5hp8 - Revision history

OCA at 10:49, 16 August 2023

OCA — Wed, 16 Aug 2023 10:49:43 GMT

←Older revision		Revision as of 10:49, 16 August 2023
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	<StructureSection load='5hp8' size='340' side='right'caption='[[5hp8]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5hp8' size='340' side='right'caption='[[5hp8]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hp8]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HP8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HP8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hp8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HP8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5hp7\|5hp7~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>RIDA, At3g20390, MQC12.15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~3702 ARATH])</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=5hp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp8 OCA], [https://pdbe.org/5hp8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hp8 RCSB], [https://www.ebi.ac.uk/pdbsum/5hp8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp8 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/2-iminobutanoate/2-iminopropanoate_deaminase 2-iminobutanoate/2-iminopropanoate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.10 3.5.99.10] </~~span~~></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=5hp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp8 OCA], [~~http~~://pdbe.org/5hp8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hp8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hp8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RIDA_ARATH RIDA_ARATH]] Hydrolyzes the Ser-derived enamine/imine product of Thr dehydratase, protecting the plastidial branched-chain aminotransferase BCAT3 (AC Q9M401) from inactivation. Involved in Ile biosynthesis.<ref>PMID:25070638</ref>	+	[https://www.uniprot.org/uniprot/RIDA_ARATH RIDA_ARATH] Hydrolyzes the Ser-derived enamine/imine product of Thr dehydratase, protecting the plastidial branched-chain aminotransferase BCAT3 (AC Q9M401) from inactivation. Involved in Ile biosynthesis.<ref>PMID:25070638</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~2-iminobutanoate/2-iminopropanoate deaminase]]~~	+	[[Category: Arabidopsis thaliana]]
-	~~[[Category: Arath~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liu, X]]	+	[[Category: Liu X]]
-	[[Category: Xie, W]]	+	[[Category: Xie W]]
-	~~[[Category: Deamination]]~~	+
-	~~[[Category: Enamine/imine]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rida~~]]	+

OCA at 08:26, 27 May 2020

OCA — Wed, 27 May 2020 08:26:43 GMT

←Older revision		Revision as of 08:26, 27 May 2020
Line 1:		Line 1:

	==Crystal structures of RidA in complex with pyruvate==		==Crystal structures of RidA in complex with pyruvate==
-	<StructureSection load='5hp8' size='340' side='right' caption='[[5hp8]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5hp8' size='340' side='right'caption='[[5hp8]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hp8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HP8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HP8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hp8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HP8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HP8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hp7\|5hp7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hp7\|5hp7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RIDA, At3g20390, MQC12.15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-iminobutanoate/2-iminopropanoate_deaminase 2-iminobutanoate/2-iminopropanoate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.10 3.5.99.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-iminobutanoate/2-iminopropanoate_deaminase 2-iminobutanoate/2-iminopropanoate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.10 3.5.99.10] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5hp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp8 OCA], [http://pdbe.org/5hp8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hp8 RCSB], [http://www.ebi.ac.uk/pdbsum/5hp8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp8 ProSAT]</span></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=5hp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp8 OCA], [http://pdbe.org/5hp8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hp8 RCSB], [http://www.ebi.ac.uk/pdbsum/5hp8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: 2-iminobutanoate/2-iminopropanoate deaminase]]		[[Category: 2-iminobutanoate/2-iminopropanoate deaminase]]
		+	[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Liu, X]]		[[Category: Liu, X]]
	[[Category: Xie, W]]		[[Category: Xie, W]]

