1umc - Revision history

OCA at 07:43, 25 October 2023

2023-10-25T07:43:03Z

←Older revision		Revision as of 07:43, 25 October 2023
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	<StructureSection load='1umc' size='340' side='right'caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1umc' size='340' side='right'caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UMC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=4MV:4~~-~~METHYL+VALERIC+ACID'>4MV</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4MV:4-METHYL+VALERIC+ACID'>4MV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </~~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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [https://pdbe.org/1umc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [https://www.ebi.ac.uk/pdbsum/1umc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1umc ProSAT], [https://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [https://pdbe.org/1umc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [https://www.ebi.ac.uk/pdbsum/1umc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1umc ProSAT], [https://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ODBA_THET8 ODBA_THET8]] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).[UniProtKB:P37940] [[https://www.uniprot.org/uniprot/ODBB_THET8 ODBB_THET8]] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).[UniProtKB:P37941]	+	[https://www.uniprot.org/uniprot/ODBA_THET8 ODBA_THET8] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).[UniProtKB:P37940]
	== 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: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kamiya, N]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Kuramitsu, S]]	+	[[Category: Kamiya N]]
-	[[Category: Maoka, N]]	+	[[Category: Kuramitsu S]]
-	[[Category: Masui, R]]	+	[[Category: Maoka N]]
-	[[Category: Nakagawa, N]]	+	[[Category: Masui R]]
-	[[Category: Nakai, T]]	+	[[Category: Nakagawa N]]
-	~~[[Category: Structural genomic]]~~	+	[[Category: Nakai T]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 06:09, 18 August 2021

2021-08-18T06:09:51Z

←Older revision		Revision as of 06:09, 18 August 2021
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	<StructureSection load='1umc' size='340' side='right'caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1umc' size='340' side='right'caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1UMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UMC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4MV:4-METHYL+VALERIC+ACID'>4MV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=~~TDP~~:~~THIAMIN~~+DIPHOSPHATE'>~~TDP~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4MV:4-METHYL+VALERIC+ACID'>4MV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [~~http~~://pdbe.org/1umc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1umc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1umc ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [https://pdbe.org/1umc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [https://www.ebi.ac.uk/pdbsum/1umc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1umc ProSAT], [https://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ODBA_THET8 ODBA_THET8]] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).[UniProtKB:P37940] [[~~http~~://www.uniprot.org/uniprot/ODBB_THET8 ODBB_THET8]] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).[UniProtKB:P37941]	+	[[https://www.uniprot.org/uniprot/ODBA_THET8 ODBA_THET8]] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).[UniProtKB:P37940] [[https://www.uniprot.org/uniprot/ODBB_THET8 ODBB_THET8]] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).[UniProtKB:P37941]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:11, 1 January 2020

2020-01-01T13:11:56Z

←Older revision		Revision as of 13:11, 1 January 2020
Line 1:		Line 1:

	==branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate==		==branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate==
-	<StructureSection load='1umc' size='340' side='right' caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1umc' size='340' side='right'caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UMC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UMC FirstGlance]. <br>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Large Structures]]
	[[Category: Kamiya, N]]		[[Category: Kamiya, N]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]

OCA at 08:01, 28 March 2018

2018-03-28T08:01:34Z

←Older revision		Revision as of 08:01, 28 March 2018
Line 1:		Line 1:
		+
	==branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate==		==branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate==
	<StructureSection load='1umc' size='340' side='right' caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1umc' size='340' side='right' caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [http://pdbe.org/1umc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [http://www.ebi.ac.uk/pdbsum/1umc PDBsum], [http://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [http://pdbe.org/1umc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [http://www.ebi.ac.uk/pdbsum/1umc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1umc ProSAT], [http://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</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/um/1umc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/um/1umc_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>
	</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=1umc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:21, 11 September 2015

2015-09-11T22:21:02Z

←Older revision		Revision as of 22:21, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1umc' size='340' side='right' caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1umc' size='340' side='right' caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UMC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4MV:4-METHYL+VALERIC+ACID'>4MV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4MV:4-METHYL+VALERIC+ACID'>4MV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [http://www.ebi.ac.uk/pdbsum/1umc PDBsum], [http://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [http://pdbe.org/1umc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [http://www.ebi.ac.uk/pdbsum/1umc PDBsum], [http://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1umc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Kamiya, N]]		[[Category: Kamiya, N]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]

OCA at 20:15, 25 December 2014

2014-12-25T20:15:40Z

←Older revision		Revision as of 20:15, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UMC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UMC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4MV:4-METHYL+VALERIC+ACID'>4MV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4MV:4-METHYL+VALERIC+ACID'>4MV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [http://www.ebi.ac.uk/pdbsum/1umc PDBsum], [http://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [http://www.ebi.ac.uk/pdbsum/1umc PDBsum], [http://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ODBA_THET8 ODBA_THET8]] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).[UniProtKB:P37940] [[http://www.uniprot.org/uniprot/ODBB_THET8 ODBB_THET8]] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3) (By similarity).[UniProtKB:P37941]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Kamiya, N.]]	+	[[Category: Kamiya, N]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Maoka, N.]]	+	[[Category: Maoka, N]]
-	[[Category: Masui, R.]]	+	[[Category: Masui, R]]
-	[[Category: Nakagawa, N.]]	+	[[Category: Nakagawa, N]]
-	[[Category: Nakai, T.]]	+	[[Category: Nakai, T]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 19:37, 29 September 2014

