5hn4 - Revision history

OCA at 10:47, 16 August 2023

OCA — Wed, 16 Aug 2023 10:47:39 GMT

←Older revision		Revision as of 10:47, 16 August 2023
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	<StructureSection load='5hn4' size='340' side='right'caption='[[5hn4]], [[Resolution\|resolution]] 2.64Å' scene=''>		<StructureSection load='5hn4' size='340' side='right'caption='[[5hn4]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hn4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HN4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hn4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HN4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=48Y:(1R,2S)-1-HYDROXYBUTANE-1,2,4-TRICARBOXYLIC+ACID'>48Y</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.64Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hn6\|5hn6]], [[5hn5\|5hn5]], [[5hn3\|5hn3]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=48Y:(1R,2S)-1-HYDROXYBUTANE-1,2,4-TRICARBOXYLIC+ACID'>48Y</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK0280 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=5hn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn4 OCA], [https://pdbe.org/5hn4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hn4 RCSB], [https://www.ebi.ac.uk/pdbsum/5hn4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn4 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5hn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn4 OCA], [~~http~~://pdbe.org/5hn4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hn4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hn4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn4 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5JFV8_THEKO Q5JFV8_THEKO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Nishiyama, M~~]]	+	[[Category: Thermococcus kodakarensis KOD1]]
-	[[Category: ~~Shimizu, T~~]]	+	[[Category: Nishiyama M]]
-	[[Category: ~~Tomita,~~ T]]	+	[[Category: Shimizu T]]
-	[[Category: ~~Beta-decarboxylating dehydrogenase]]~~	+	[[Category: Tomita T]]
-	~~[[Category: Homoisocitrate dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:15, 19 February 2020

OCA — Wed, 19 Feb 2020 07:15:59 GMT

←Older revision		Revision as of 07:15, 19 February 2020
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	==Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and homoisocitrate==		==Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and homoisocitrate==
-	<StructureSection load='5hn4' size='340' side='right' caption='[[5hn4]], [[Resolution\|resolution]] 2.64Å' scene=''>	+	<StructureSection load='5hn4' size='340' side='right'caption='[[5hn4]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hn4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HN4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hn4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HN4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=48Y:(1R,2S)-1-HYDROXYBUTANE-1,2,4-TRICARBOXYLIC+ACID'>48Y</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=48Y:(1R,2S)-1-HYDROXYBUTANE-1,2,4-TRICARBOXYLIC+ACID'>48Y</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hn6\|5hn6]], [[5hn5\|5hn5]], [[5hn3\|5hn3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hn6\|5hn6]], [[5hn5\|5hn5]], [[5hn3\|5hn3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK0280 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=5hn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn4 OCA], [http://pdbe.org/5hn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hn4 RCSB], [http://www.ebi.ac.uk/pdbsum/5hn4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn4 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5hn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn4 OCA], [http://pdbe.org/5hn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hn4 RCSB], [http://www.ebi.ac.uk/pdbsum/5hn4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn4 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Nishiyama, M]]		[[Category: Nishiyama, M]]
	[[Category: Shimizu, T]]		[[Category: Shimizu, T]]

