3zhv - Revision history

OCA at 11:02, 20 December 2023

OCA — Wed, 20 Dec 2023 11:02:17 GMT

←Older revision		Revision as of 11:02, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='3zhv' size='340' side='right'caption='[[3zhv]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3zhv' size='340' side='right'caption='[[3zhv]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zhv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_smegmatis"_trevisan_1889 "bacillus~~ smegmatis~~" trevisan 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zhv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDW:2-[3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-[(1S)-1-OXIDANYLETHYL]-1,3-THIAZOL-3-IUM-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDW</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]] 2.3Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zhq\|3zhq]], [[3zhr\|3zhr]], [[3zhs\|3zhs]], [[3zht\|3zht]], [[3zhu\|3zhu]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDW:2-[3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-[(1S)-1-OXIDANYLETHYL]-1,3-THIAZOL-3-IUM-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDW</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=3zhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhv OCA], [https://pdbe.org/3zhv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zhv RCSB], [https://www.ebi.ac.uk/pdbsum/3zhv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhv 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=3zhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhv OCA], [https://pdbe.org/3zhv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zhv RCSB], [https://www.ebi.ac.uk/pdbsum/3zhv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KGD_MYCS2 KGD_MYCS2]] Shows three enzymatic activities that share a first common step, the attack of thiamine-PP on 2-oxoglutarate (alpha-ketoglutarate, KG), leading to the formation of an enamine-thiamine-PP intermediate upon decarboxylation. Thus, displays KGD activity, catalyzing the decarboxylation from five-carbon 2-oxoglutarate to four-carbon succinate semialdehyde (SSA). Also catalyzes C-C bond formation between the activated aldehyde formed after decarboxylation of alpha-ketoglutarate and the carbonyl of glyoxylate (GLX), to yield 2-hydroxy-3-oxoadipate (HOA), which spontaneously decarboxylates to form 5-hydroxylevulinate (HLA). And is also a component of the 2-oxoglutarate dehydrogenase (ODH) complex, that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). The KG decarboxylase and KG dehydrogenase reactions provide two alternative, tightly regulated, pathways connecting the oxidative and reductive branches of the TCA cycle.<ref>PMID:19019160</ref> <ref>PMID:21867916</ref>	+	[https://www.uniprot.org/uniprot/KGD_MYCS2 KGD_MYCS2] Shows three enzymatic activities that share a first common step, the attack of thiamine-PP on 2-oxoglutarate (alpha-ketoglutarate, KG), leading to the formation of an enamine-thiamine-PP intermediate upon decarboxylation. Thus, displays KGD activity, catalyzing the decarboxylation from five-carbon 2-oxoglutarate to four-carbon succinate semialdehyde (SSA). Also catalyzes C-C bond formation between the activated aldehyde formed after decarboxylation of alpha-ketoglutarate and the carbonyl of glyoxylate (GLX), to yield 2-hydroxy-3-oxoadipate (HOA), which spontaneously decarboxylates to form 5-hydroxylevulinate (HLA). And is also a component of the 2-oxoglutarate dehydrogenase (ODH) complex, that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). The KG decarboxylase and KG dehydrogenase reactions provide two alternative, tightly regulated, pathways connecting the oxidative and reductive branches of the TCA cycle.<ref>PMID:19019160</ref> <ref>PMID:21867916</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus smegmatis trevisan 1889]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Alzari~~, P M~~]]	+	[[Category: Mycolicibacterium smegmatis]]
-	[[Category: Barilone, N]]	+	[[Category: Alzari PM]]
-	[[Category: Bellinzoni, M]]	+	[[Category: Barilone N]]
-	[[Category: Wagner, T]]	+	[[Category: Bellinzoni M]]
-	~~[[Category: E1o]]~~	+	[[Category: Wagner T]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 05:47, 10 August 2022

OCA — Wed, 10 Aug 2022 05:47:04 GMT

←Older revision		Revision as of 05:47, 10 August 2022
Line 1:		Line 1:

	==Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)==		==Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)==
-	<StructureSection load='3zhv' size='340' side='right' caption='[[3zhv]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3zhv' size='340' side='right'caption='[[3zhv]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zhv]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ZHV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zhv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDW:2-[3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-[(1S)-1-OXIDANYLETHYL]-1,3-THIAZOL-3-IUM-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDW</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDW:2-[3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-[(1S)-1-OXIDANYLETHYL]-1,3-THIAZOL-3-IUM-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDW</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhq\|3zhq]], [[3zhr\|3zhr]], [[3zhs\|3zhs]], [[3zht\|3zht]], [[3zhu\|3zhu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zhq\|3zhq]], [[3zhr\|3zhr]], [[3zhs\|3zhs]], [[3zht\|3zht]], [[3zhu\|3zhu]]</div></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=3zhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhv OCA], [~~http~~://pdbe.org/3zhv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3zhv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3zhv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhv 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=3zhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhv OCA], [https://pdbe.org/3zhv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zhv RCSB], [https://www.ebi.ac.uk/pdbsum/3zhv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KGD_MYCS2 KGD_MYCS2]] Shows three enzymatic activities that share a first common step, the attack of thiamine-PP on 2-oxoglutarate (alpha-ketoglutarate, KG), leading to the formation of an enamine-thiamine-PP intermediate upon decarboxylation. Thus, displays KGD activity, catalyzing the decarboxylation from five-carbon 2-oxoglutarate to four-carbon succinate semialdehyde (SSA). Also catalyzes C-C bond formation between the activated aldehyde formed after decarboxylation of alpha-ketoglutarate and the carbonyl of glyoxylate (GLX), to yield 2-hydroxy-3-oxoadipate (HOA), which spontaneously decarboxylates to form 5-hydroxylevulinate (HLA). And is also a component of the 2-oxoglutarate dehydrogenase (ODH) complex, that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). The KG decarboxylase and KG dehydrogenase reactions provide two alternative, tightly regulated, pathways connecting the oxidative and reductive branches of the TCA cycle.<ref>PMID:19019160</ref> <ref>PMID:21867916</ref>	+	[[https://www.uniprot.org/uniprot/KGD_MYCS2 KGD_MYCS2]] Shows three enzymatic activities that share a first common step, the attack of thiamine-PP on 2-oxoglutarate (alpha-ketoglutarate, KG), leading to the formation of an enamine-thiamine-PP intermediate upon decarboxylation. Thus, displays KGD activity, catalyzing the decarboxylation from five-carbon 2-oxoglutarate to four-carbon succinate semialdehyde (SSA). Also catalyzes C-C bond formation between the activated aldehyde formed after decarboxylation of alpha-ketoglutarate and the carbonyl of glyoxylate (GLX), to yield 2-hydroxy-3-oxoadipate (HOA), which spontaneously decarboxylates to form 5-hydroxylevulinate (HLA). And is also a component of the 2-oxoglutarate dehydrogenase (ODH) complex, that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). The KG decarboxylase and KG dehydrogenase reactions provide two alternative, tightly regulated, pathways connecting the oxidative and reductive branches of the TCA cycle.<ref>PMID:19019160</ref> <ref>PMID:21867916</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus smegmatis trevisan 1889]]		[[Category: Bacillus smegmatis trevisan 1889]]
		+	[[Category: Large Structures]]
	[[Category: Alzari, P M]]		[[Category: Alzari, P M]]
	[[Category: Barilone, N]]		[[Category: Barilone, N]]

