6w1h - Revision history

OCA at 14:14, 18 October 2023

OCA — Wed, 18 Oct 2023 14:14:54 GMT

←Older revision		Revision as of 14:14, 18 October 2023
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	==Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Pseudomonas putida==		==Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Pseudomonas putida==
-	<StructureSection load='6w1h' size='340' side='right'caption='[[6w1h]]' scene=''>	+	<StructureSection load='6w1h' size='340' side='right'caption='[[6w1h]], [[Resolution\|resolution]] 1.42Å' 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=6W1H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6W1H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w1h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W1H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W1H 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=6w1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w1h OCA], [~~http~~://pdbe.org/6w1h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6w1h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6w1h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6w1h 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]] 1.42Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OOG:2-OXOADIPIC+ACID'>OOG</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=6w1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w1h OCA], [https://pdbe.org/6w1h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w1h RCSB], [https://www.ebi.ac.uk/pdbsum/6w1h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w1h ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q88CC1_PSEPK Q88CC1_PSEPK]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Despite intensive study, plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remains unvalidated. Recently we described a missing step in the D-lysine catabolism of Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (2HG) via hydroxyglutarate synthase (HglS), a DUF1338 family protein. Here we solve the structure of HglS to 1.1 A resolution in substrate-free form and in complex with 2OA. We propose a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O2-dependent manner. Specificity is mediated by a single arginine, highly conserved across most DUF1338 proteins. An Arabidopsis thaliana HglS homolog coexpresses with known lysine catabolism enzymes, and mutants show phenotypes consistent with disrupted lysine catabolism. Structural and biochemical analysis of Oryza sativa homolog FLO7 reveals identical activity to HglS despite low sequence identity. Our results suggest DUF1338-containing enzymes catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes.
		+
		+	An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism.,Thompson MG, Blake-Hedges JM, Pereira JH, Hangasky JA, Belcher MS, Moore WM, Barajas JF, Cruz-Morales P, Washington LJ, Haushalter RW, Eiben CB, Liu Y, Skyrud W, Benites VT, Barnum TP, Baidoo EEK, Scheller HV, Marletta MA, Shih PM, Adams PD, Keasling JD Nat Commun. 2020 Jun 10;11(1):2931. doi: 10.1038/s41467-020-16815-3. PMID:32523014<ref>PMID:32523014</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6w1h" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pseudomonas putida]]
	[[Category: Adams PD]]		[[Category: Adams PD]]
	[[Category: Blake-Hedges JM]]		[[Category: Blake-Hedges JM]]

OCA at 06:26, 25 June 2020

OCA — Thu, 25 Jun 2020 06:26:25 GMT

←Older revision		Revision as of 06:26, 25 June 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6w1h ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Pseudomonas putida==
-		+	<StructureSection load='6w1h' size='340' side='right'caption='[[6w1h]]' scene=''>
-	~~Authors~~: ~~Pereira, J~~.H.~~, Thompson, M~~.G., ~~Blake~~-~~Hedges~~, J.M., ~~Keasling, J~~.D., ~~Adams, P~~.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W1H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W1H FirstGlance]. <br>
-	~~Description: Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Pseudomonas putida~~	+	</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=6w1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w1h OCA], [http://pdbe.org/6w1h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w1h RCSB], [http://www.ebi.ac.uk/pdbsum/6w1h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w1h ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Pereira, J.H~~]]	+	__TOC__
-	[[Category: ~~Keasling, J.D~~]]	+	</StructureSection>
-	[[Category: ~~Adams, P.D~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Thompson, M.G~~]]	+	[[Category: Adams PD]]
-	[[Category: ~~Blake-Hedges, J.M~~]]	+	[[Category: Blake-Hedges JM]]
		+	[[Category: Keasling JD]]
		+	[[Category: Pereira JH]]
		+	[[Category: Thompson MG]]

OCA at 03:56, 13 May 2020

OCA — Wed, 13 May 2020 03:56:15 GMT

←Older revision		Revision as of 03:56, 13 May 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6w1h is ON HOLD	+	The entry 6w1h is ON HOLD until Paper Publication

	Authors: Pereira, J.H., Thompson, M.G., Blake-Hedges, J.M., Keasling, J.D., Adams, P.D.		Authors: Pereira, J.H., Thompson, M.G., Blake-Hedges, J.M., Keasling, J.D., Adams, P.D.

OCA: Protected "6w1h" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2020 06:09:33 GMT

Protected "6w1h" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:09, 11 March 2020

OCA: New page: '''Unreleased structure''' The entry 6w1h is ON HOLD Authors: Pereira, J.H., Thompson, M.G., Blake-Hedges, J.M., Keasling, J.D., Adams, P.D. Description: Crystal structure of the hydro...

OCA — Wed, 11 Mar 2020 06:09:32 GMT

New page: '''Unreleased structure''' The entry 6w1h is ON HOLD Authors: Pereira, J.H., Thompson, M.G., Blake-Hedges, J.M., Keasling, J.D., Adams, P.D. Description: Crystal structure of the hydro...

New page

'''Unreleased structure'''

The entry 6w1h is ON HOLD

Authors: Pereira, J.H., Thompson, M.G., Blake-Hedges, J.M., Keasling, J.D., Adams, P.D.

Description: Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Pseudomonas putida
[[Category: Unreleased Structures]]
[[Category: Pereira, J.H]]
[[Category: Keasling, J.D]]
[[Category: Adams, P.D]]
[[Category: Thompson, M.G]]
[[Category: Blake-Hedges, J.M]]