2w93 - Revision history

OCA at 15:48, 13 December 2023

2023-12-13T15:48:33Z

←Older revision		Revision as of 15:48, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2w93' size='340' side='right'caption='[[2w93]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2w93' size='340' side='right'caption='[[2w93]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2w93]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W93 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2w93]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W93 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=PY0:(1S,2S)-1-AMINO-1,2-DIHYDROXYPROPAN-1-OLATE'>PY0</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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]] 1.6Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</div></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=PY0:(1S,2S)-1-AMINO-1,2-DIHYDROXYPROPAN-1-OLATE'>PY0</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyruvate_decarboxylase Pyruvate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [https://pdbe.org/2w93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [https://www.ebi.ac.uk/pdbsum/2w93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w93 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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [https://pdbe.org/2w93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [https://www.ebi.ac.uk/pdbsum/2w93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w93 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PDC1_YEAST PDC1_YEAST]] Major of three pyruvate decarboxylases (PDC1, PDC5, PDC6) implicated in the nonoxidative conversion of pyruvate to acetaldehyde and carbon dioxide during alcoholic fermentation. Most of the produced acetaldehyde is subsequently reduced to ethanol, but some is required for cytosolic acetyl-CoA production for biosynthetic pathways. The enzyme is also one of five 2-oxo acid decarboxylases (PDC1, PDC5, PDC6, ARO10, and THI3) able to decarboxylate more complex 2-oxo acids (alpha-ketoacids) than pyruvate, which seem mainly involved in amino acid catabolism. Here the enzyme catalyzes the decarboxylation of amino acids, which, in a first step, have been transaminated to the corresponding 2-oxo acids. In a third step, the resulting aldehydes are reduced to alcohols, collectively referred to as fusel oils or alcohols. Its preferred substrates are the transaminated amino acids valine, isoleucine, phenylalanine, and tryptophan, whereas leucine is no substrate. In a side-reaction the carbanionic intermediate (or active aldehyde) generated by decarboxylation or by activation of an aldehyde can react with an aldehyde via condensation (or carboligation) yielding a 2-hydroxy ketone, collectively called acyloins.<ref>PMID:4687392</ref> <ref>PMID:8866484</ref> <ref>PMID:9341119</ref> <ref>PMID:9748245</ref> <ref>PMID:10234824</ref> <ref>PMID:10231381</ref> <ref>PMID:10753893</ref> <ref>PMID:11141278</ref> <ref>PMID:12499363</ref> <ref>PMID:12902239</ref>	+	[https://www.uniprot.org/uniprot/PDC1_YEAST PDC1_YEAST] Major of three pyruvate decarboxylases (PDC1, PDC5, PDC6) implicated in the nonoxidative conversion of pyruvate to acetaldehyde and carbon dioxide during alcoholic fermentation. Most of the produced acetaldehyde is subsequently reduced to ethanol, but some is required for cytosolic acetyl-CoA production for biosynthetic pathways. The enzyme is also one of five 2-oxo acid decarboxylases (PDC1, PDC5, PDC6, ARO10, and THI3) able to decarboxylate more complex 2-oxo acids (alpha-ketoacids) than pyruvate, which seem mainly involved in amino acid catabolism. Here the enzyme catalyzes the decarboxylation of amino acids, which, in a first step, have been transaminated to the corresponding 2-oxo acids. In a third step, the resulting aldehydes are reduced to alcohols, collectively referred to as fusel oils or alcohols. Its preferred substrates are the transaminated amino acids valine, isoleucine, phenylalanine, and tryptophan, whereas leucine is no substrate. In a side-reaction the carbanionic intermediate (or active aldehyde) generated by decarboxylation or by activation of an aldehyde can react with an aldehyde via condensation (or carboligation) yielding a 2-hydroxy ketone, collectively called acyloins.<ref>PMID:4687392</ref> <ref>PMID:8866484</ref> <ref>PMID:9341119</ref> <ref>PMID:9748245</ref> <ref>PMID:10234824</ref> <ref>PMID:10231381</ref> <ref>PMID:10753893</ref> <ref>PMID:11141278</ref> <ref>PMID:12499363</ref> <ref>PMID:12902239</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyruvate decarboxylase~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Konig, S]]	+	[[Category: Konig S]]
-	[[Category: Kutter, S]]	+	[[Category: Kutter S]]
-	[[Category: Weiss~~, M S]]~~	+	[[Category: Weiss MS]]
-	~~[[Category: Acetylation]]~~	+
-	~~[[Category: Allosteric enzyme]]~~	+
-	~~[[Category: Branched-chain amino acid catabolism]]~~	+
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Decarboxylase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phenylalanine catabolism]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Substrate activation]]~~	+
-	~~[[Category: Substrate regulation]]~~	+
-	~~[[Category: Thiamine pyrophosphate]]~~	+
-	~~[[Category: Thiohemiketal]]~~	+
-	~~[[Category: Tryptophan catabolism~~]]	+