OCA at 16:33, 4 August 2016

OCA — Thu, 04 Aug 2016 16:33:32 GMT

←Older revision		Revision as of 16:33, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)==		==Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)==
	<StructureSection load='3zhv' size='340' side='right' caption='[[3zhv]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3zhv' size='340' side='right' caption='[[3zhv]], [[Resolution\|resolution]] 2.30Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDW:2-[3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-[(1S)-1-OXIDANYLETHYL]-1,3-THIAZOL-3-IUM-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDW</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDW:2-[3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-[(1S)-1-OXIDANYLETHYL]-1,3-THIAZOL-3-IUM-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDW</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhq\|3zhq]], [[3zhr\|3zhr]], [[3zhs\|3zhs]], [[3zht\|3zht]], [[3zhu\|3zhu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhq\|3zhq]], [[3zhr\|3zhr]], [[3zhs\|3zhs]], [[3zht\|3zht]], [[3zhu\|3zhu]]</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=3zhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhv RCSB], [http://www.ebi.ac.uk/pdbsum/3zhv 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=3zhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhv OCA], [http://pdbe.org/3zhv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zhv RCSB], [http://www.ebi.ac.uk/pdbsum/3zhv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 3zhv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:01, 25 December 2014

OCA — Thu, 25 Dec 2014 11:01:39 GMT

←Older revision		Revision as of 11:01, 25 December 2014
Line 7:		Line 7:
	<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=3zhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhv RCSB], [http://www.ebi.ac.uk/pdbsum/3zhv 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=3zhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhv RCSB], [http://www.ebi.ac.uk/pdbsum/3zhv PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KGD_MYCS2 KGD_MYCS2]] Shows three enzymatic activities that share a first common step, the attack of thiamine-PP on 2-oxoglutarate (alpha-ketoglutarate, KG), leading to the formation of an enamine-thiamine-PP intermediate upon decarboxylation. Thus, displays KGD activity, catalyzing the decarboxylation from five-carbon 2-oxoglutarate to four-carbon succinate semialdehyde (SSA). Also catalyzes C-C bond formation between the activated aldehyde formed after decarboxylation of alpha-ketoglutarate and the carbonyl of glyoxylate (GLX), to yield 2-hydroxy-3-oxoadipate (HOA), which spontaneously decarboxylates to form 5-hydroxylevulinate (HLA). And is also a component of the 2-oxoglutarate dehydrogenase (ODH) complex, that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). The KG decarboxylase and KG dehydrogenase reactions provide two alternative, tightly regulated, pathways connecting the oxidative and reductive branches of the TCA cycle.<ref>PMID:19019160</ref> <ref>PMID:21867916</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:42, 21 December 2014

OCA — Sun, 21 Dec 2014 18:42:57 GMT

←Older revision		Revision as of 18:42, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3zhv\| PDB=3zhv \| SCENE= }}~~	+	==Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)==
-	===Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)===	+	<StructureSection load='3zhv' size='340' side='right' caption='[[3zhv]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24171907}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3zhv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZHV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDW:2-[3-[(4-AZANYL-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-2-[(1S)-1-OXIDANYLETHYL]-1,3-THIAZOL-3-IUM-5-YL]ETHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>TDW</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhq\|3zhq]], [[3zhr\|3zhr]], [[3zhs\|3zhs]], [[3zht\|3zht]], [[3zhu\|3zhu]]</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=3zhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhv RCSB], [http://www.ebi.ac.uk/pdbsum/3zhv PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	alpha-ketoacid dehydrogenases are large multi-enzyme machineries that orchestrate the oxidative decarboxylation of alpha-ketoacids with the concomitant production of acyl-CoA and NADH. The first reaction, catalysed by alpha-ketoacid decarboxylases (E1 enzymes), needs a thiamine diphosphate cofactor and represents the overall rate-limiting step. Although the catalytic cycles of E1 from the pyruvate dehydrogenase (E1p) and branched chain alpha-ketoacid dehydrogenase (E1b) complexes have been elucidated, little structural information is available on E1o, the first component of the alpha-ketoglutarate dehydrogenase complex, despite the central role of this complex at the branching point between the TCA cycle and glutamate metabolism. Here, we provide structural evidence that MsKGD, the E1o from Mycobacterium smegmatis, shows two conformations of the post-decarboxylation intermediate, each one associated with a distinct enzyme state. We also report an overall picture of the catalytic cycle, reconstructed by either crystallographic snapshots or modelling. Our results show that the conformational change leading the enzyme from the initial (early) to the late state, although not required for decarboxylation, plays an essential role in catalysis, and possibly in the regulation of mycobacterial E1o.

