7ool - Revision history

OCA at 12:53, 1 February 2024

2024-02-01T12:53:46Z

←Older revision		Revision as of 12:53, 1 February 2024
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	<StructureSection load='7ool' size='340' side='right'caption='[[7ool]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='7ool' size='340' side='right'caption='[[7ool]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ool]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ool]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Photodesmus_katoptron Candidatus Photodesmus katoptron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OOL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.85Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ool FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ool OCA], [https://pdbe.org/7ool PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ool RCSB], [https://www.ebi.ac.uk/pdbsum/7ool PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ool 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=7ool FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ool OCA], [https://pdbe.org/7ool PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ool RCSB], [https://www.ebi.ac.uk/pdbsum/7ool PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ool ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/S3DGC4_9GAMM S3DGC4_9GAMM]
	<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: Candidatus Photodesmus katoptron]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gamiz-Arco, G]]	+	[[Category: Gamiz-Arco G]]
-	[[Category: Gavira~~, J A~~]]	+	[[Category: Gavira JA]]
-	[[Category: Ibarra-Molero, B]]	+	[[Category: Ibarra-Molero B]]
-	[[Category: Risso, V]]	+	[[Category: Risso V]]
-	[[Category: Sanchez-Ruiz~~, J M]]~~	+	[[Category: Sanchez-Ruiz JM]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Quimera from ancestral lpbca~~]]	+

OCA at 12:49, 24 November 2021

2021-11-24T12:49:33Z

←Older revision		Revision as of 12:49, 24 November 2021
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	==Crystal structure of a Candidatus photodesmus katoptron thioredoxin chimera containing an ancestral loop==		==Crystal structure of a Candidatus photodesmus katoptron thioredoxin chimera containing an ancestral loop==
-	<StructureSection load='7ool' size='340' side='right'caption='[[7ool]]' scene=''>	+	<StructureSection load='7ool' size='340' side='right'caption='[[7ool]], [[Resolution\|resolution]] 2.85Å' 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=7OOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ool]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OOL 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=7ool FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ool OCA], [https://pdbe.org/7ool PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ool RCSB], [https://www.ebi.ac.uk/pdbsum/7ool PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ool 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ool FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ool OCA], [https://pdbe.org/7ool PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ool RCSB], [https://www.ebi.ac.uk/pdbsum/7ool PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ool ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Obligate symbionts typically exhibit high evolutionary rates. Consequently, their proteins may differ considerably from their modern and ancestral homologs in terms of both sequence and properties, thus providing excellent models to study protein evolution. Also, obligate symbionts are challenging to culture in the lab and proteins from uncultured organisms must be produced in heterologous hosts using recombinant DNA technology. Obligate symbionts thus replicate a fundamental scenario of metagenomics studies aimed at the functional characterization and biotechnological exploitation of proteins from the bacteria in soil. Here, we use the thioredoxin from Candidatus Photodesmus katoptron, an uncultured symbiont of flashlight fish, to explore evolutionary and engineering aspects of protein folding in heterologous hosts. The symbiont protein is a standard thioredoxin in terms of 3D-structure, stability and redox activity. However, its folding outside the original host is severely impaired, as shown by a very slow refolding in vitro and an inefficient expression in E. coli that leads mostly to insoluble protein. By contrast, resurrected Precambrian thioredoxins express efficiently in E. coli, plausibly reflecting an ancient adaptation to unassisted folding. We have used a statistical-mechanical model of the folding landscape to guide back-to-ancestor engineering of the symbiont protein. Remarkably, we find that the efficiency of heterologous expression correlates with the in vitro (i.e., unassisted) folding rate and that the ancestral expression efficiency can be achieved with only 1-2 back-to-ancestor replacements. These results demonstrate a minimal-perturbation, sequence-engineering approach to rescue inefficient heterologous expression which may potentially be useful in metagenomics efforts targeting recent adaptations.
		+
		+	Combining ancestral reconstruction with folding-landscape simulations to engineer heterologous protein expression.,Gamiz-Arco G, Risso VA, Gaucher EA, Gavira JA, Naganathan AN, Ibarra-Molero B, Sanchez-Ruiz JM J Mol Biol. 2021 Oct 20:167321. doi: 10.1016/j.jmb.2021.167321. PMID:34687715<ref>PMID:34687715</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ool" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gamiz-Arco G]]	+	[[Category: Gamiz-Arco, G]]
-	[[Category: Gavira JA]]	+	[[Category: Gavira, J A]]
-	[[Category: Ibarra-Molero B]]	+	[[Category: Ibarra-Molero, B]]
-	[[Category: Risso V]]	+	[[Category: Risso, V]]
-	[[Category: Sanchez-Ruiz JM]]	+	[[Category: Sanchez-Ruiz, J M]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Quimera from ancestral lpbca]]