OCA at 10:53, 7 July 2021

2021-07-07T10:53:15Z

←Older revision		Revision as of 10:53, 7 July 2021
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	<StructureSection load='2w93' size='340' side='right'caption='[[2w93]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2w93' size='340' side='right'caption='[[2w93]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2w93]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2W93 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2w93]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W93 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PY0:(1S,2S)-1-AMINO-1,2-DIHYDROXYPROPAN-1-OLATE'>PY0</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=PY0:(1S,2S)-1-AMINO-1,2-DIHYDROXYPROPAN-1-OLATE'>PY0</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Pyruvate_decarboxylase Pyruvate decarboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyruvate_decarboxylase Pyruvate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [~~http~~://pdbe.org/2w93 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2w93 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2w93 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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [https://pdbe.org/2w93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [https://www.ebi.ac.uk/pdbsum/2w93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w93 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PDC1_YEAST PDC1_YEAST]] Major of three pyruvate decarboxylases (PDC1, PDC5, PDC6) implicated in the nonoxidative conversion of pyruvate to acetaldehyde and carbon dioxide during alcoholic fermentation. Most of the produced acetaldehyde is subsequently reduced to ethanol, but some is required for cytosolic acetyl-CoA production for biosynthetic pathways. The enzyme is also one of five 2-oxo acid decarboxylases (PDC1, PDC5, PDC6, ARO10, and THI3) able to decarboxylate more complex 2-oxo acids (alpha-ketoacids) than pyruvate, which seem mainly involved in amino acid catabolism. Here the enzyme catalyzes the decarboxylation of amino acids, which, in a first step, have been transaminated to the corresponding 2-oxo acids. In a third step, the resulting aldehydes are reduced to alcohols, collectively referred to as fusel oils or alcohols. Its preferred substrates are the transaminated amino acids valine, isoleucine, phenylalanine, and tryptophan, whereas leucine is no substrate. In a side-reaction the carbanionic intermediate (or active aldehyde) generated by decarboxylation or by activation of an aldehyde can react with an aldehyde via condensation (or carboligation) yielding a 2-hydroxy ketone, collectively called acyloins.<ref>PMID:4687392</ref> <ref>PMID:8866484</ref> <ref>PMID:9341119</ref> <ref>PMID:9748245</ref> <ref>PMID:10234824</ref> <ref>PMID:10231381</ref> <ref>PMID:10753893</ref> <ref>PMID:11141278</ref> <ref>PMID:12499363</ref> <ref>PMID:12902239</ref>	+	[[https://www.uniprot.org/uniprot/PDC1_YEAST PDC1_YEAST]] Major of three pyruvate decarboxylases (PDC1, PDC5, PDC6) implicated in the nonoxidative conversion of pyruvate to acetaldehyde and carbon dioxide during alcoholic fermentation. Most of the produced acetaldehyde is subsequently reduced to ethanol, but some is required for cytosolic acetyl-CoA production for biosynthetic pathways. The enzyme is also one of five 2-oxo acid decarboxylases (PDC1, PDC5, PDC6, ARO10, and THI3) able to decarboxylate more complex 2-oxo acids (alpha-ketoacids) than pyruvate, which seem mainly involved in amino acid catabolism. Here the enzyme catalyzes the decarboxylation of amino acids, which, in a first step, have been transaminated to the corresponding 2-oxo acids. In a third step, the resulting aldehydes are reduced to alcohols, collectively referred to as fusel oils or alcohols. Its preferred substrates are the transaminated amino acids valine, isoleucine, phenylalanine, and tryptophan, whereas leucine is no substrate. In a side-reaction the carbanionic intermediate (or active aldehyde) generated by decarboxylation or by activation of an aldehyde can react with an aldehyde via condensation (or carboligation) yielding a 2-hydroxy ketone, collectively called acyloins.<ref>PMID:4687392</ref> <ref>PMID:8866484</ref> <ref>PMID:9341119</ref> <ref>PMID:9748245</ref> <ref>PMID:10234824</ref> <ref>PMID:10231381</ref> <ref>PMID:10753893</ref> <ref>PMID:11141278</ref> <ref>PMID:12499363</ref> <ref>PMID:12902239</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:05, 10 July 2019