-	~~==Function==~~	+	A dual conformation of the post-decarboxylation intermediate is associated with distinct enzyme states in mycobacterial alpha-ketoglutarate decarboxylase (KGD).,Wagner T, Barilone N, Alzari PM, Bellinzoni M Biochem J. 2013 Oct 31. PMID:24171907<ref>PMID:24171907</ref>
-	~~[[http://www.uniprot.org/uniprot/KGD_MYCS2 KGD_MYCS2]] Shows three enzymatic activities that share a first common step, the attack~~ of ~~thiamine-PP on 2-oxoglutarate (alpha-ketoglutarate, KG), leading to~~ the ~~formation of an enamine~~-~~thiamine-PP~~ intermediate upon decarboxylation. Thus, displays KGD activity, catalyzing the decarboxylation from five-carbon 2-oxoglutarate to four-carbon succinate semialdehyde (SSA). Also catalyzes C-C bond formation between the activated aldehyde formed after decarboxylation of alpha-ketoglutarate ~~and the carbonyl of glyoxylate~~ (~~GLX~~), ~~to yield 2-hydroxy-3-oxoadipate (HOA)~~, ~~which spontaneously decarboxylates to form 5-hydroxylevulinate (HLA). And is also a component of the 2-oxoglutarate dehydrogenase (ODH) complex~~, ~~that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2)~~. ~~The KG decarboxylase and KG dehydrogenase reactions provide two alternative, tightly regulated, pathways connecting the oxidative and reductive branches of the TCA cycle~~.~~<ref>~~PMID:~~19019160</ref>~~ <ref>PMID:~~21867916~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3zhv]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHV OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024171907</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus smegmatis trevisan 1889]]		[[Category: Bacillus smegmatis trevisan 1889]]
-	[[Category: Alzari, P M.]]	+	[[Category: Alzari, P M]]
-	[[Category: Barilone, N.]]	+	[[Category: Barilone, N]]
-	[[Category: Bellinzoni, M.]]	+	[[Category: Bellinzoni, M]]
-	[[Category: Wagner, T.]]	+	[[Category: Wagner, T]]
	[[Category: E1o]]		[[Category: E1o]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 05:39, 29 January 2014

OCA — Wed, 29 Jan 2014 05:39:34 GMT

←Older revision		Revision as of 05:39, 29 January 2014
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3zhv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHV OCA].	+	[[3zhv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHV OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:024171907</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024171907</ref><references group="xtra"/><references/>
		+	[[Category: Bacillus smegmatis trevisan 1889]]
	[[Category: Alzari, P M.]]		[[Category: Alzari, P M.]]
	[[Category: Barilone, N.]]		[[Category: Barilone, N.]]

OCA at 08:13, 13 November 2013

OCA — Wed, 13 Nov 2013 08:13:59 GMT

←Older revision		Revision as of 08:13, 13 November 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3zhv\| PDB=3zhv \| SCENE= }}
		+	===Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)===
		+	{{ABSTRACT_PUBMED_24171907}}

