts H]]
-	[[Category: Tittmann, K]]	+	[[Category: Tittmann K]]
-	~~[[Category: Carbanion]]~~	+
-	~~[[Category: Oxidation-reduction]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Reaction intermediate]]~~	+
-	~~[[Category: Structure activity relationship]]~~	+
-	~~[[Category: Thiamine diphosphate]]~~	+
-	~~[[Category: Umpolung~~]]	+

OCA at 12:53, 11 August 2016

2016-08-11T12:53:34Z

←Older revision		Revision as of 12:53, 11 August 2016
Line 1:		Line 1:
		+
	==High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal A==		==High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal A==
	<StructureSection load='4feg' size='340' side='right' caption='[[4feg]], [[Resolution\|resolution]] 1.09Å' scene=''>		<StructureSection load='4feg' size='340' side='right' caption='[[4feg]], [[Resolution\|resolution]] 1.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4feg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Lactobacillus_plantarum Lactobacillus plantarum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FEG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4feg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lacpj Lacpj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FEG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TDM:2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TDM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TDM:2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TDM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pow\|1pow]], [[1pox\|1pox]], [[2ez4\|2ez4]], [[2ezt\|2ezt]], [[2ez8\|2ez8]], [[2ez9\|2ez9]], [[2ezu\|2ezu]], [[4fee\|4fee]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pow\|1pow]], [[1pox\|1pox]], [[2ez4\|2ez4]], [[2ezt\|2ezt]], [[2ez8\|2ez8]], [[2ez9\|2ez9]], [[2ezu\|2ezu]], [[4fee\|4fee]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pox5, JDM1_2870 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1590 Lactobacillus plantarum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pox5, JDM1_2870 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644042 LACPJ])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_oxidase Pyruvate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.3.3 1.2.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_oxidase Pyruvate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.3.3 1.2.3.3] </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=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [http://www.ebi.ac.uk/pdbsum/4feg PDBsum]</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=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [http://pdbe.org/4feg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [http://www.ebi.ac.uk/pdbsum/4feg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4feg ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4feg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lactobacillus plantarum~~]]	+	[[Category: Lacpj]]
	[[Category: Pyruvate oxidase]]		[[Category: Pyruvate oxidase]]
	[[Category: Ficner, R]]		[[Category: Ficner, R]]

OCA at 12:59, 4 January 2015

2015-01-04T12:59:43Z

←Older revision		Revision as of 12:59, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4feg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_plantarum Lactobacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FEG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4feg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_plantarum Lactobacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FEG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TDM:2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TDM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TDM:2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TDM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pow\|1pow]], [[1pox\|1pox]], [[2ez4\|2ez4]], [[2ezt\|2ezt]], [[2ez8\|2ez8]], [[2ez9\|2ez9]], [[2ezu\|2ezu]], [[4fee\|4fee]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pow\|1pow]], [[1pox\|1pox]], [[2ez4\|2ez4]], [[2ezt\|2ezt]], [[2ez8\|2ez8]], [[2ez9\|2ez9]], [[2ezu\|2ezu]], [[4fee\|4fee]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pox5, JDM1_2870 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 Lactobacillus plantarum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pox5, JDM1_2870 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 Lactobacillus plantarum])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_oxidase Pyruvate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.3.3 1.2.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_oxidase Pyruvate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.3.3 1.2.3.3] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [http://www.ebi.ac.uk/pdbsum/4feg PDBsum]</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=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [http://www.ebi.ac.uk/pdbsum/4feg PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	[[Category: Lactobacillus plantarum]]		[[Category: Lactobacillus plantarum]]
	[[Category: Pyruvate oxidase]]		[[Category: Pyruvate oxidase]]
-	[[Category: Ficner, R.]]	+	[[Category: Ficner, R]]
-	[[Category: Koers, E.]]	+	[[Category: Koers, E]]
-	[[Category: Luedtke, S.]]	+	[[Category: Luedtke, S]]
-	[[Category: Meyer, D.]]	+	[[Category: Meyer, D]]
-	[[Category: Neumann, P.]]	+	[[Category: Neumann, P]]
-	[[Category: Sheldrick, G M.]]	+	[[Category: Sheldrick, G M]]
-	[[Category: Sjuts, H.]]	+	[[Category: Sjuts, H]]
-	[[Category: Tittmann, K.]]	+	[[Category: Tittmann, K]]
	[[Category: Carbanion]]		[[Category: Carbanion]]
	[[Category: Oxidation-reduction]]		[[Category: Oxidation-reduction]]

