6y88 - Revision history

OCA at 13:21, 24 January 2024

OCA — Wed, 24 Jan 2024 13:21:31 GMT

←Older revision		Revision as of 13:21, 24 January 2024
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-	====	+	==IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP==
-	<StructureSection load='6y88' size='340' side='right'caption='[[6y88]]' scene=''>	+	<StructureSection load='6y88' size='340' side='right'caption='[[6y88]], [[Resolution\|resolution]] 2.10Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y88]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y88 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=6y88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y88 OCA], [~~http~~://pdbe.org/6y88 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y88 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y88 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y88 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]] 2.0998344Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=137:1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE'>137</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=6y88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y88 OCA], [https://pdbe.org/6y88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y88 RCSB], [https://www.ebi.ac.uk/pdbsum/6y88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y88 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TRPC_PSEAE TRPC_PSEAE]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In tryptophan biosynthesis, the reaction catalyzed by the enzyme indole-3-glycerol phosphate synthase (IGP synthase, IGPS) starts with a condensation step where the substrate's carboxylated phenyl group makes a nucleophilic attack to form the pyrrole ring of the indole, followed by a decarboxylation which restores the aromaticity of the phenyl. IGPS from Pseudomonas aeruginosa has the highest turnover number of all characterized IGPS enzymes, providing an excellent model system to test the necessity of the decarboxylation step. This step was since the 1960s considered to be mechanistically essential based on studies of the IGPS:PRAI fusion protein from Escherichia coli. Here, we present the crystal structure of P. aeruginosa IGPS in complex with reduced CdRP, a non-reactive substrate analogue, and using a sensitive discontinuous assay, we demonstrate weak promiscuous activity on the decarboxylated substrate 1-(phenylamino)-1-deoxyribulose-5-phosphate (PAdRP) - with approximately 1000' lower rate of IGP formation than from the native substrate. We also show that E. coli IGPS, at even lower rate, can produce IGP from decarboxylated substrate. Our structure of P. aeruginosa IGPS has eight molecules in the asymmetric unit, out of which seven contain ligand, and one displays a previously unobserved conformation closer to the reactive state. One of the few non-conserved active-site residues, Phe201 in P. aeruginosa IGPS, is by mutagenesis demonstrated to be important for the higher turnover of this enzyme on both substrates. Our results demonstrate that, despite IGPS's classification as a carboxylyase (i.e. decarboxylase), decarboxylation not a completely essential step in its catalysis.
		+
		+	Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa - decarboxylation is not essential for indole formation.,Soderholm A, Newton MS, Patrick WM, Selmer M J Biol Chem. 2020 Sep 14. pii: RA120.014936. doi: 10.1074/jbc.RA120.014936. PMID:32928960<ref>PMID:32928960</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y88" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[IGPS 3D structures\|IGPS 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Pseudomonas aeruginosa]]
		+	[[Category: Selmer M]]
		+	[[Category: Soderholm A]]

OCA at 11:13, 23 September 2020

OCA — Wed, 23 Sep 2020 11:13:58 GMT

←Older revision		Revision as of 11:13, 23 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6y88 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6y88' size='340' side='right'caption='[[6y88]]' scene=''>
-	~~Authors~~: ~~Soderholm, A~~.~~, Selmer, M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~IGPS (Indole-3~~-~~glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP~~	+	</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=6y88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y88 OCA], [http://pdbe.org/6y88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y88 RCSB], [http://www.ebi.ac.uk/pdbsum/6y88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y88 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Soderholm, A~~]]	+	__TOC__
-	[[Category: ~~Selmer, M~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 09:26, 29 July 2020

OCA — Wed, 29 Jul 2020 09:26:30 GMT

←Older revision		Revision as of 09:26, 29 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y88 is ON HOLD	+	The entry 6y88 is ON HOLD until Paper Publication

	Authors: Soderholm, A., Selmer, M.		Authors: Soderholm, A., Selmer, M.
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	Description: IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP		Description: IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Selmer, M]]
	[[Category: Soderholm, A]]		[[Category: Soderholm, A]]
		+	[[Category: Selmer, M]]

OCA: Protected "6y88" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2020 06:16:34 GMT

Protected "6y88" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:16, 11 March 2020

OCA: New page: '''Unreleased structure''' The entry 6y88 is ON HOLD Authors: Soderholm, A., Selmer, M. Description: IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex ...

OCA — Wed, 11 Mar 2020 06:16:33 GMT

New page: '''Unreleased structure''' The entry 6y88 is ON HOLD Authors: Soderholm, A., Selmer, M. Description: IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex ...

New page

'''Unreleased structure'''

The entry 6y88 is ON HOLD

Authors: Soderholm, A., Selmer, M.

Description: IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP
[[Category: Unreleased Structures]]
[[Category: Selmer, M]]
[[Category: Soderholm, A]]