7f4c - Revision history

OCA at 17:09, 29 November 2023

2023-11-29T17:09:19Z

←Older revision		Revision as of 17:09, 29 November 2023
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	<StructureSection load='7f4c' size='340' side='right'caption='[[7f4c]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='7f4c' size='340' side='right'caption='[[7f4c]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7f4c]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F4C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7f4c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F4C FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BU1:1,4~~-~~BUTANEDIOL'>BU1</scene>~~, ~~<scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[7f4b\|7f4b]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Homoserine_dehydrogenase Homoserine dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.3 1.1.1.3]~~ </~~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=7f4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f4c OCA], [https://pdbe.org/7f4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f4c RCSB], [https://www.ebi.ac.uk/pdbsum/7f4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f4c 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=7f4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f4c OCA], [https://pdbe.org/7f4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f4c RCSB], [https://www.ebi.ac.uk/pdbsum/7f4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f4c ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F9VNG5_SULTO F9VNG5_SULTO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Homoserine dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Goto, M]]	+	[[Category: Sulfurisphaera tokodaii str. 7]]
-	[[Category: Kaneko, R]]	+	[[Category: Goto M]]
-	[[Category: Kubota, T]]	+	[[Category: Kaneko R]]
-	[[Category: Kurihara, E]]	+	[[Category: Kubota T]]
-	[[Category: Ogata, K]]	+	[[Category: Kurihara E]]
-	[[Category: Oshima, T]]	+	[[Category: Ogata K]]
-	[[Category: Watanabe, K]]	+	[[Category: Oshima T]]
-	[[Category: Yoshimune, K]]	+	[[Category: Watanabe K]]
-	~~[[Category: Heat-induced activation]]~~	+	[[Category: Yoshimune K]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 05:06, 10 August 2022

2022-08-10T05:06:29Z

←Older revision		Revision as of 05:06, 10 August 2022
Line 1:		Line 1:

	==The crystal structure of the immature holo-enzyme of homoserine dehydrogenase complexed with NADP and 1,4-butandiol from the hyperthermophilic archaeon Sulfurisphaera tokodaii.==		==The crystal structure of the immature holo-enzyme of homoserine dehydrogenase complexed with NADP and 1,4-butandiol from the hyperthermophilic archaeon Sulfurisphaera tokodaii.==
-	<StructureSection load='7f4c' size='340' side='right'caption='[[7f4c]]' scene=''>	+	<StructureSection load='7f4c' size='340' side='right'caption='[[7f4c]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F4C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7f4c]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F4C FirstGlance]. <br>
-	</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=7f4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f4c OCA], [https://pdbe.org/7f4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f4c RCSB], [https://www.ebi.ac.uk/pdbsum/7f4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f4c ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU1:1,4-BUTANEDIOL'>BU1</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7f4b\|7f4b]]</div></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Homoserine_dehydrogenase Homoserine dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.3 1.1.1.3] </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=7f4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f4c OCA], [https://pdbe.org/7f4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f4c RCSB], [https://www.ebi.ac.uk/pdbsum/7f4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f4c ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	When overexpressed as an immature enzyme in the mesophilic bacterium Escherichia coli, recombinant homoserine dehydrogenase from the hyperthermophilic archaeon Sulfurisphaera tokodaii (StHSD) was markedly activated by heat treatment. Both the apo- and holo-forms of the immature enzyme were successively crystallized, and the two structures were determined. Comparison among the structures of the immature enzyme and previously reported structures of mature enzymes revealed that a conformational change in a flexible part (residues 160-190) of the enzyme, which encloses substrates within the substrate-binding pocket, is smaller in the immature enzyme. The immature enzyme, but not the mature enzyme, formed a complex that included NADP(+), despite its absence during crystallization. This indicates that the opening to the substrate-binding pocket in the immature enzyme is not sufficient for substrate-binding, efficient catalytic turnover or release of NADP(+). Thus, specific conformational changes within the catalytic region appear to be responsible for heat-induced activation.
		+
		+	Conformational changes in the catalytic region are responsible for heat-induced activation of hyperthermophilic homoserine dehydrogenase.,Kubota T, Kurihara E, Watanabe K, Ogata K, Kaneko R, Goto M, Ohshima T, Yoshimune K Commun Biol. 2022 Jul 14;5(1):704. doi: 10.1038/s42003-022-03656-7. PMID:35835834<ref>PMID:35835834</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7f4c" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homoserine dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Goto M]]	+	[[Category: Goto, M]]
-	[[Category: Kaneko R]]	+	[[Category: Kaneko, R]]
-	[[Category: Kubota T]]	+	[[Category: Kubota, T]]
-	[[Category: Kurihara E]]	+	[[Category: Kurihara, E]]
-	[[Category: Ogata K]]	+	[[Category: Ogata, K]]
-	[[Category: Oshima T]]	+	[[Category: Oshima, T]]
-	[[Category: Watanabe K]]	+	[[Category: Watanabe, K]]
-	[[Category: Yoshimune K]]	+	[[Category: Yoshimune, K]]
		+	[[Category: Heat-induced activation]]
		+	[[Category: Oxidoreductase]]

