7xyl - Revision history

OCA at 18:03, 29 November 2023

2023-11-29T18:03:33Z

←Older revision		Revision as of 18:03, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7xyl]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_luteocolor Streptomyces luteocolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XYL FirstGlance]. <br>		<table><tr><td colspan='2'>[[7xyl]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_luteocolor Streptomyces luteocolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XYL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=I55:[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(~{E})-[(3~{a}~{S},7~{R},7~{a}~{S})-7-oxidanyl-4-oxidanylidene-3,3~{a},5,6,7,7~{a}-hexahydro-1~{H}-imidazo[4,5-c]pyridin-2-ylidene]amino]-5-(2-azanylethanoylamino)-2-(hydroxymethyl)-4-oxidanyl-oxan-3-yl]+carbamate'>I55</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]] 2.099Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=I55:[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(~{E})-[(3~{a}~{S},7~{R},7~{a}~{S})-7-oxidanyl-4-oxidanylidene-3,3~{a},5,6,7,7~{a}-hexahydro-1~{H}-imidazo[4,5-c]pyridin-2-ylidene]amino]-5-(2-azanylethanoylamino)-2-(hydroxymethyl)-4-oxidanyl-oxan-3-yl]+carbamate'>I55</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=7xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xyl OCA], [https://pdbe.org/7xyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xyl RCSB], [https://www.ebi.ac.uk/pdbsum/7xyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xyl 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=7xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xyl OCA], [https://pdbe.org/7xyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xyl RCSB], [https://www.ebi.ac.uk/pdbsum/7xyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xyl ProSAT]</span></td></tr>
	</table>		</table>

OCA at 05:35, 31 May 2023

2023-05-31T05:35:03Z

←Older revision		Revision as of 05:35, 31 May 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 7xyl is ~~ON HOLD until Paper~~ Publication	+	==E426Q-glycine-glycylthricin complex==
		+	<StructureSection load='7xyl' size='340' side='right'caption='[[7xyl]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7xyl]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_luteocolor Streptomyces luteocolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XYL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=I55:[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(~{E})-[(3~{a}~{S},7~{R},7~{a}~{S})-7-oxidanyl-4-oxidanylidene-3,3~{a},5,6,7,7~{a}-hexahydro-1~{H}-imidazo[4,5-c]pyridin-2-ylidene]amino]-5-(2-azanylethanoylamino)-2-(hydroxymethyl)-4-oxidanyl-oxan-3-yl]+carbamate'>I55</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=7xyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xyl OCA], [https://pdbe.org/7xyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xyl RCSB], [https://www.ebi.ac.uk/pdbsum/7xyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xyl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A125SZC1_9ACTN A0A125SZC1_9ACTN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Oxidized cysteine residues are highly reactive and can form functional covalent conjugates, of which the allosteric redox switch formed by the lysine-cysteine NOS bridge is an example. Here, we report a noncanonical FAD-dependent enzyme Orf1 that adds a glycine-derived N-formimidoyl group to glycinothricin to form the antibiotic BD-12. X-ray crystallography was used to investigate this complex enzymatic process, which showed Orf1 has two substrate-binding sites that sit 13.5 A apart unlike canonical FAD-dependent oxidoreductases. One site could accommodate glycine and the other glycinothricin or glycylthricin. Moreover, an intermediate-enzyme adduct with a NOS-covalent linkage was observed in the later site, where it acts as a two-scissile-bond linkage facilitating nucleophilic addition and cofactor-free decarboxylation. The chain length of nucleophilic acceptors vies with bond cleavage sites at either N-O or O-S accounting for N-formimidoylation or N-iminoacetylation. The resultant product is no longer sensitive to aminoglycoside-modifying enzymes, a strategy that antibiotic-producing species employ to counter drug resistance in competing species.

-	~~Authors~~:	+	N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry.,Wang YL, Chang CY, Hsu NS, Lo IW, Lin KH, Chen CL, Chang CF, Wang ZC, Ogasawara Y, Dairi T, Maruyama C, Hamano Y, Li TL Nat Commun. 2023 May 3;14(1):2528. doi: 10.1038/s41467-023-38218-w. PMID:37137912<ref>PMID:37137912</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 7xyl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Streptomyces luteocolor]]
		+	[[Category: Li TL]]
		+	[[Category: Wang YL]]

OCA at 06:07, 29 June 2022

2022-06-29T06:07:26Z

←Older revision		Revision as of 06:07, 29 June 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2022-06-08T04:05:39Z

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

←Older revision

Revision as of 04:05, 8 June 2022

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

2022-06-08T04:05:38Z

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

New page

'''Unreleased structure'''

The entry 7xyl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]