-	~~The entry 3zhv~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/KGD_MYCS2 KGD_MYCS2]] Shows three enzymatic activities that share a first common step, the attack of thiamine-PP on 2-oxoglutarate (alpha-ketoglutarate, KG), leading to the formation of an enamine-thiamine-PP intermediate upon decarboxylation. Thus, displays KGD activity, catalyzing the decarboxylation from five-carbon 2-oxoglutarate to four-carbon succinate semialdehyde (SSA). Also catalyzes C-C bond formation between the activated aldehyde formed after decarboxylation of alpha-ketoglutarate and the carbonyl of glyoxylate (GLX), to yield 2-hydroxy-3-oxoadipate (HOA), which spontaneously decarboxylates to form 5-hydroxylevulinate (HLA). And is also a component of the 2-oxoglutarate dehydrogenase (ODH) complex, that catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2). The KG decarboxylase and KG dehydrogenase reactions provide two alternative, tightly regulated, pathways connecting the oxidative and reductive branches of the TCA cycle.<ref>PMID:19019160</ref> <ref>PMID:21867916</ref>

-	~~Authors: Wagner, T~~.~~, Barilone, N~~.~~, Bellinzoni, M~~.~~, Alzari, P~~.M.	+	==About this Structure==
		+	[[3zhv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHV OCA].

-	~~Description~~: ~~Crystal structure of the SucA domain of Mycobacterium smegmatis KGD showing an alpha-carbanion reaction intermediate from pyruvate (2-hydroxyethyl-ThDP)~~	+	==Reference==
		+	<ref group="xtra">PMID:024171907</ref><references group="xtra"/><references/>
		+	[[Category: Alzari, P M.]]
		+	[[Category: Barilone, N.]]
		+	[[Category: Bellinzoni, M.]]
		+	[[Category: Wagner, T.]]
		+	[[Category: E1o]]
		+	[[Category: Oxidoreductase]]

OCA at 13:34, 6 March 2013

OCA — Wed, 06 Mar 2013 13:34:26 GMT

←Older revision		Revision as of 13:34, 6 March 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3zhv is ON HOLD	+	The entry 3zhv is ON HOLD until Paper Publication

	Authors: Wagner, T., Barilone, N., Bellinzoni, M., Alzari, P.M.		Authors: Wagner, T., Barilone, N., Bellinzoni, M., Alzari, P.M.

	Description: Crystal structure of the SucA domain of Mycobacterium smegmatis KGD showing an alpha-carbanion reaction intermediate from pyruvate (2-hydroxyethyl-ThDP)		Description: Crystal structure of the SucA domain of Mycobacterium smegmatis KGD showing an alpha-carbanion reaction intermediate from pyruvate (2-hydroxyethyl-ThDP)

OCA at 13:11, 20 February 2013

OCA — Wed, 20 Feb 2013 13:11:59 GMT

←Older revision		Revision as of 13:11, 20 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3zhv is ON HOLD ~~until sometime in the future~~	+	The entry 3zhv is ON HOLD

	Authors: Wagner, T., Barilone, N., Bellinzoni, M., Alzari, P.M.		Authors: Wagner, T., Barilone, N., Bellinzoni, M., Alzari, P.M.

	Description: Crystal structure of the SucA domain of Mycobacterium smegmatis KGD showing an alpha-carbanion reaction intermediate from pyruvate (2-hydroxyethyl-ThDP)		Description: Crystal structure of the SucA domain of Mycobacterium smegmatis KGD showing an alpha-carbanion reaction intermediate from pyruvate (2-hydroxyethyl-ThDP)

OCA at 09:52, 13 February 2013

OCA — Wed, 13 Feb 2013 09:52:21 GMT

←Older revision		Revision as of 09:52, 13 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3zhv is ON HOLD	+	The entry 3zhv is ON HOLD until sometime in the future

	Authors: Wagner, T., Barilone, N., Bellinzoni, M., Alzari, P.M.		Authors: Wagner, T., Barilone, N., Bellinzoni, M., Alzari, P.M.

	Description: Crystal structure of the SucA domain of Mycobacterium smegmatis KGD showing an alpha-carbanion reaction intermediate from pyruvate (2-hydroxyethyl-ThDP)		Description: Crystal structure of the SucA domain of Mycobacterium smegmatis KGD showing an alpha-carbanion reaction intermediate from pyruvate (2-hydroxyethyl-ThDP)