7kjj - Revision history

OCA at 10:58, 15 November 2023

2023-11-15T10:58:25Z

←Older revision		Revision as of 10:58, 15 November 2023
Line 3:		Line 3:
	<StructureSection load='7kjj' size='340' side='right'caption='[[7kjj]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='7kjj' size='340' side='right'caption='[[7kjj]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7kjj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Miscellaneous_nucleic_acid Miscellaneous nucleic acid~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KJJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kjj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KJJ 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=T44:3,5,3,5-TETRAIODO-L-THYRONINE'>T44</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]] 1.55Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height~~: ~~3em;~~'>~~[[7kcn\|7kcn]]~~</~~div~~></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=T44:3,5,3,5-TETRAIODO-L-THYRONINE'>T44</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=7kjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kjj OCA], [https://pdbe.org/7kjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kjj RCSB], [https://www.ebi.ac.uk/pdbsum/7kjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kjj 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=7kjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kjj OCA], [https://pdbe.org/7kjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kjj RCSB], [https://www.ebi.ac.uk/pdbsum/7kjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kjj ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Miscellaneous nucleic acid~~]]	+	[[Category: Unidentified]]
-	[[Category: Bleicher, L]]	+	[[Category: Bleicher L]]
-	[[Category: Costa~~, M A.F~~]]	+	[[Category: Costa MAF]]
-	[[Category: Nagem~~, R A.P]]~~	+	[[Category: Nagem RAP]]
-	~~[[Category: Hormone transport]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 03:49, 2 July 2021

2021-07-02T03:49:41Z

←Older revision		Revision as of 03:49, 2 July 2021
Line 1:		Line 1:

	==Reconstructed ancestor of HIUases and Transthyretins==		==Reconstructed ancestor of HIUases and Transthyretins==
-	<StructureSection load='7kjj' size='340' side='right'caption='[[7kjj]]' scene=''>	+	<StructureSection load='7kjj' size='340' side='right'caption='[[7kjj]], [[Resolution\|resolution]] 1.55Å' 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=7KJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KJJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kjj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Miscellaneous_nucleic_acid Miscellaneous nucleic acid]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KJJ 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=7kjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kjj OCA], [https://pdbe.org/7kjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kjj RCSB], [https://www.ebi.ac.uk/pdbsum/7kjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kjj 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=T44:3,5,3,5-TETRAIODO-L-THYRONINE'>T44</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;'>[[7kcn\|7kcn]]</div></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=7kjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kjj OCA], [https://pdbe.org/7kjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kjj RCSB], [https://www.ebi.ac.uk/pdbsum/7kjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kjj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transthyretin was discovered in the 1940s, named after its ability to bind thyroid hormones and retinol. In the genomic era, transthyretins were found to be part of a larger family with homologs of no obvious function, then called transthyretin-related proteins. Thus, it was proposed that the transthyretin gene could be the result of gene duplication of an ancestral of this newly identified homolog, later found out to be an enzyme involved in uric acid degradation, then named HIUase (5-hydroxy-isourate hydrolase). Here, we sought to re-enact the evolutionary history of this protein family by reconstructing, from a phylogeny inferred from 123 vertebrate sequences, three ancestors corresponding to key moments in their evolution-before duplication; the common transthyretin ancestor after gene duplication and the common ancestor of Eutheria transthyretins. Experimental and computational characterization showed the reconstructed ancestor before duplication was unable to bind thyroxine and likely presented the modern HIUase reaction mechanism, while the substitutions after duplication prevented that activity and were enough to provide stable thyroxine binding, as confirmed by calorimetry and x-ray diffraction. The Eutheria transthyretin ancestor was less prone to characterization, but limited data suggested thyroxine binding as expected. Sequence/structure analysis suggests an early ability to bind the Retinol Binding Protein. We solved the X-ray structures from the two first ancestors, the first at 1.46 resolution, the second at 1.55 resolution with well-defined electron density for thyroxine, providing a useful tool for the understanding of structural adaptation from enzyme to hormone distributor.
		+
		+	Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies.,Carrijo de Oliveira L, Figueiredo Costa MA, Goncalves Pedersolli N, Heleno Batista FA, Migliorini Figueira AC, Salgado Ferreira R, Alves Pinto Nagem R, Alves Nahum L, Bleicher L J Mol Evol. 2021 May 6. pii: 10.1007/s00239-021-10010-8. doi:, 10.1007/s00239-021-10010-8. PMID:33956179<ref>PMID:33956179</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kjj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bleicher L]]	+	[[Category: Miscellaneous nucleic acid]]
-	[[Category: Costa ~~MAF~~]]	+	[[Category: Bleicher, L]]
-	[[Category: Nagem ~~RAP~~]]	+	[[Category: Costa, M A.F]]
		+	[[Category: Nagem, R A.P]]
		+	[[Category: Hormone transport]]
		+	[[Category: Transport protein]]

OCA at 10:09, 19 May 2021

2021-05-19T10:09:54Z

←Older revision		Revision as of 10:09, 19 May 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7kjj ~~is ON HOLD until Paper Publication~~	+	==Reconstructed ancestor of HIUases and Transthyretins==
-		+	<StructureSection load='7kjj' size='340' side='right'caption='[[7kjj]]' scene=''>
-	~~Authors~~: ~~Nagem~~, R.A.P., ~~Bleicher~~, L., ~~Costa, M~~.A.F.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KJJ FirstGlance]. <br>
-	~~Description: Reconstructed ancestor of HIUases and Transthyretins~~	+	</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=7kjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kjj OCA], [https://pdbe.org/7kjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kjj RCSB], [https://www.ebi.ac.uk/pdbsum/7kjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kjj ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Costa, M.A.F~~]]	+	__TOC__
-	[[Category: ~~Nagem, R.A.P~~]]	+	</StructureSection>
-	[[Category: ~~Bleicher, L~~]]	+	[[Category: Large Structures]]
		+	[[Category: Bleicher L]]
		+	[[Category: Costa MAF]]
		+	[[Category: Nagem RAP]]

OCA at 08:07, 18 November 2020

2020-11-18T08:07:39Z

←Older revision		Revision as of 08:07, 18 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Nagem, R.A.P., Bleicher, L., Costa, M.A.F.		Authors: Nagem, R.A.P., Bleicher, L., Costa, M.A.F.

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

2020-11-04T05:38:49Z

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

←Older revision

Revision as of 05:38, 4 November 2020

OCA: New page: '''Unreleased structure''' The entry 7kjj is ON HOLD Authors: Nagem, R.A.P., Bleicher, L., Costa, M.A.F. Description: Reconstructed ancestor of HIUases and Transthyretins [[Category: U...

2020-11-04T05:38:48Z

New page: '''Unreleased structure''' The entry 7kjj is ON HOLD Authors: Nagem, R.A.P., Bleicher, L., Costa, M.A.F. Description: Reconstructed ancestor of HIUases and Transthyretins [[Category: U...

New page

'''Unreleased structure'''

The entry 7kjj is ON HOLD

Authors: Nagem, R.A.P., Bleicher, L., Costa, M.A.F.

Description: Reconstructed ancestor of HIUases and Transthyretins
[[Category: Unreleased Structures]]
[[Category: Costa, M.A.F]]
[[Category: Nagem, R.A.P]]
[[Category: Bleicher, L]]