OCA at 07:58, 5 June 2014

2014-06-05T07:58:24Z

←Older revision		Revision as of 07:58, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~4feg.~~png~~\|~~left~~\|~~200px~~]]	+	==High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal A==
		+	<StructureSection load='4feg' size='340' side='right' caption='[[4feg]], [[Resolution\|resolution]] 1.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4feg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_plantarum Lactobacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FEG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TDM:2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TDM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pow\|1pow]], [[1pox\|1pox]], [[2ez4\|2ez4]], [[2ezt\|2ezt]], [[2ez8\|2ez8]], [[2ez9\|2ez9]], [[2ezu\|2ezu]], [[4fee\|4fee]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pox5, JDM1_2870 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 Lactobacillus plantarum])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_oxidase Pyruvate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.3.3 1.2.3.3] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4feg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4feg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4feg RCSB], [http://www.ebi.ac.uk/pdbsum/4feg PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Thiamin diphosphate, the vitamin B1 coenzyme, plays critical roles in fundamental metabolic pathways that require acyl carbanion equivalents. Studies on chemical models and enzymes had suggested that these carbanions are resonance-stabilized as enamines. A crystal structure of this intermediate in pyruvate oxidase at 1.1 A resolution now challenges this paradigm by revealing that the enamine does not accumulate. Instead, the intermediate samples between the ketone and the carbanion both interlocked in a tautomeric equilibrium. Formation of the keto tautomer is associated with a loss of aromaticity of the cofactor. The alternate confinement of electrons to neighboring atoms rather than pi-conjugation seems to be of importance for the enzyme-catalyzed, redox-coupled acyl transfer to phosphate, which requires a dramatic inversion of polarity of the reacting substrate carbon in two subsequent catalytic steps. The ability to oscillate between a nucleophilic (carbanion) and an electrophilic (ketone) substrate center highlights a hitherto unrecognized versatility of the thiamin cofactor. It remains to be studied whether formation of the keto tautomer is a general feature of all thiamin enzymes, as it could provide for stable storage of the carbanion state, or whether this feature represents a specific trait of thiamin oxidases. In addition, the protonation state of the two-electron reduced flavin cofactor can be fully assigned, demonstrating the power of high-resolution cryocrystallography for elucidation of enzymatic mechanisms.

-	~~{{STRUCTURE_4feg\| PDB=4feg \| SCENE= }}~~	+	Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin.,Meyer D, Neumann P, Koers E, Sjuts H, Ludtke S, Sheldrick GM, Ficner R, Tittmann K Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10867-72. Epub 2012 Jun 22. PMID:22730460<ref>PMID:22730460</ref>

-	~~===High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine~~, ~~crystal A===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22730460}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[4feg]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Lactobacillus_plantarum Lactobacillus plantarum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022730460<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Lactobacillus plantarum]]		[[Category: Lactobacillus plantarum]]
	[[Category: Pyruvate oxidase]]		[[Category: Pyruvate oxidase]]

OCA at 07:26, 11 July 2012

2012-07-11T07:26:48Z

←Older revision		Revision as of 07:26, 11 July 2012
Line 1:		Line 1:
-	[[Image:4feg.~~jpg~~\|left\|200px]]	+	[[Image:4feg.png\|left\|200px]]

	{{STRUCTURE_4feg\| PDB=4feg \| SCENE= }}		{{STRUCTURE_4feg\| PDB=4feg \| SCENE= }}
Line 5:		Line 5:
	===High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal A===		===High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal A===

		+	{{ABSTRACT_PUBMED_22730460}}

	==About this Structure==		==About this Structure==
	[[4feg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_plantarum Lactobacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA].		[[4feg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_plantarum Lactobacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022730460</ref><references group="xtra"/>
	[[Category: Lactobacillus plantarum]]		[[Category: Lactobacillus plantarum]]
	[[Category: Pyruvate oxidase]]		[[Category: Pyruvate oxidase]]

OCA at 08:01, 20 June 2012

2012-06-20T08:01:06Z

←Older revision		Revision as of 08:01, 20 June 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4feg.jpg\|left\|200px]]

-	~~The entry~~ 4feg ~~is ON HOLD~~	+	{{STRUCTURE_4feg\| PDB=4feg \| SCENE= }}

-	~~Authors: Meyer~~, ~~D., Neumann, P., Koers, E., Sjuts, H., Luedtke, S., Sheldrick, G. M., Ficner, R., Tittmann, K.~~	+	===High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal A===

-	~~Description~~: ~~Unexpected tautomeric equilibria of the carbanion~~-~~enamine intermediate in pyruvate~~ oxidase ~~highlight unrecognized chemical versatility of the thiamin cofactor~~	+
		+	==About this Structure==
		+	[[4feg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_plantarum Lactobacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FEG OCA].
		+	[[Category: Lactobacillus plantarum]]
		+	[[Category: Pyruvate oxidase]]
		+	[[Category: Ficner, R.]]
		+	[[Category: Koers, E.]]
		+	[[Category: Luedtke, S.]]
		+	[[Category: Meyer, D.]]
		+	[[Category: Neumann, P.]]
		+	[[Category: Sheldrick, G M.]]
		+	[[Category: Sjuts, H.]]
		+	[[Category: Tittmann, K.]]
		+	[[Category: Carbanion]]
		+	[[Category: Oxidation-reduction]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Reaction intermediate]]
		+	[[Category: Structure activity relationship]]
		+	[[Category: Thiamine diphosphate]]
		+	[[Category: Umpolung]]

OCA: Protected "4feg" [edit=sysop:move=sysop]

2012-06-06T07:23:07Z

Protected "4feg" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:23, 6 June 2012

OCA: New page: '''Unreleased structure''' The entry 4feg is ON HOLD Authors: Meyer, D., Neumann, P., Koers, E., Sjuts, H., Luedtke, S., Sheldrick, G. M., Ficner, R., Tittmann, K. Description: Unexpec...

2012-06-06T07:23:06Z

New page: '''Unreleased structure''' The entry 4feg is ON HOLD Authors: Meyer, D., Neumann, P., Koers, E., Sjuts, H., Luedtke, S., Sheldrick, G. M., Ficner, R., Tittmann, K. Description: Unexpec...

New page

'''Unreleased structure'''

The entry 4feg is ON HOLD

Authors: Meyer, D., Neumann, P., Koers, E., Sjuts, H., Luedtke, S., Sheldrick, G. M., Ficner, R., Tittmann, K.

Description: Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of the thiamin cofactor