6hl8 - Revision history

OCA at 06:53, 8 February 2023

2023-02-08T06:53:27Z

←Older revision		Revision as of 06:53, 8 February 2023
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	==Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate==		==Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate==
-	<StructureSection load='6hl8' size='340' side='right' caption='[[6hl8]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='6hl8' size='340' side='right'caption='[[6hl8]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hl8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HL8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HL8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hl8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HL8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GUA:GLUTARIC+ACID'>GUA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GUA:GLUTARIC+ACID'>GUA</scene></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=6hl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hl8 OCA], [~~http~~://pdbe.org/6hl8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6hl8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6hl8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6hl8 ProSAT]</span></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=6hl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hl8 OCA], [https://pdbe.org/6hl8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hl8 RCSB], [https://www.ebi.ac.uk/pdbsum/6hl8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hl8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~CSID_ECOLI CSID_ECOLI~~]~~] May be involved~~ in the ~~control~~ of ~~utilization of gamma-aminobutyric acid~~.~~[HAMAP~~-~~Rule~~:~~MF_01083]~~	+	[https://www.uniprot.org/uniprot/GLAH_ECOLI GLAH_ECOLI] Acts as an alpha-ketoglutarate-dependent dioxygenase catalyzing hydroxylation of glutarate (GA) to L-2-hydroxyglutarate (L2HG) in the stationary phase of E.coli. Functions in a L-lysine degradation pathway that proceeds via cadaverine, glutarate and L-2-hydroxyglutarate. Other dicarboxylic acids (oxalate, malonate, succinate, adipate, and pimelate) are not substrates for this enzyme.<ref>PMID:30498244</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: ~~Hartig, J S~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Mayans, O~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Williams, R M~~]]	+	[[Category: Hartig JS]]
-	[[Category: ~~Alpha-ketoglutarate-dependent~~]]	+	[[Category: Mayans O]]
-	[[Category: ~~Glutarate hydroxylase]]~~	+	[[Category: Williams RM]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Jelly roll~~]]	+

OCA at 06:51, 12 December 2018

2018-12-12T06:51:15Z

←Older revision		Revision as of 06:51, 12 December 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6hl8 is ~~ON HOLD~~	+	==Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate==
		+	<StructureSection load='6hl8' size='340' side='right' caption='[[6hl8]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6hl8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HL8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HL8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GUA:GLUTARIC+ACID'>GUA</scene></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=6hl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hl8 OCA], [http://pdbe.org/6hl8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hl8 RCSB], [http://www.ebi.ac.uk/pdbsum/6hl8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hl8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CSID_ECOLI CSID_ECOLI]] May be involved in the control of utilization of gamma-aminobutyric acid.[HAMAP-Rule:MF_01083]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lysine degradation has remained elusive in many organisms including Escherichia coli. Here we report catabolism of lysine to succinate in E. coli involving glutarate and L-2-hydroxyglutarate as intermediates. We show that CsiD acts as an alpha-ketoglutarate-dependent dioxygenase catalysing hydroxylation of glutarate to L-2-hydroxyglutarate. CsiD is found widespread in bacteria. We present crystal structures of CsiD in complex with glutarate, succinate, and the inhibitor N-oxalyl-glycine, demonstrating strong discrimination between the structurally related ligands. We show that L-2-hydroxyglutarate is converted to alpha-ketoglutarate by LhgO acting as a membrane-bound, ubiquinone-linked dehydrogenase. Lysine enters the pathway via 5-aminovalerate by the promiscuous enzymes GabT and GabD. We demonstrate that repression of the pathway by CsiR is relieved upon glutarate binding. In conclusion, lysine degradation provides an important link in central metabolism. Our results imply the gut microbiome as a potential source of glutarate and L-2-hydroxyglutarate associated with human diseases such as cancer and organic acidurias.

-	~~Authors: Williams, R~~.M., ~~Mayans~~, O., ~~Hartig~~, J.S.	+	Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate.,Knorr S, Sinn M, Galetskiy D, Williams RM, Wang C, Muller N, Mayans O, Schleheck D, Hartig JS Nat Commun. 2018 Nov 29;9(1):5071. doi: 10.1038/s41467-018-07563-6. PMID:30498244<ref>PMID:30498244</ref>

-	~~Description: Crystal Structure~~ of the ~~CsiD Glutarate Hydroxylase in complex with Glutarate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6hl8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hartig, J S]]
	[[Category: Mayans, O]]		[[Category: Mayans, O]]
-	[[Category: Williams, R.M]]	+	[[Category: Williams, R M]]
-	[[Category: ~~Hartig, J.S~~]]	+	[[Category: Alpha-ketoglutarate-dependent]]
		+	[[Category: Glutarate hydroxylase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Jelly roll]]

OCA at 18:28, 2 December 2018

2018-12-02T18:28:07Z

←Older revision		Revision as of 18:28, 2 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6hl8 is ON HOLD ~~until Paper Publication~~	+	The entry 6hl8 is ON HOLD

	Authors: Williams, R.M., Mayans, O., Hartig, J.S.		Authors: Williams, R.M., Mayans, O., Hartig, J.S.
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	Description: Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate		Description: Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Hartig, J.S]]
	[[Category: Mayans, O]]		[[Category: Mayans, O]]
	[[Category: Williams, R.M]]		[[Category: Williams, R.M]]
		+	[[Category: Hartig, J.S]]

OCA at 06:10, 26 September 2018

2018-09-26T06:10:19Z

←Older revision		Revision as of 06:10, 26 September 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6hl8 is ON HOLD	+	The entry 6hl8 is ON HOLD until Paper Publication

	Authors: Williams, R.M., Mayans, O., Hartig, J.S.		Authors: Williams, R.M., Mayans, O., Hartig, J.S.
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	Description: Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate		Description: Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Mayans, O]]
	[[Category: Hartig, J.S]]		[[Category: Hartig, J.S]]
		+	[[Category: Mayans, O]]
	[[Category: Williams, R.M]]		[[Category: Williams, R.M]]

OCA: Protected "6hl8" [edit=sysop:move=sysop]

2018-09-19T18:10:43Z

Protected "6hl8" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:10, 19 September 2018

OCA: New page: '''Unreleased structure''' The entry 6hl8 is ON HOLD Authors: Williams, R.M., Mayans, O., Hartig, J.S. Description: Crystal Structure of the CsiD Glutarate Hydroxylase in complex with ...

2018-09-19T18:10:41Z

New page: '''Unreleased structure''' The entry 6hl8 is ON HOLD Authors: Williams, R.M., Mayans, O., Hartig, J.S. Description: Crystal Structure of the CsiD Glutarate Hydroxylase in complex with ...

New page

'''Unreleased structure'''

The entry 6hl8 is ON HOLD

Authors: Williams, R.M., Mayans, O., Hartig, J.S.

Description: Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate
[[Category: Unreleased Structures]]
[[Category: Mayans, O]]
[[Category: Hartig, J.S]]
[[Category: Williams, R.M]]