6r1o - Revision history

OCA at 12:13, 24 January 2024

2024-01-24T12:13:20Z

←Older revision		Revision as of 12:13, 24 January 2024
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	<StructureSection load='6r1o' size='340' side='right'caption='[[6r1o]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6r1o' size='340' side='right'caption='[[6r1o]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r1o]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R1O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R1O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r1o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R1O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R1O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=JPE:[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-pyridin-3-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate'>JPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.6Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=JPE:[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-pyridin-3-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate'>JPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=6r1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r1o OCA], [~~http~~://pdbe.org/6r1o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r1o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r1o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r1o 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=6r1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r1o OCA], [https://pdbe.org/6r1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r1o RCSB], [https://www.ebi.ac.uk/pdbsum/6r1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r1o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A1X3JK72_ECOLX A0A1X3JK72_ECOLX]~~] Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).~~[HAMAP-Rule~~:~~MF_00176]~~	+	[https://www.uniprot.org/uniprot/SYS_ECOLI SYS_ECOLI] Catalyzes the attachment of serine to tRNA(Ser) (PubMed:7537870). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).<ref>PMID:2963963</ref> <ref>PMID:7537870</ref> <ref>PMID:8065908</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6r1o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6r1o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Serine--tRNA ligase]]~~	+	[[Category: Cain R]]
-	[[Category: Cain, R]]	+	[[Category: Roper DI]]
-	[[Category: Roper~~, D I~~]]	+	[[Category: Salimraj R]]
-	[[Category: Salimraj, R]]	+
-	~~[[Category: Aminoacyl-trna synthetase]]~~	+
-	~~[[Category: Class ii]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Protein synthesis~~]]	+

OCA at 16:16, 22 January 2020

2020-01-22T16:16:14Z

←Older revision		Revision as of 16:16, 22 January 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6r1o is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of E. coli seryl-tRNA synthetase complexed to a seryl sulfamoyl adenosine derivative==
		+	<StructureSection load='6r1o' size='340' side='right'caption='[[6r1o]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r1o]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R1O FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=JPE:[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-pyridin-3-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate'>JPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </span></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=6r1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r1o OCA], [http://pdbe.org/6r1o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r1o RCSB], [http://www.ebi.ac.uk/pdbsum/6r1o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r1o ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A1X3JK72_ECOLX A0A1X3JK72_ECOLX]] Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).[HAMAP-Rule:MF_00176]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aminoacyl-tRNA synthetases are ubiquitous and essential enzymes for protein synthesis and also a variety of other metabolic processes, especially in bacterial species. Bacterial aminoacyl-tRNA synthetases represent attractive and validated targets for antimicrobial drug discovery if issues of prokaryotic versus eukaryotic selectivity and antibiotic resistance generation can be addressed. We have determined high-resolution X-ray crystal structures of the Escherichia coli and Staphylococcus aureus seryl-tRNA synthetases in complex with aminoacyl adenylate analogues and applied a structure-based drug discovery approach to explore and identify a series of small molecule inhibitors that selectively inhibit bacterial seryl-tRNA synthetases with greater than 2 orders of magnitude compared to their human homologue, demonstrating a route to the selective chemical inhibition of these bacterial targets.

-	~~Authors: Salimraj, R~~., Cain, R., ~~Roper~~, D.I.	+	Structure-Guided Enhancement of Selectivity of Chemical Probe Inhibitors Targeting Bacterial Seryl-tRNA Synthetase.,Cain R, Salimraj R, Punekar AS, Bellini D, Fishwick CWG, Czaplewski L, Scott DJ, Harris G, Dowson CG, Lloyd AJ, Roper DI J Med Chem. 2019 Nov 14;62(21):9703-9717. doi: 10.1021/acs.jmedchem.9b01131. Epub, 2019 Nov 5. PMID:31626547<ref>PMID:31626547</ref>

-	~~Description: Crystal structure~~ of E. ~~coli seryl~~-~~tRNA synthetase complexed to a seryl sulfamoyl adenosine derivative~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Roper, D.I~~]]	+	<div class="pdbe-citations 6r1o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Serine--tRNA ligase]]
	[[Category: Cain, R]]		[[Category: Cain, R]]
		+	[[Category: Roper, D I]]
	[[Category: Salimraj, R]]		[[Category: Salimraj, R]]
		+	[[Category: Aminoacyl-trna synthetase]]
		+	[[Category: Class ii]]
		+	[[Category: Inhibitor]]
		+	[[Category: Ligase]]
		+	[[Category: Protein synthesis]]

OCA at 05:37, 10 April 2019

2019-04-10T05:37:21Z

←Older revision		Revision as of 05:37, 10 April 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6r1o is ON HOLD	+	The entry 6r1o is ON HOLD until Paper Publication

	Authors: Salimraj, R., Cain, R., Roper, D.I.		Authors: Salimraj, R., Cain, R., Roper, D.I.
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	Description: Crystal structure of E. coli seryl-tRNA synthetase complexed to a seryl sulfamoyl adenosine derivative		Description: Crystal structure of E. coli seryl-tRNA synthetase complexed to a seryl sulfamoyl adenosine derivative
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Salimraj, R]]
	[[Category: Roper, D.I]]		[[Category: Roper, D.I]]
	[[Category: Cain, R]]		[[Category: Cain, R]]
		+	[[Category: Salimraj, R]]

OCA: Protected "6r1o" [edit=sysop:move=sysop]

2019-03-20T06:19:34Z

Protected "6r1o" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:19, 20 March 2019

OCA: New page: '''Unreleased structure''' The entry 6r1o is ON HOLD Authors: Salimraj, R., Cain, R., Roper, D.I. Description: Crystal structure of E. coli seryl-tRNA synthetase complexed to a seryl s...

2019-03-20T06:19:33Z

New page: '''Unreleased structure''' The entry 6r1o is ON HOLD Authors: Salimraj, R., Cain, R., Roper, D.I. Description: Crystal structure of E. coli seryl-tRNA synthetase complexed to a seryl s...

New page

'''Unreleased structure'''

The entry 6r1o is ON HOLD

Authors: Salimraj, R., Cain, R., Roper, D.I.

Description: Crystal structure of E. coli seryl-tRNA synthetase complexed to a seryl sulfamoyl adenosine derivative
[[Category: Unreleased Structures]]
[[Category: Salimraj, R]]
[[Category: Roper, D.I]]
[[Category: Cain, R]]