6ora - Revision history

OCA at 07:15, 11 October 2023

OCA — Wed, 11 Oct 2023 07:15:37 GMT

←Older revision		Revision as of 07:15, 11 October 2023
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	<StructureSection load='6ora' size='340' side='right'caption='[[6ora]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6ora' size='340' side='right'caption='[[6ora]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ora]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ORA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ora]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ORA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XR:2-hydroxy-N-[(1S)-1-hydroxy-3-oxopropyl]-L-aspartic+acid'>5XR</scene>, <scene name='pdbligand=5XW:(2~{Z})-2-(1-oxidanyl-3-oxidanylidene-propyl)iminobutanedioic+acid'>5XW</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zk6\|4zk6]], [[4zkz\|4zkz]], [[5fev\|5fev]], [[5ffk\|5ffk]], [[6nso\|6nso]], [[6nsu\|6nsu]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5XR:2-hydroxy-N-[(1S)-1-hydroxy-3-oxopropyl]-L-aspartic+acid'>5XR</scene>, <scene name='pdbligand=5XW:(2~{Z})-2-(1-oxidanyl-3-oxidanylidene-propyl)iminobutanedioic+acid'>5XW</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nadA, PH0013 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=6ora FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ora OCA], [https://pdbe.org/6ora PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ora RCSB], [https://www.ebi.ac.uk/pdbsum/6ora PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ora 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/Quinolinate_synthase Quinolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.72 2.5.1.72] </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=6ora FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ora OCA], [~~http~~://pdbe.org/6ora PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ora RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ora PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ora ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NADA_PYRHO NADA_PYRHO]] Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate (By similarity).	+	[https://www.uniprot.org/uniprot/NADA_PYRHO NADA_PYRHO] Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pyrococcus horikoshii]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	~~[[Category: Quinolinate synthase~~]]	+	[[Category: Booker SJ]]
-	[[Category: Booker~~, S J~~]]	+	[[Category: Esakova OA]]
-	[[Category: Esakova~~, O A~~]]	+	[[Category: Grove TL]]
-	[[Category: Grove~~, T L~~]]	+	[[Category: Silakov A]]
-	[[Category: Silakov, A]]	+	[[Category: Yennawar NH]]
-	[[Category: Yennawar~~, N H]]~~	+
-	~~[[Category: Biosynthesis]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 17:45, 20 November 2019

OCA — Wed, 20 Nov 2019 17:45:29 GMT

←Older revision		Revision as of 17:45, 20 November 2019
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	<StructureSection load='6ora' size='340' side='right'caption='[[6ora]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6ora' size='340' side='right'caption='[[6ora]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ora]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ORA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ora]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ORA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XR:2-hydroxy-N-[(1S)-1-hydroxy-3-oxopropyl]-L-aspartic+acid'>5XR</scene>, <scene name='pdbligand=5XW:(2~{Z})-2-(1-oxidanyl-3-oxidanylidene-propyl)iminobutanedioic+acid'>5XW</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XR:2-hydroxy-N-[(1S)-1-hydroxy-3-oxopropyl]-L-aspartic+acid'>5XR</scene>, <scene name='pdbligand=5XW:(2~{Z})-2-(1-oxidanyl-3-oxidanylidene-propyl)iminobutanedioic+acid'>5XW</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zk6\|4zk6]], [[4zkz\|4zkz]], [[5fev\|5fev]], [[5ffk\|5ffk]], [[6nso\|6nso]], [[6nsu\|6nsu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zk6\|4zk6]], [[4zkz\|4zkz]], [[5fev\|5fev]], [[5ffk\|5ffk]], [[6nso\|6nso]], [[6nsu\|6nsu]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nadA, PH0013 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Quinolinate_synthase Quinolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.72 2.5.1.72] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Quinolinate_synthase Quinolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.72 2.5.1.72] </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=6ora FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ora OCA], [http://pdbe.org/6ora PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ora RCSB], [http://www.ebi.ac.uk/pdbsum/6ora PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ora 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=6ora FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ora OCA], [http://pdbe.org/6ora PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ora RCSB], [http://www.ebi.ac.uk/pdbsum/6ora PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ora ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pyrococcus horikoshii]]
	[[Category: Quinolinate synthase]]		[[Category: Quinolinate synthase]]
	[[Category: Booker, S J]]		[[Category: Booker, S J]]

