6aim - Revision history

OCA at 09:31, 22 November 2023

OCA — Wed, 22 Nov 2023 09:31:47 GMT

←Older revision		Revision as of 09:31, 22 November 2023
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	<StructureSection load='6aim' size='340' side='right'caption='[[6aim]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='6aim' size='340' side='right'caption='[[6aim]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6aim]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6AIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6aim]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AIM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=9Z3:N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl-L-cysteine'>9Z3</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]] 2.04Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ai8\|6ai8]]~~, [[~~6ai9~~\|~~6ai9]], [[6aik\|6aik]], [[6aip\|6aip~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9Z3:N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl-L-cysteine'>9Z3</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CAB2, YIL083C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=559292 Baker's yeast])</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=6aim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aim OCA], [https://pdbe.org/6aim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6aim RCSB], [https://www.ebi.ac.uk/pdbsum/6aim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6aim 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/Phosphopantothenate~~--~~cysteine_ligase Phosphopantothenate~~--~~cysteine ligase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=6.3.2.5 6.3.2.5~~] </~~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=6aim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aim OCA], [~~http~~://pdbe.org/6aim PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6aim RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6aim PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6aim ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PPCS_YEAST PPCS_YEAST]] Catalyzes the first step in the biosynthesis of coenzyme A from vitamin B5, where cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine.<ref>PMID:19266201</ref>	+	[https://www.uniprot.org/uniprot/PPCS_YEAST PPCS_YEAST] Catalyzes the first step in the biosynthesis of coenzyme A from vitamin B5, where cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine.<ref>PMID:19266201</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: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Phosphopantothenate--cysteine ligase~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Zheng, P]]	+	[[Category: Zheng P]]
-	[[Category: Zhu, Z]]	+	[[Category: Zhu Z]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Phosphopantothenate--cysteine~~]]	+

OCA at 17:08, 20 November 2019

OCA — Wed, 20 Nov 2019 17:08:35 GMT

←Older revision		Revision as of 17:08, 20 November 2019
Line 3:		Line 3:
	<StructureSection load='6aim' size='340' side='right'caption='[[6aim]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='6aim' size='340' side='right'caption='[[6aim]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6aim]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6aim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AIM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9Z3:N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl-L-cysteine'>9Z3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9Z3:N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl-L-cysteine'>9Z3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ai8\|6ai8]], [[6ai9\|6ai9]], [[6aik\|6aik]], [[6aip\|6aip]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ai8\|6ai8]], [[6ai9\|6ai9]], [[6aik\|6aik]], [[6aip\|6aip]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB2, YIL083C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphopantothenate--cysteine_ligase Phosphopantothenate--cysteine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.5 6.3.2.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphopantothenate--cysteine_ligase Phosphopantothenate--cysteine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.5 6.3.2.5] </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=6aim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aim OCA], [http://pdbe.org/6aim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aim RCSB], [http://www.ebi.ac.uk/pdbsum/6aim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aim ProSAT]</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=6aim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aim OCA], [http://pdbe.org/6aim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aim RCSB], [http://www.ebi.ac.uk/pdbsum/6aim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aim ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Phosphopantothenate--cysteine ligase]]		[[Category: Phosphopantothenate--cysteine ligase]]