OCA at 06:16, 10 November 2021

2021-11-10T06:16:16Z

←Older revision		Revision as of 06:16, 10 November 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7ool ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of a Candidatus photodesmus katoptron thioredoxin chimera containing an ancestral loop==
-		+	<StructureSection load='7ool' size='340' side='right'caption='[[7ool]]' scene=''>
-	~~Authors~~: ~~Gavira, J~~.A.~~, Ibarra~~-~~Molero, B~~., ~~Gamiz~~-~~Arco~~, G., ~~Risso~~, V., ~~Sanchez~~-~~Ruiz, J.M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OOL FirstGlance]. <br>
-	~~Description: Crystal structure of a Candidatus photodesmus katoptron thioredoxin chimera containing an ancestral loop~~	+	</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=7ool FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ool OCA], [https://pdbe.org/7ool PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ool RCSB], [https://www.ebi.ac.uk/pdbsum/7ool PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ool ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Risso, V~~]]	+	__TOC__
-	[[Category: Gavira~~, J.A~~]]	+	</StructureSection>
-	[[Category: Ibarra-Molero, B]]	+	[[Category: Large Structures]]
-	[[Category: ~~Gamiz-Arco, G~~]]	+	[[Category: Gamiz-Arco G]]
-	[[Category: Sanchez-Ruiz~~, J.M~~]]	+	[[Category: Gavira JA]]
		+	[[Category: Ibarra-Molero B]]
		+	[[Category: Risso V]]
		+	[[Category: Sanchez-Ruiz JM]]

OCA at 11:13, 9 June 2021

2021-06-09T11:13:04Z

←Older revision		Revision as of 11:13, 9 June 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Gavira, J.A., Ibarra-Molero, B., Gamiz-Arco, G., Risso, V., Sanchez-Ruiz, J.M.		Authors: Gavira, J.A., Ibarra-Molero, B., Gamiz-Arco, G., Risso, V., Sanchez-Ruiz, J.M.

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

2021-06-02T13:41:29Z

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

←Older revision

Revision as of 13:41, 2 June 2021

OCA: New page: '''Unreleased structure''' The entry 7ool is ON HOLD Authors: Gavira, J.A., Ibarra-Molero, B., Gamiz-Arco, G., Risso, V., Sanchez-Ruiz, J.M. Description: Crystal structure of a Candida...

2021-06-02T13:41:28Z

New page: '''Unreleased structure''' The entry 7ool is ON HOLD Authors: Gavira, J.A., Ibarra-Molero, B., Gamiz-Arco, G., Risso, V., Sanchez-Ruiz, J.M. Description: Crystal structure of a Candida...

New page

'''Unreleased structure'''

The entry 7ool is ON HOLD

Authors: Gavira, J.A., Ibarra-Molero, B., Gamiz-Arco, G., Risso, V., Sanchez-Ruiz, J.M.

Description: Crystal structure of a Candidatus photodesmus katoptron thioredoxin chimera containing an ancestral loop
[[Category: Unreleased Structures]]
[[Category: Risso, V]]
[[Category: Gavira, J.A]]
[[Category: Ibarra-Molero, B]]
[[Category: Gamiz-Arco, G]]
[[Category: Sanchez-Ruiz, J.M]]