7uk8 - Revision history

OCA at 09:54, 25 October 2023

OCA — Wed, 25 Oct 2023 09:54:06 GMT

←Older revision		Revision as of 09:54, 25 October 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7uk8]] is a 1 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=7UK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UK8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7uk8]] is a 1 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=7UK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UK8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.85Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7uk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uk8 OCA], [https://pdbe.org/7uk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uk8 RCSB], [https://www.ebi.ac.uk/pdbsum/7uk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uk8 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=7uk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uk8 OCA], [https://pdbe.org/7uk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uk8 RCSB], [https://www.ebi.ac.uk/pdbsum/7uk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uk8 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:22, 15 February 2023

OCA — Wed, 15 Feb 2023 10:22:19 GMT

←Older revision		Revision as of 10:22, 15 February 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7uk8 is ~~ON HOLD until Paper~~ Publication	+	==Apo form of YgiC from Escherichia coli K-12==
		+	<StructureSection load='7uk8' size='340' side='right'caption='[[7uk8]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7uk8]] is a 1 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=7UK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UK8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7uk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uk8 OCA], [https://pdbe.org/7uk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uk8 RCSB], [https://www.ebi.ac.uk/pdbsum/7uk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uk8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YGIC_ECOLI YGIC_ECOLI] May be a ligase forming an amide bond. Shows ATPase activity. Despite its similarity to the C-terminal synthetase domain of Gss, is not a glutathionylspermidine (Gsp) synthetase. Cannot synthesize Gsp, glutathione (GSH), or GSH intermediates, from GSH and spermidine, cysteine and glutamate, gamma-glutamylcysteine and spermidine, and gamma-glutamylcysteine and glycine. Does not bind to Gsp.<ref>PMID:23097746</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Polyamines and polyamine-containing metabolites are involved in many cellular processes related to bacterial cell growth and survival. In Escherichia coli, the bifunctional enzyme glutathionylspermidine synthetase/amidase (GspSA) controls the production of glutathionylspermidine, which has a protective role against oxidative stress. E. coli also encodes two enzymes with homology to the synthetase domain of GspSA, YgiC, and YjfC; however, these do not catalyze the formation of glutathionylspermidine, and their catalytic function remained unknown. Here, we detail the structural and functional characterization of YgiC and YjfC. Using X-ray crystallography, the high-resolution crystal structures of YgiC and YjfC were obtained. This revealed that YgiC and YjfC possess multiple substitutions in key residues required for binding of glutathione in GspSA. Despite this difference, these enzymes share a similar active site structure to GspSA, suggesting that they catalyze the formation of an alternate peptide horizontal line spermidine conjugate. As the physiological substrates of YgiC and YjfC are unknown, this was probed using the peptide triglycine as a model substrate. A combination of enzyme activity assays and mass spectrometry revealed that YgiC and YjfC can function as peptide-spermidine ligases, forming a triglycine-spermidine conjugate. For both enzymes, conjugate formation was only observed in the presence of spermidine, but not other common polyamines, supporting that spermidine or a spermidine derivative is the physiological substrate. Importantly, since YgiC and YjfC are widely distributed in Gram-negative bacterial species, this suggests that these enzymes function in a conserved cellular process, representing a currently unknown aspect of bacterial polyamine metabolism.

-	~~Authors~~:	+	Escherichia coli YgiC and YjfC Possess Peptide horizontal line Spermidine Ligase Activity.,Pederick JL, Klose J, Jovcevski B, Pukala TL, Bruning JB Biochemistry. 2023 Feb 6. doi: 10.1021/acs.biochem.2c00592. PMID:36745518<ref>PMID:36745518</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 7uk8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli K-12]]
		+	[[Category: Large Structures]]
		+	[[Category: Bruning JB]]
		+	[[Category: Pederick JL]]

OCA at 04:44, 12 May 2022

OCA — Thu, 12 May 2022 04:44:13 GMT

←Older revision		Revision as of 04:44, 12 May 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7uk8 is ON HOLD	+	The entry 7uk8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7uk8" [edit=sysop:move=sysop]

OCA — Wed, 06 Apr 2022 09:09:00 GMT

Protected "7uk8" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:09, 6 April 2022

OCA: New page: '''Unreleased structure''' The entry 7uk8 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 06 Apr 2022 09:08:59 GMT

New page: '''Unreleased structure''' The entry 7uk8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7uk8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]