2014-09-29T19:37:38Z

←Older revision		Revision as of 19:37, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1umc.~~png~~\|~~left~~\|200px]]	+	==branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate==
		+	<StructureSection load='1umc' size='340' side='right' caption='[[1umc]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1umc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UMC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4MV:4-METHYL+VALERIC+ACID'>4MV</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1um9\|1um9]], [[1umb\|1umb]], [[1umd\|1umd]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_dehydrogenase_(2-methylpropanoyl-transferring) 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.4 1.2.4.4] </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=1umc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1umc RCSB], [http://www.ebi.ac.uk/pdbsum/1umc PDBsum], [http://www.topsan.org/Proteins/RSGI/1umc TOPSAN]</span></td></tr>
		+	<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/um/1umc_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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The alpha(2)beta(2) tetrameric E1 component of the branched-chain 2-oxo acid (BCOA) dehydrogenase multienzyme complex is a thiamin diphosphate (ThDP)-dependent enzyme. E1 catalyzes the decarboxylation of a BCOA concomitant with the formation of the alpha-carbanion/enamine intermediate, 2-(1-hydroxyalkyl)-ThDP, followed by transfer of the 1-hydroxyalkyl group to the distal sulfur atom on the lipoamide of the E2 component. In order to elucidate the catalytic mechanism of E1, the alpha- and beta-subunits of E1 from Thermus thermophilus HB8 have been co-expressed in Escherichia coli, purified and crystallized as a stable complex, and the following crystal structures have been analyzed: the apoenzyme (E1(apo)), the holoenzyme (E1(holo)), E1(holo) in complex with the substrate analogue 4-methylpentanoate (MPA) as an ES complex model, and E1(holo) in complex with 4-methyl-2-oxopentanoate (MOPA) as the alpha-carbanion/enamine intermediate (E1(ceim)). Binding of cofactors to E1(apo) induces a disorder-order transition in two loops adjacent to the active site. Furthermore, upon binding of MPA to E1(holo), the loop comprised of Gly121beta-Gln131beta moves close to the active site and interacts with MPA. The carboxylate group of MPA is recognized mainly by Tyr86beta and N4' of ThDP. The hydrophobic moiety of MPA is recognized by Phe66alpha, Tyr95alpha, Met128alpha and His131alpha. As an intermediate, MOPA is decarboxylated and covalently linked to ThDP, and the conformation of the protein loop is almost the same as in the substrate-free (holoenzyme) form. These results suggest that E1 undergoes an open-closed conformational change upon formation of the ES complex with a BCOA, and the mobile region participates in the recognition of the carboxylate group of the BCOA. ES complex models of E1(holo).MOPA and of E1(ceim).lipoamide built from the above structures suggest that His273alpha and His129beta' are potential proton donors to the carbonyl group of a BCOA and to the proximal sulfur atom on the lipoamide, respectively.

-	~~{{STRUCTURE_1umc\| PDB=1umc \| SCENE= }}~~	+	Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8, as revealed by X-ray crystallography.,Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N J Mol Biol. 2004 Apr 2;337(4):1011-33. PMID:15033367<ref>PMID:15033367</ref>

-	~~===branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15033367}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1umc]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015033367<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kamiya, N.]]		[[Category: Kamiya, N.]]

OCA: Protected "1umc" [edit=sysop:move=sysop]

2013-01-05T12:50:42Z

Protected "1umc" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:50, 5 January 2013

OCA at 12:50, 5 January 2013

2013-01-05T12:50:39Z

←Older revision		Revision as of 12:50, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1umc.png\|left\|200px]]		[[Image:1umc.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1umc", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1umc\| PDB=1umc \| SCENE= }}		{{STRUCTURE_1umc\| PDB=1umc \| SCENE= }}

	===branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate===		===branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15033367}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15033367 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15033367}}		{{ABSTRACT_PUBMED_15033367}}

	==About this Structure==		==About this Structure==
-	~~1UMC~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA].	+	[[1umc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMC OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15033367~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015033367</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kamiya, N.]]		[[Category: Kamiya, N.]]
Line 32:		Line 20:
	[[Category: Nakai, T.]]		[[Category: Nakai, T.]]
	[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]		[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
		+	[[Category: Oxidoreductase]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:52:20 2009''

OCA at 03:52, 18 February 2009

2009-02-18T03:52:23Z

←Older revision		Revision as of 03:52, 18 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8, as revealed by X-ray crystallography., Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N, J Mol Biol. 2004 Apr 2;337(4):1011-33. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15033367 15033367]~~	+	<ref group="xtra">PMID:15033367</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kamiya, N.]]		[[Category: Kamiya, N.]]
Line 36:		Line 36:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 12~~:48:~~24 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:52:20 2009''