OCA at 19:38, 9 December 2016

OCA — Fri, 09 Dec 2016 19:38:35 GMT

←Older revision		Revision as of 19:38, 9 December 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5hn4 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and homoisocitrate==
		+	<StructureSection load='5hn4' size='340' side='right' caption='[[5hn4]], [[Resolution\|resolution]] 2.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hn4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HN4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HN4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=48Y:(1R,2S)-1-HYDROXYBUTANE-1,2,4-TRICARBOXYLIC+ACID'>48Y</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hn6\|5hn6]], [[5hn5\|5hn5]], [[5hn3\|5hn3]]</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=5hn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hn4 OCA], [http://pdbe.org/5hn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hn4 RCSB], [http://www.ebi.ac.uk/pdbsum/5hn4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hn4 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	beta-Decarboxylating dehydrogenases, which are involved in central metabolism, are considered to have diverged from a common ancestor with broad substrate specificity. In a molecular phylogenetic analysis of 183 beta-decarboxylating dehydrogenase homologs from 84 species, TK0280 from Thermococcus kodakarensis was selected as a candidate for an ancestral-type beta-decarboxylating dehydrogenase. The biochemical characterization of recombinant TK0280 revealed that the enzyme exhibited dehydrogenase activities toward homoisocitrate, isocitrate, and 3-isopropylmalate, which correspond to key reactions involved in the lysine biosynthetic pathway, tricarboxylic acid cycle, and leucine biosynthetic pathway, respectively. In T. kodakarensis , the growth characteristics of the KUW1 host strain and a TK0280 deletion strain suggested that TK0280 is involved in lysine biosynthesis in this archaeon. On the other hand, gene complementation analyses using Thermus thermophilus as a host revealed that TK0280 functions as both an isocitrate dehydrogenase and homoisocitrate dehydrogenase in this organism, but not as 3-isopropylmalate dehydrogenase, most likely reflecting its low catalytic efficiency towards 3-isopropylmalate. A crystallographic study on TK0280 binding each substrate indicated that Thr71 and Ser80 played important roles in the recognition of homoisocitrate and isocitrate while the hydrophobic region consisting of Ile82 and Leu83 was responsible for the recognition of 3-isopropylmalate. These analyses also suggested the importance of a water-mediated hydrogen bond network for the stabilization of the beta3-alpha4 loop, including the Thr71 residue, with respect to the promiscuity of the substrate specificity of TK0280.

-	~~Authors:~~ Shimizu, T., Tomita, T., Nishiyama, M.	+	Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis.,Shimizu T, Yin L, Yoshida A, Yokooji Y, Hachisuka SI, Sato T, Tomita T, Nishida H, Atomi H, Kuzuyama T, Nishiyama M Biochem J. 2016 Nov 9. pii: BCJ20160699. PMID:27831491<ref>PMID:27831491</ref>

-	~~Description: Crystal structure~~ of ~~beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and homoisocitrate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Tomita, T]]~~	+	<div class="pdbe-citations 5hn4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Nishiyama, M]]		[[Category: Nishiyama, M]]
	[[Category: Shimizu, T]]		[[Category: Shimizu, T]]
		+	[[Category: Tomita, T]]
		+	[[Category: Beta-decarboxylating dehydrogenase]]
		+	[[Category: Homoisocitrate dehydrogenase]]
		+	[[Category: Oxidoreductase]]

OCA at 14:02, 3 February 2016

OCA — Wed, 03 Feb 2016 14:02:13 GMT

←Older revision		Revision as of 14:02, 3 February 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hn4 is ON HOLD	+	The entry 5hn4 is ON HOLD until Paper Publication

	Authors: Shimizu, T., Tomita, T., Nishiyama, M.		Authors: Shimizu, T., Tomita, T., Nishiyama, M.

OCA: Protected "5hn4" [edit=sysop:move=sysop]

OCA — Thu, 28 Jan 2016 00:54:56 GMT

Protected "5hn4" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:54, 28 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hn4 is ON HOLD Authors: Shimizu, T., Tomita, T., Nishiyama, M. Description: Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from ...

OCA — Thu, 28 Jan 2016 00:54:54 GMT

New page: '''Unreleased structure''' The entry 5hn4 is ON HOLD Authors: Shimizu, T., Tomita, T., Nishiyama, M. Description: Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from ...

New page

'''Unreleased structure'''

The entry 5hn4 is ON HOLD

Authors: Shimizu, T., Tomita, T., Nishiyama, M.

Description: Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and homoisocitrate
[[Category: Unreleased Structures]]
[[Category: Tomita, T]]
[[Category: Nishiyama, M]]
[[Category: Shimizu, T]]