2019-07-10T06:05:03Z

←Older revision		Revision as of 06:05, 10 July 2019
Line 1:		Line 1:

	==Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide==		==Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide==
-	<StructureSection load='2w93' size='340' side='right' caption='[[2w93]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='2w93' size='340' side='right'caption='[[2w93]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2w93]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W93 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2w93]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W93 FirstGlance]. <br>
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Pyruvate decarboxylase]]		[[Category: Pyruvate decarboxylase]]
	[[Category: Konig, S]]		[[Category: Konig, S]]

OCA at 09:31, 26 September 2018

2018-09-26T09:31:10Z

←Older revision		Revision as of 09:31, 26 September 2018
Line 1:		Line 1:
		+
	==Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide==		==Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide==
	<StructureSection load='2w93' size='340' side='right' caption='[[2w93]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2w93' size='340' side='right' caption='[[2w93]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_decarboxylase Pyruvate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </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_decarboxylase Pyruvate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [http://pdbe.org/2w93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [http://www.ebi.ac.uk/pdbsum/2w93 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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [http://pdbe.org/2w93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [http://www.ebi.ac.uk/pdbsum/2w93 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w93 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w9/2w93_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w9/2w93_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 32:		Line 33:
	[[Category: Kutter, S]]		[[Category: Kutter, S]]
	[[Category: Weiss, M S]]		[[Category: Weiss, M S]]
		+	[[Category: Acetylation]]
	[[Category: Allosteric enzyme]]		[[Category: Allosteric enzyme]]
	[[Category: Branched-chain amino acid catabolism]]		[[Category: Branched-chain amino acid catabolism]]
		+	[[Category: Cytoplasm]]
	[[Category: Decarboxylase]]		[[Category: Decarboxylase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 03:01, 8 February 2016

2016-02-08T03:01:18Z

←Older revision		Revision as of 03:01, 8 February 2016
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_decarboxylase Pyruvate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </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_decarboxylase Pyruvate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [http://www.ebi.ac.uk/pdbsum/2w93 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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [http://pdbe.org/2w93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [http://www.ebi.ac.uk/pdbsum/2w93 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2w93 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>

