8i1z - Revision history

OCA at 19:52, 29 May 2024

OCA — Wed, 29 May 2024 19:52:37 GMT

←Older revision		Revision as of 19:52, 29 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8i1z]] 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=8I1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8I1Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[8i1z]] 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=8I1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8I1Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=O7R:1-(2,3-dihydro-1-benzofuran-5-yl)ethanone'>O7R</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYM:TRYPTOPHANYL-5AMP'>TYM</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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=O7R:1-(2,3-dihydro-1-benzofuran-5-yl)ethanone'>O7R</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYM:TRYPTOPHANYL-5AMP'>TYM</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=8i1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8i1z OCA], [https://pdbe.org/8i1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8i1z RCSB], [https://www.ebi.ac.uk/pdbsum/8i1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8i1z 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=8i1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8i1z OCA], [https://pdbe.org/8i1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8i1z RCSB], [https://www.ebi.ac.uk/pdbsum/8i1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8i1z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SYW_ECOLI SYW_ECOLI] Catalyzes the attachment of tryptophan to tRNA(Trp). Amino acylates tRNA(Trp) with both L- and D-tryptophan, although D-tryptophan is a poor substrate (PubMed:10918062).[HAMAP-Rule:MF_00140]<ref>PMID:10918062</ref>		[https://www.uniprot.org/uniprot/SYW_ECOLI SYW_ECOLI] Catalyzes the attachment of tryptophan to tRNA(Trp). Amino acylates tRNA(Trp) with both L- and D-tryptophan, although D-tryptophan is a poor substrate (PubMed:10918062).[HAMAP-Rule:MF_00140]<ref>PMID:10918062</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tryptophanyl-tRNA synthetase (TrpRS) links tryptophan to tRNATrp, thereby playing an indispensable role in protein translation. Unlike most class I aminoacyl-tRNA synthetases (AARSs), TrpRS functions as a homodimer. Herein, we captured an 'open-closed' asymmetric structure of Escherichia coli TrpRS (EcTrpRS) with one active site occupied by a copurified intermediate product and the other remaining empty, providing structural evidence for the long-discussed half-of-the-sites reactivity of bacterial TrpRS. In contrast to its human counterpart, bacterial TrpRS may rely on this asymmetric conformation to functionally bind with substrate tRNA. As this asymmetric conformation is probably a dominant form of TrpRS purified from bacterial cells, we performed fragment screening against asymmetric EcTrpRS to support antibacterial discovery. Nineteen fragment hits were identified, and 8 of them were successfully cocrystallized with EcTrpRS. While a fragment named niraparib bound to the L-Trp binding site of the 'open' subunit, the other 7 fragments all bound to an unprecedented pocket at the interface between two TrpRS subunits. Binding of these fragments relies on residues specific to bacterial TrpRS, avoiding undesired interactions with human TrpRS. These findings improve our understanding of the catalytic mechanism of this important enzyme and will also facilitate the discovery of bacterial TrpRS inhibitors with therapeutic potential.
		+
		+	An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening.,Xiang M, Xia K, Chen B, Luo Z, Yu Y, Jiang L, Zhou H Nucleic Acids Res. 2023 May 22;51(9):4637-4649. doi: 10.1093/nar/gkad278. PMID:37070195<ref>PMID:37070195</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 8i1z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:35, 12 April 2023

OCA — Wed, 12 Apr 2023 20:35:40 GMT

←Older revision		Revision as of 20:35, 12 April 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8i1z is ~~ON HOLD until Paper Publication~~	+	==E. coli tryptophanyl-tRNA synthetase bound with a chemical fragment==
-		+	<StructureSection load='8i1z' size='340' side='right'caption='[[8i1z]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[8i1z]] 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=8I1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8I1Z FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=O7R:1-(2,3-dihydro-1-benzofuran-5-yl)ethanone'>O7R</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYM:TRYPTOPHANYL-5AMP'>TYM</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8i1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8i1z OCA], [https://pdbe.org/8i1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8i1z RCSB], [https://www.ebi.ac.uk/pdbsum/8i1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8i1z ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SYW_ECOLI SYW_ECOLI] Catalyzes the attachment of tryptophan to tRNA(Trp). Amino acylates tRNA(Trp) with both L- and D-tryptophan, although D-tryptophan is a poor substrate (PubMed:10918062).[HAMAP-Rule:MF_00140]<ref>PMID:10918062</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli K-12]]
		+	[[Category: Large Structures]]
		+	[[Category: Xiang M]]
		+	[[Category: Zhou H]]

OCA at 05:25, 8 February 2023

OCA — Wed, 08 Feb 2023 05:25:01 GMT

←Older revision		Revision as of 05:25, 8 February 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8i1z is ON HOLD	+	The entry 8i1z is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8i1z" [edit=sysop:move=sysop]

OCA — Wed, 18 Jan 2023 05:31:56 GMT

Protected "8i1z" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:31, 18 January 2023

OCA: New page: '''Unreleased structure''' The entry 8i1z is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 18 Jan 2023 05:31:54 GMT

New page: '''Unreleased structure''' The entry 8i1z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8i1z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]