OCA at 07:44, 20 March 2019

OCA — Wed, 20 Mar 2019 07:44:47 GMT

←Older revision		Revision as of 07:44, 20 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6aim is ~~ON HOLD~~ ~~until Aug 24 2020~~	+	==Cab2 mutant H337A complex with phosphopantothenate-cysteine==
		+	<StructureSection load='6aim' size='340' side='right'caption='[[6aim]], [[Resolution\|resolution]] 2.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6aim]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AIM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9Z3:N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl-L-cysteine'>9Z3</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ai8\|6ai8]], [[6ai9\|6ai9]], [[6aik\|6aik]], [[6aip\|6aip]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphopantothenate--cysteine_ligase Phosphopantothenate--cysteine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.5 6.3.2.5] </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=6aim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aim OCA], [http://pdbe.org/6aim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aim RCSB], [http://www.ebi.ac.uk/pdbsum/6aim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aim ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PPCS_YEAST PPCS_YEAST]] Catalyzes the first step in the biosynthesis of coenzyme A from vitamin B5, where cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine.<ref>PMID:19266201</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphopantothenoylcysteine (PPC) synthetase (PPCS) catalyzes nucleoside triphosphate-dependent condensation reaction between 4'-phosphopantothenate (PPA) and l-cysteine to form PPC in CoA biosynthesis. The catalytic mechanism of PPCS has not been resolved yet. Coenzyme A biosynthesis protein 2 (Cab2) possesses activity of PPCS in Saccharomyces cerevisiae. Our enzymatic assays suggest that Cab2 could utilize both ATP and CTP to activate PPA in vitro. The results of isothermal titration calorimetry indicate that PPA, CTP, and ATP could bind to Cab2 individually, with PPA having the highest binding affinity. To provide further insight into the catalytic mechanism of Cab2, we determined the crystal structures of Cab2 and its complex with PPA, the reaction intermediate 4'-phosphopantothenoyl-CMP, the final reaction product PPC, and the product analogue phosphopantothenoylcystine. Except for PPA, all other ligands were generated in situ and present in the active-site pocket of Cab2. Structures of Cab2 in complex with ligands provide insight into substrates binding and its catalytic mechanism. Analysis of structures indicates that the carboxyl of PPA-moiety of ligands and the gamma-amino group of Asn97 possess different conformations in these complex structures. The cysteine/cystine/serine selectivity assays for Cab2 indicate that the amino group rather than the thiol group of l-cysteine attacks the carbonyl of 4'-phosphopantothenoyl-CMP to form PPC. Based on structural and biochemical data, the catalytic mechanism of Cab2 was proposed for the first time.

-	~~Authors: Zheng~~, P., ~~Zhu~~, Z.	+	Crystallographic Analysis of the Catalytic Mechanism of Phosphopantothenoylcysteine Synthetase from Saccharomyces cerevisiae.,Zheng P, Zhang M, Khan MH, Liu H, Jin Y, Yue J, Gao Y, Teng M, Zhu Z, Niu L J Mol Biol. 2019 Feb 15;431(4):764-776. doi: 10.1016/j.jmb.2019.01.012. Epub 2019, Jan 14. PMID:30653991<ref>PMID:30653991</ref>

-	~~Description: Cab2 mutant H337A complex with phosphopantothenate~~-~~cysteine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6aim" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Phosphopantothenate--cysteine ligase]]
	[[Category: Zheng, P]]		[[Category: Zheng, P]]
	[[Category: Zhu, Z]]		[[Category: Zhu, Z]]
		+	[[Category: Complex]]
		+	[[Category: Ligase]]
		+	[[Category: Phosphopantothenate--cysteine]]

OCA at 04:46, 2 January 2019

OCA — Wed, 02 Jan 2019 04:46:50 GMT

←Older revision		Revision as of 04:46, 2 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6aim is ON HOLD	+	The entry 6aim is ON HOLD until Aug 24 2020

	Authors: Zheng, P., Zhu, Z.		Authors: Zheng, P., Zhu, Z.

OCA at 08:35, 5 September 2018

OCA — Wed, 05 Sep 2018 08:35:42 GMT

←Older revision		Revision as of 08:35, 5 September 2018
Line 3:		Line 3:
	The entry 6aim is ON HOLD		The entry 6aim is ON HOLD

-	Authors: ~~Peiyi~~, Z., ~~Zhongliang~~, Z.	+	Authors: Zheng, P., Zhu, Z.

-	Description: Cab2 mutant-H337A complex with phosphopantothenate	+	Description: Cab2 mutant H337A complex with phosphopantothenate-cysteine
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Peiyi~~, Z]]	+	[[Category: Zheng, P]]
-	[[Category: ~~Zhongliang~~, Z]]	+	[[Category: Zhu, Z]]

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

OCA — Wed, 29 Aug 2018 05:36:30 GMT

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

←Older revision

Revision as of 05:36, 29 August 2018

OCA: New page: '''Unreleased structure''' The entry 6aim is ON HOLD Authors: Peiyi, Z., Zhongliang, Z. Description: Cab2 mutant-H337A complex with phosphopantothenate [[Category: Unreleased Structure...

OCA — Wed, 29 Aug 2018 05:36:28 GMT

New page: '''Unreleased structure''' The entry 6aim is ON HOLD Authors: Peiyi, Z., Zhongliang, Z. Description: Cab2 mutant-H337A complex with phosphopantothenate [[Category: Unreleased Structure...

New page

'''Unreleased structure'''

The entry 6aim is ON HOLD

Authors: Peiyi, Z., Zhongliang, Z.

Description: Cab2 mutant-H337A complex with phosphopantothenate
[[Category: Unreleased Structures]]
[[Category: Peiyi, Z]]
[[Category: Zhongliang, Z]]