OCA at 09:43, 22 June 2022

2022-06-22T09:43:09Z

←Older revision		Revision as of 09:43, 22 June 2022
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-	'''Unreleased structure'''

-	~~The entry 7f4c is ON HOLD until Paper Publication~~	+	==The crystal structure of the immature holo-enzyme of homoserine dehydrogenase complexed with NADP and 1,4-butandiol from the hyperthermophilic archaeon Sulfurisphaera tokodaii.==
-		+	<StructureSection load='7f4c' size='340' side='right'caption='[[7f4c]]' scene=''>
-	~~Authors: Ogata, K., Kaneko, R., Kubota, T., Watanabe, K., Kurihara, E., Oshima, T., Yoshimune, K., Goto, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F4C FirstGlance]. <br>
-	~~Description:~~ The crystal structure of the immature holo-enzyme of homoserine dehydrogenase complexed with NADP and 1,4-butandiol from the hyperthermophilic archaeon Sulfurisphaera tokodaii.	+	</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=7f4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f4c OCA], [https://pdbe.org/7f4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f4c RCSB], [https://www.ebi.ac.uk/pdbsum/7f4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f4c ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Watanabe, K~~]]	+	__TOC__
-	[[Category: Kaneko, R]]	+	</StructureSection>
-	[[Category: ~~Oshima,~~ T]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kubota, T~~]]	+	[[Category: Goto M]]
-	[[Category: ~~Yoshimune,~~ K]]	+	[[Category: Kaneko R]]
-	[[Category: ~~Goto, M~~]]	+	[[Category: Kubota T]]
-	[[Category: ~~Kurihara, E~~]]	+	[[Category: Kurihara E]]
-	[[Category: ~~Ogata,~~ K]]	+	[[Category: Ogata K]]
		+	[[Category: Oshima T]]
		+	[[Category: Watanabe K]]
		+	[[Category: Yoshimune K]]

OCA at 11:57, 17 November 2021

2021-11-17T11:57:13Z

←Older revision		Revision as of 11:57, 17 November 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7f4c is ON HOLD	+	The entry 7f4c is ON HOLD until Paper Publication

	Authors: Ogata, K., Kaneko, R., Kubota, T., Watanabe, K., Kurihara, E., Oshima, T., Yoshimune, K., Goto, M.		Authors: Ogata, K., Kaneko, R., Kubota, T., Watanabe, K., Kurihara, E., Oshima, T., Yoshimune, K., Goto, M.

OCA: Protected "7f4c" [edit=sysop:move=sysop]

2021-06-25T06:08:18Z

Protected "7f4c" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:08, 25 June 2021

OCA: New page: '''Unreleased structure''' The entry 7f4c is ON HOLD Authors: Ogata, K., Kaneko, R., Kubota, T., Watanabe, K., Kurihara, E., Oshima, T., Yoshimune, K., Goto, M. Description: The crysta...

2021-06-25T06:08:17Z

New page: '''Unreleased structure''' The entry 7f4c is ON HOLD Authors: Ogata, K., Kaneko, R., Kubota, T., Watanabe, K., Kurihara, E., Oshima, T., Yoshimune, K., Goto, M. Description: The crysta...

New page

'''Unreleased structure'''

The entry 7f4c is ON HOLD

Authors: Ogata, K., Kaneko, R., Kubota, T., Watanabe, K., Kurihara, E., Oshima, T., Yoshimune, K., Goto, M.

Description: The crystal structure of the immature holo-enzyme of homoserine dehydrogenase complexed with NADP and 1,4-butandiol from the hyperthermophilic archaeon Sulfurisphaera tokodaii.
[[Category: Unreleased Structures]]
[[Category: Watanabe, K]]
[[Category: Kaneko, R]]
[[Category: Oshima, T]]
[[Category: Kubota, T]]
[[Category: Yoshimune, K]]
[[Category: Goto, M]]
[[Category: Kurihara, E]]
[[Category: Ogata, K]]