OCA at 17:40, 19 October 2016

OCA — Wed, 19 Oct 2016 17:40:34 GMT

←Older revision		Revision as of 17:40, 19 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hp8 is ~~ON HOLD~~ ~~until Jan 20 2018~~	+	==Crystal structures of RidA in complex with pyruvate==
		+	<StructureSection load='5hp8' size='340' side='right' caption='[[5hp8]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hp8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HP8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HP8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hp7\|5hp7]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-iminobutanoate/2-iminopropanoate_deaminase 2-iminobutanoate/2-iminopropanoate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.10 3.5.99.10] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5hp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp8 OCA], [http://pdbe.org/5hp8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hp8 RCSB], [http://www.ebi.ac.uk/pdbsum/5hp8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RIDA_ARATH RIDA_ARATH]] Hydrolyzes the Ser-derived enamine/imine product of Thr dehydratase, protecting the plastidial branched-chain aminotransferase BCAT3 (AC Q9M401) from inactivation. Involved in Ile biosynthesis.<ref>PMID:25070638</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The YjgF/YER057c/UK114 family proteins are highly conserved across all three domains of life, and most of them currently have no clearly defined biological roles. In vitro, these proteins were found to hydrolyze the enamine/imine intermediates generated from serine or threonine, and were renamed Reactive Intermediate Deaminase A (RidA). RidA was recently discovered in Arabidopsis thaliana, and by deaminating the toxic enamine/imine intermediates, it prevents the inactivation of many functionally important pyridoxal 5'-phosphate (PLP)-containing enzymes in plants such as branched-chain aminotransferase BCAT (IlvE). In this study, we determined the crystal structure of Arabidopsis thaliana RidA in the apo form, as well as RidA complexed with the ligand pyruvate. RidA forms the trimeric, barrel-like quaternary structure and inter-subunit cavities, and resembles most RidA family members. Each pyruvate molecule binds to the interface between two subunits, and the recognition of pyruvate is achieved by the interactions with R165 and T167. From sequence alignment and structural superposition, we identified a series of key residues responsible for the trimer assembly, whose importance was confirmed by enzymatic assays. This study provides structural insight into RidA functions in plants.

-	~~Authors: Xie~~, W., Liu, X.	+	Crystal structures of RidA, an important enzyme for the prevention of toxic side products.,Liu X, Zeng J, Chen X, Xie W Sci Rep. 2016 Jul 26;6:30494. doi: 10.1038/srep30494. PMID:27458092<ref>PMID:27458092</ref>

-	~~Description: Crystal structures~~ of ~~RidA in complex with pyruvate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5hp8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 2-iminobutanoate/2-iminopropanoate deaminase]]
	[[Category: Liu, X]]		[[Category: Liu, X]]
	[[Category: Xie, W]]		[[Category: Xie, W]]
		+	[[Category: Deamination]]
		+	[[Category: Enamine/imine]]
		+	[[Category: Hydrolase]]
		+	[[Category: Rida]]

OCA at 15:33, 10 February 2016

OCA — Wed, 10 Feb 2016 15:33:01 GMT

←Older revision		Revision as of 15:33, 10 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hp8 is ON HOLD	+	The entry 5hp8 is ON HOLD until Jan 20 2018

	Authors: Xie, W., Liu, X.		Authors: Xie, W., Liu, X.

OCA at 14:06, 3 February 2016

OCA — Wed, 03 Feb 2016 14:06:58 GMT

←Older revision		Revision as of 14:06, 3 February 2016
Line 3:		Line 3:
	The entry 5hp8 is ON HOLD		The entry 5hp8 is ON HOLD

-	Authors: Xie, W, Liu, X	+	Authors: Xie, W., Liu, X.

	Description: Crystal structures of RidA in complex with pyruvate		Description: Crystal structures of RidA in complex with pyruvate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Xie, W~~, Liu, X~~]]	+	[[Category: Liu, X]]
		+	[[Category: Xie, W]]

OCA: Protected "5hp8" [edit=sysop:move=sysop]

OCA — Thu, 28 Jan 2016 01:01:41 GMT

Protected "5hp8" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:01, 28 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hp8 is ON HOLD Authors: Xie, W, Liu, X Description: Crystal structures of RidA in complex with pyruvate Category: Unreleased Structures [[Cate...

OCA — Thu, 28 Jan 2016 01:01:39 GMT

New page: '''Unreleased structure''' The entry 5hp8 is ON HOLD Authors: Xie, W, Liu, X Description: Crystal structures of RidA in complex with pyruvate Category: Unreleased Structures [[Cate...

New page

'''Unreleased structure'''

The entry 5hp8 is ON HOLD

Authors: Xie, W, Liu, X

Description: Crystal structures of RidA in complex with pyruvate
[[Category: Unreleased Structures]]
[[Category: Xie, W, Liu, X]]