OCA at 05:57, 21 August 2019

OCA — Wed, 21 Aug 2019 05:57:38 GMT

←Older revision		Revision as of 05:57, 21 August 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6ora is ~~ON HOLD until Paper~~ Publication	+	==An Unexpected Intermediate in the Reaction Catalyzed by Quinolinate Synthase==
		+	<StructureSection load='6ora' size='340' side='right'caption='[[6ora]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ora]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ORA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XR:2-hydroxy-N-[(1S)-1-hydroxy-3-oxopropyl]-L-aspartic+acid'>5XR</scene>, <scene name='pdbligand=5XW:(2~{Z})-2-(1-oxidanyl-3-oxidanylidene-propyl)iminobutanedioic+acid'>5XW</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zk6\|4zk6]], [[4zkz\|4zkz]], [[5fev\|5fev]], [[5ffk\|5ffk]], [[6nso\|6nso]], [[6nsu\|6nsu]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Quinolinate_synthase Quinolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.72 2.5.1.72] </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=6ora FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ora OCA], [http://pdbe.org/6ora PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ora RCSB], [http://www.ebi.ac.uk/pdbsum/6ora PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ora ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NADA_PYRHO NADA_PYRHO]] Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Quinolinic acid (QA) is a common intermediate in the biosynthesis of nicotinamide adenine dinucleotide (NAD+) and its derivatives in all organisms that synthesize the molecule de novo. In most prokaryotes, it is formed from the condensation of dihydroxyacetone phosphate (DHAP) and iminoaspartate (IA) by the action of quinolinate synthase (NadA). NadA contains a [4Fe-4S] cluster cofactor with a unique non-cysteinyl-ligated iron ion (Fea), which is proposed to bind the hydroxyl group of an intermediate in its reaction to facilitate a dehydration step. However, direct evidence for this role in catalysis has yet to be provided, and the exact chemical mechanism that underlies this transformation remains elusive. Herein, we present a structure of NadA from Pyrococcus horikoshii (PhNadA) in complex with IA and show that a carboxylate group of the molecule is ligated to Fea of the iron-sulfur cluster, occupying the site to which DHAP has been proposed to bind during catalysis. When crystals of PhNadA in complex with IA are soaked briefly in DHAP before freezing, electron density for a new molecule is observed, which we suggest is related to an intermediate in the reaction. Similar, but slightly different "intermediates" are observed when crystals of a PhNadA Glu198Gln variant are incubated with DHAP, oxaloacetate, and ammonium chloride, conditions under which IA is formed chemically. Continuous-wave and pulse electron paramagnetic resonance techniques are used to verify the binding mode of substrates and proposed intermediates in frozen solution.

-	~~Authors:~~ Esakova, O.A., Grove, ~~T.L., Silakov, A.~~, Yennawar, N.H.~~, Booker, S~~.J.	+	An Unexpected Species Determined by X-ray Crystallography that May Represent an Intermediate in the Reaction Catalyzed by Quinolinate Synthase.,Esakova OA, Silakov A, Grove TL, Warui DM, Yennawar NH, Booker SJ J Am Chem Soc. 2019 Aug 7. doi: 10.1021/jacs.9b02513. PMID:31390192<ref>PMID:31390192</ref>

-	~~Description: An Unexpected Intermediate in~~ the ~~Reaction Catalyzed by Quinolinate Synthase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Grove~~, ~~T.L~~]]	+	<div class="pdbe-citations 6ora" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Yennawar~~, ~~N.H~~]]	+	== References ==
-	[[Category: ~~Booker~~, ~~S.J~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Quinolinate synthase]]
		+	[[Category: Booker, S J]]
		+	[[Category: Esakova, O A]]
		+	[[Category: Grove, T L]]
	[[Category: Silakov, A]]		[[Category: Silakov, A]]
-	[[Category: ~~Esakova~~, ~~O.A~~]]	+	[[Category: Yennawar, N H]]
		+	[[Category: Biosynthesis]]
		+	[[Category: Transferase]]

OCA at 08:52, 17 July 2019

OCA — Wed, 17 Jul 2019 08:52:48 GMT

←Older revision		Revision as of 08:52, 17 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Esakova, O.A., Grove, T.L., Silakov, A., Yennawar, N.H., Booker, S.J.		Authors: Esakova, O.A., Grove, T.L., Silakov, A., Yennawar, N.H., Booker, S.J.

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

OCA — Fri, 10 May 2019 08:02:01 GMT

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

←Older revision

Revision as of 08:02, 10 May 2019

OCA: New page: '''Unreleased structure''' The entry 6ora is ON HOLD Authors: Esakova, O.A., Grove, T.L., Silakov, A., Yennawar, N.H., Booker, S.J. Description: An Unexpected Intermediate in the React...

OCA — Fri, 10 May 2019 08:01:59 GMT

New page: '''Unreleased structure''' The entry 6ora is ON HOLD Authors: Esakova, O.A., Grove, T.L., Silakov, A., Yennawar, N.H., Booker, S.J. Description: An Unexpected Intermediate in the React...

New page

'''Unreleased structure'''

The entry 6ora is ON HOLD

Authors: Esakova, O.A., Grove, T.L., Silakov, A., Yennawar, N.H., Booker, S.J.

Description: An Unexpected Intermediate in the Reaction Catalyzed by Quinolinate Synthase
[[Category: Unreleased Structures]]
[[Category: Grove, T.L]]
[[Category: Yennawar, N.H]]
[[Category: Booker, S.J]]
[[Category: Silakov, A]]
[[Category: Esakova, O.A]]