OCA at 12:59, 24 January 2024

OCA — Wed, 24 Jan 2024 12:59:33 GMT

←Older revision		Revision as of 12:59, 24 January 2024
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	==Crystal structure of Salmo salar RidA-2==		==Crystal structure of Salmo salar RidA-2==
-	<StructureSection load='6tcd' size='340' side='right'caption='[[6tcd]]' scene=''>	+	<StructureSection load='6tcd' size='340' side='right'caption='[[6tcd]], [[Resolution\|resolution]] 1.36Å' 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=6TCD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TCD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tcd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmo_salar Salmo salar]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TCD FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6tcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tcd OCA], [~~http~~://pdbe.org/6tcd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tcd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tcd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tcd 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]] 1.36Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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=6tcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tcd OCA], [https://pdbe.org/6tcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tcd RCSB], [https://www.ebi.ac.uk/pdbsum/6tcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tcd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/C0H8I4_SALSA C0H8I4_SALSA] Catalyzes the hydrolytic deamination of enamine/imine intermediates that form during the course of normal metabolism. May facilitate the release of ammonia from these potentially toxic reactive metabolites, reducing their impact on cellular components. It may act on enamine/imine intermediates formed by several types of pyridoxal-5'-phosphate-dependent dehydratases including L-threonine dehydratase.[ARBA:ARBA00002596]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Reactive Intermediate Deaminase (Rid) protein superfamily includes eight families among which the RidA is conserved in all domains of life. RidA proteins accelerate the deamination of the reactive 2-aminoacrylate (2AA), an enamine produced by some pyridoxal phosphate (PLP)-dependent enzymes. 2AA accumulation inhibits target enzymes with a detrimental impact on fitness. As a consequence of whole genome duplication, teleost fish have two ridA paralogs, while other extant vertebrates contain a single-copy gene. We investigated the biochemical properties of the products of two paralogs, identified in Salmo salar. SsRidA-1 and SsRidA-2 complemented the growth defect of a Salmonella enterica ridA mutant, an in vivo model of 2AA stress. In vitro, both proteins hydrolyzed 2-imino acids (IA) to keto-acids and ammonia. SsRidA-1 was active on IA derived from nonpolar amino acids and poorly active or inactive on IA derived from other amino acids tested. In contrast, SsRidA-2 had a generally low catalytic efficiency, but showed a relatively higher activity with IA derived from L-Glu and aromatic amino acids. The crystal structures of SsRidA-1 and SsRidA-2 provided hints of the remarkably different conformational stability and substrate specificity. Overall, SsRidA-1 is similar to the mammalian orthologs whereas SsRidA-2 displays unique properties likely generated by functional specialization of a duplicated ancestral gene.
		+
		+	Two novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage.,Digiovanni S, Visentin C, Degani G, Barbiroli A, Chiara M, Regazzoni L, Di Pisa F, Borchert AJ, Downs DM, Ricagno S, Vanoni MA, Popolo L Sci Rep. 2020 Jun 23;10(1):10135. doi: 10.1038/s41598-020-66663-w. PMID:32576850<ref>PMID:32576850</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tcd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Salmo salar]]
	[[Category: Bartorelli A]]		[[Category: Bartorelli A]]
	[[Category: Degani G]]		[[Category: Degani G]]

OCA at 11:08, 29 July 2020

OCA — Wed, 29 Jul 2020 11:08:31 GMT

←Older revision		Revision as of 11:08, 29 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6tcd is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Salmo salar RidA-2==
-		+	<StructureSection load='6tcd' size='340' side='right'caption='[[6tcd]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TCD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TCD FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tcd OCA], [http://pdbe.org/6tcd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tcd RCSB], [http://www.ebi.ac.uk/pdbsum/6tcd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tcd ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bartorelli A]]
		+	[[Category: Degani G]]
		+	[[Category: Di Pisa F]]
		+	[[Category: Digiovanni S]]
		+	[[Category: Oberti L]]
		+	[[Category: Popolo L]]
		+	[[Category: Ricagno S]]
		+	[[Category: Visentin C]]

OCA at 06:11, 22 July 2020

OCA — Wed, 22 Jul 2020 06:11:32 GMT

←Older revision		Revision as of 06:11, 22 July 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6tcd is ON HOLD	+	The entry 6tcd is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6tcd" [edit=sysop:move=sysop]

OCA — Wed, 13 Nov 2019 09:28:25 GMT

Protected "6tcd" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:28, 13 November 2019

OCA: New page: '''Unreleased structure''' The entry 6tcd is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Nov 2019 09:28:24 GMT

New page: '''Unreleased structure''' The entry 6tcd is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6tcd is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6tcd - Revision history

OCA at 12:59, 24 January 2024

OCA at 11:08, 29 July 2020

OCA at 06:11, 22 July 2020

OCA: Protected "6tcd" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6tcd is ON HOLD Authors: Description: Category: Unreleased Structures