5hp7 - Revision history

OCA at 10:49, 16 August 2023

OCA — Wed, 16 Aug 2023 10:49:41 GMT

←Older revision		Revision as of 10:49, 16 August 2023
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	<StructureSection load='5hp7' size='340' side='right'caption='[[5hp7]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5hp7' size='340' side='right'caption='[[5hp7]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hp7]] is a 1 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=5HP7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HP7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hp7]] is a 1 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=5HP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HP7 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5hp8\|5hp8]]</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]] 2Å</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=5hp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp7 OCA], [https://pdbe.org/5hp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hp7 RCSB], [https://www.ebi.ac.uk/pdbsum/5hp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp7 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=5hp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp7 OCA], [~~http~~://pdbe.org/5hp7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hp7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hp7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp7 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 ==
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	__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 08:26:41 GMT

←Older revision		Revision as of 08:26, 27 May 2020
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	==Crystal structures of RidA in the apo form==		==Crystal structures of RidA in the apo form==
-	<StructureSection load='5hp7' size='340' side='right' caption='[[5hp7]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5hp7' size='340' side='right'caption='[[5hp7]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hp7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HP7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HP7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hp7]] is a 1 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=5HP7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HP7 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hp8\|5hp8]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hp8\|5hp8]]</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=5hp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp7 OCA], [http://pdbe.org/5hp7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hp7 RCSB], [http://www.ebi.ac.uk/pdbsum/5hp7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp7 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=5hp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp7 OCA], [http://pdbe.org/5hp7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hp7 RCSB], [http://www.ebi.ac.uk/pdbsum/5hp7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</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 17:40:31 GMT

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

-	~~The entry~~ 5hp7 is ~~ON HOLD~~ ~~until Jan 20 2018~~	+	==Crystal structures of RidA in the apo form==
		+	<StructureSection load='5hp7' size='340' side='right' caption='[[5hp7]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hp7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HP7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HP7 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hp8\|5hp8]]</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=5hp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp7 OCA], [http://pdbe.org/5hp7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hp7 RCSB], [http://www.ebi.ac.uk/pdbsum/5hp7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp7 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~~:	+	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~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5hp7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 2-iminobutanoate/2-iminopropanoate deaminase]]
		+	[[Category: Liu, X]]
		+	[[Category: Xie, W]]
		+	[[Category: Deamination]]
		+	[[Category: Enamine/imine]]
		+	[[Category: Hydrolase]]
		+	[[Category: Rida]]

OCA at 13:47, 15 May 2016

OCA — Sun, 15 May 2016 13:47:18 GMT

←Older revision		Revision as of 13:47, 15 May 2016
Line 3:		Line 3:
	The entry 5hp7 is ON HOLD until Jan 20 2018		The entry 5hp7 is ON HOLD until Jan 20 2018

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

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Liu, X]]
-	[[Category: Xie, W]]

OCA at 15:32, 10 February 2016

OCA — Wed, 10 Feb 2016 15:32:58 GMT

←Older revision		Revision as of 15:32, 10 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hp7 is ON HOLD	+	The entry 5hp7 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 14:06:55 GMT

←Older revision		Revision as of 14:06, 3 February 2016
Line 3:		Line 3:
	The entry 5hp7 is ON HOLD		The entry 5hp7 is ON HOLD

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

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Xie, W~~, Liu, X~~]]	+	[[Category: Liu, X]]
		+	[[Category: Xie, W]]

OCA: Protected "5hp7" [edit=sysop:move=sysop]

OCA — Thu, 28 Jan 2016 01:01:34 GMT

Protected "5hp7" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:01, 28 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hp7 is ON HOLD Authors: Xie, W, Liu, X Description: Category: Unreleased Structures Category: Xie, W, Liu, X

OCA — Thu, 28 Jan 2016 01:01:33 GMT

New page: '''Unreleased structure''' The entry 5hp7 is ON HOLD Authors: Xie, W, Liu, X Description: Category: Unreleased Structures Category: Xie, W, Liu, X

New page

'''Unreleased structure'''

The entry 5hp7 is ON HOLD

Authors: Xie, W, Liu, X

Description:
[[Category: Unreleased Structures]]
[[Category: Xie, W, Liu, X]]