7eps - Revision history

OCA at 16:59, 29 November 2023

2023-11-29T16:59:34Z

←Older revision		Revision as of 16:59, 29 November 2023
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	==Partial Consensus L-threonine 3-dehydrogenase (E-change)==		==Partial Consensus L-threonine 3-dehydrogenase (E-change)==
-	<StructureSection load='7eps' size='340' side='right'caption='[[7eps]]' scene=''>	+	<StructureSection load='7eps' size='340' side='right'caption='[[7eps]], [[Resolution\|resolution]] 2.10Å' 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=7EPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7eps]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPS 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=7eps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eps OCA], [https://pdbe.org/7eps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eps RCSB], [https://www.ebi.ac.uk/pdbsum/7eps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eps ProSAT]</span></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]] 2.102Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=THR:THREONINE'>THR</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=7eps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eps OCA], [https://pdbe.org/7eps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eps RCSB], [https://www.ebi.ac.uk/pdbsum/7eps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eps ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Consensus design (CD) is a representative sequence-based protein design method that enables the design of highly functional proteins by analyzing vast amounts of protein sequence data. This study proposes a partial consensus design (PCD) of a protein as a derivative approach of CD. The method replaces the target protein sequence with a consensus sequence in a secondary-structure-dependent manner (i.e., regionally dependent and divided into alpha-helix, beta-sheet, and loop regions). In this study, we generated several artificial partial consensus l-threonine 3-dehydrogenases (PcTDHs) by PCD using the TDH from Cupriavidus necator (CnTDH) as a target protein. Structural and functional analysis of PcTDHs suggested that thermostability would be independently improved when consensus mutations are introduced into the loop region of TDHs. On the other hand, enzyme kinetic parameters (kcat/Km) and average productivity would be synergistically enhanced by changing the combination of the mutations-replacement of one region of CnTDH with a consensus sequence provided only negative effects, but the negative effects were nullified when the two regions were replaced simultaneously. Taken together, we propose the hypothesis that there are protein regions that encode individual protein properties, such as thermostability and activity, and that the introduction of consensus mutations into these regions could additively or synergistically modify their functions.
		+
		+	Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations.,Kozuka K, Nakano S, Asano Y, Ito S Biochemistry. 2021 Jul 27;60(29):2309-2319. doi: 10.1021/acs.biochem.1c00309., Epub 2021 Jul 13. PMID:34254784<ref>PMID:34254784</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7eps" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Synthetic construct]]
	[[Category: Asano Y]]		[[Category: Asano Y]]
	[[Category: Ito S]]		[[Category: Ito S]]
	[[Category: Kozuka K]]		[[Category: Kozuka K]]
	[[Category: Nakano S]]		[[Category: Nakano S]]

OCA at 06:06, 11 August 2021

2021-08-11T06:06:35Z

←Older revision		Revision as of 06:06, 11 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7eps ~~is ON HOLD until Paper Publication~~	+	==Partial Consensus L-threonine 3-dehydrogenase (E-change)==
-		+	<StructureSection load='7eps' size='340' side='right'caption='[[7eps]]' scene=''>
-	~~Authors~~: ~~Kozuka~~, K., ~~Nakano, S~~., ~~Asano, Y~~., ~~Ito~~, S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPS FirstGlance]. <br>
-	~~Description: Partial Consensus L-threonine 3-dehydrogenase (E-change)~~	+	</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=7eps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eps OCA], [https://pdbe.org/7eps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eps RCSB], [https://www.ebi.ac.uk/pdbsum/7eps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eps ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Asano, Y]]	+	__TOC__
-	[[Category: Ito, S]]	+	</StructureSection>
-	[[Category: ~~Nakano, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kozuka, K~~]]	+	[[Category: Asano Y]]
		+	[[Category: Ito S]]
		+	[[Category: Kozuka K]]
		+	[[Category: Nakano S]]

OCA at 08:41, 19 May 2021

2021-05-19T08:41:31Z

←Older revision		Revision as of 08:41, 19 May 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kozuka, K., Nakano, S., Asano, Y., Ito, S.		Authors: Kozuka, K., Nakano, S., Asano, Y., Ito, S.

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

2021-05-05T07:19:47Z

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

←Older revision

Revision as of 07:19, 5 May 2021

OCA: New page: '''Unreleased structure''' The entry 7eps is ON HOLD Authors: Kozuka, K., Nakano, S., Asano, Y., Ito, S. Description: Partial Consensus L-threonine 3-dehydrogenase (E-change) [[Categor...

2021-05-05T07:19:46Z

New page: '''Unreleased structure''' The entry 7eps is ON HOLD Authors: Kozuka, K., Nakano, S., Asano, Y., Ito, S. Description: Partial Consensus L-threonine 3-dehydrogenase (E-change) [[Categor...

New page

'''Unreleased structure'''

The entry 7eps is ON HOLD

Authors: Kozuka, K., Nakano, S., Asano, Y., Ito, S.

Description: Partial Consensus L-threonine 3-dehydrogenase (E-change)
[[Category: Unreleased Structures]]
[[Category: Asano, Y]]
[[Category: Ito, S]]
[[Category: Nakano, S]]
[[Category: Kozuka, K]]