OCA at 20:06, 24 December 2014

2014-12-24T20:06:06Z

←Older revision		Revision as of 20:06, 24 December 2014
Line 8:		Line 8:
	<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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [http://www.ebi.ac.uk/pdbsum/2w93 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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [http://www.ebi.ac.uk/pdbsum/2w93 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDC1_YEAST PDC1_YEAST]] Major of three pyruvate decarboxylases (PDC1, PDC5, PDC6) implicated in the nonoxidative conversion of pyruvate to acetaldehyde and carbon dioxide during alcoholic fermentation. Most of the produced acetaldehyde is subsequently reduced to ethanol, but some is required for cytosolic acetyl-CoA production for biosynthetic pathways. The enzyme is also one of five 2-oxo acid decarboxylases (PDC1, PDC5, PDC6, ARO10, and THI3) able to decarboxylate more complex 2-oxo acids (alpha-ketoacids) than pyruvate, which seem mainly involved in amino acid catabolism. Here the enzyme catalyzes the decarboxylation of amino acids, which, in a first step, have been transaminated to the corresponding 2-oxo acids. In a third step, the resulting aldehydes are reduced to alcohols, collectively referred to as fusel oils or alcohols. Its preferred substrates are the transaminated amino acids valine, isoleucine, phenylalanine, and tryptophan, whereas leucine is no substrate. In a side-reaction the carbanionic intermediate (or active aldehyde) generated by decarboxylation or by activation of an aldehyde can react with an aldehyde via condensation (or carboligation) yielding a 2-hydroxy ketone, collectively called acyloins.<ref>PMID:4687392</ref> <ref>PMID:8866484</ref> <ref>PMID:9341119</ref> <ref>PMID:9748245</ref> <ref>PMID:10234824</ref> <ref>PMID:10231381</ref> <ref>PMID:10753893</ref> <ref>PMID:11141278</ref> <ref>PMID:12499363</ref> <ref>PMID:12902239</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 23:
	==See Also==		==See Also==
	*[[Pyruvate decarboxylase\|Pyruvate decarboxylase]]		*[[Pyruvate decarboxylase\|Pyruvate decarboxylase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
	[[Category: Pyruvate decarboxylase]]		[[Category: Pyruvate decarboxylase]]
-	[[Category: Konig, S.]]	+	[[Category: Konig, S]]
-	[[Category: Kutter, S.]]	+	[[Category: Kutter, S]]
-	[[Category: Weiss, M S.]]	+	[[Category: Weiss, M S]]
	[[Category: Allosteric enzyme]]		[[Category: Allosteric enzyme]]
	[[Category: Branched-chain amino acid catabolism]]		[[Category: Branched-chain amino acid catabolism]]
Line 37:		Line 41:
	[[Category: Phenylalanine catabolism]]		[[Category: Phenylalanine catabolism]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
-	[[Category: Pyruvate decarboxylase]]
	[[Category: Substrate activation]]		[[Category: Substrate activation]]
	[[Category: Substrate regulation]]		[[Category: Substrate regulation]]

OCA at 06:07, 10 October 2014

2014-10-10T06:07:23Z

←Older revision		Revision as of 06:07, 10 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2w93]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W93 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2w93]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W93 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PY0:(1S,2S)-1-AMINO-1,2-DIHYDROXYPROPAN-1-OLATE'>PY0</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PY0:(1S,2S)-1-AMINO-1,2-DIHYDROXYPROPAN-1-OLATE'>PY0</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_decarboxylase Pyruvate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </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_decarboxylase Pyruvate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [http://www.ebi.ac.uk/pdbsum/2w93 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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [http://www.ebi.ac.uk/pdbsum/2w93 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:38, 30 July 2014

2014-07-30T06:38:13Z

←Older revision		Revision as of 06:38, 30 July 2014
Line 1:		Line 1:
-	~~[[Image:2w93.png\|left\|200px]]~~	+	==Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide==
-		+	<StructureSection load='2w93' size='340' side='right' caption='[[2w93]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{STRUCTURE_2w93\| PDB~~=~~2w93 \| SCENE~~= }}	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[2w93]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W93 FirstGlance]. <br>
-	===~~CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PYRUVATE DECARBOXYLASE VARIANT E477Q IN COMPLEX WITH THE SURROGATE PYRUVAMIDE~~===	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PY0:(1S,2S)-1-AMINO-1,2-DIHYDROXYPROPAN-1-OLATE'>PY0</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qpb\|1qpb]], [[1pyd\|1pyd]], [[2vk8\|2vk8]], [[1pvd\|1pvd]], [[2vk1\|2vk1]]</td></tr>
-		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_decarboxylase Pyruvate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </span></td></tr>
-	==~~About this Structure~~==	+	<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=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [http://www.ebi.ac.uk/pdbsum/2w93 PDBsum]</span></td></tr>
-	[[2w93]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA].	+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w9/2w93_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>

	==See Also==		==See Also==
	*[[Pyruvate decarboxylase\|Pyruvate decarboxylase]]		*[[Pyruvate decarboxylase\|Pyruvate decarboxylase]]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Pyruvate decarboxylase]]		[[Category: Pyruvate decarboxylase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Konig, S.]]		[[Category: Konig, S.]]
	[[Category: Kutter, S.]]		[[Category: Kutter, S.]]

OCA at 08:40, 20 October 2012

2012-10-20T08:40:54Z

←Older revision		Revision as of 08:40, 20 October 2012
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[2w93]] is a 4 chain structure ~~of [[Pyruvate decarboxylase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA].	+	[[2w93]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA].

	==See Also==		==See Also==

OCA: Protected "2w93" [edit=sysop:move=sysop]

2012-07-25T20:25:29Z

Protected "2w93" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:25, 25 July 2012