7ot3 - Revision history

OCA at 12:55, 1 February 2024

OCA — Thu, 01 Feb 2024 12:55:49 GMT

←Older revision		Revision as of 12:55, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7ot3' size='340' side='right'caption='[[7ot3]], [[Resolution\|resolution]] 2.53Å' scene=''>		<StructureSection load='7ot3' size='340' side='right'caption='[[7ot3]], [[Resolution\|resolution]] 2.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ot3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OT3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ot3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OT3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0W4:~{N}-[(2-chlorophenyl)methyl]-3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide'>0W4</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.53Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7ot2\|7ot2]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0W4:~{N}-[(2-chlorophenyl)methyl]-3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide'>0W4</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=7ot3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ot3 OCA], [https://pdbe.org/7ot3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ot3 RCSB], [https://www.ebi.ac.uk/pdbsum/7ot3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ot3 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=7ot3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ot3 OCA], [https://pdbe.org/7ot3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ot3 RCSB], [https://www.ebi.ac.uk/pdbsum/7ot3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ot3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SYEP_HUMAN SYEP_HUMAN]] Catalyzes the attachment of the cognate amino acid to the corresponding tRNA in a two-step reaction: the amino acid is first activated by ATP to form a covalent intermediate with AMP and is then transferred to the acceptor end of the cognate tRNA. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation and subsequent phosphorylation dissociates from the multisynthetase complex and assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation.<ref>PMID:1756734</ref> <ref>PMID:15479637</ref> <ref>PMID:23071094</ref>	+	[https://www.uniprot.org/uniprot/SYEP_HUMAN SYEP_HUMAN] Catalyzes the attachment of the cognate amino acid to the corresponding tRNA in a two-step reaction: the amino acid is first activated by ATP to form a covalent intermediate with AMP and is then transferred to the acceptor end of the cognate tRNA. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation and subsequent phosphorylation dissociates from the multisynthetase complex and assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation.<ref>PMID:1756734</ref> <ref>PMID:15479637</ref> <ref>PMID:23071094</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7ot3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7ot3" 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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pang, L]]	+	[[Category: Pang L]]
-	[[Category: Strelkov~~, S V~~]]	+	[[Category: Strelkov SV]]
-	[[Category: Weeks~~, S D~~]]	+	[[Category: Weeks SD]]
-	[[Category: Zitko, J]]	+	[[Category: Zitko J]]
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Protein-inhibitor complex]]~~	+
-	~~[[Category: Trna synthetase~~]]	+

OCA at 07:05, 22 September 2021

OCA — Wed, 22 Sep 2021 07:05:15 GMT

←Older revision		Revision as of 07:05, 22 September 2021
Line 1:		Line 1:

	==Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 3b==		==Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 3b==
-	<StructureSection load='7ot3' size='340' side='right'caption='[[7ot3]]' scene=''>	+	<StructureSection load='7ot3' size='340' side='right'caption='[[7ot3]], [[Resolution\|resolution]] 2.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OT3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ot3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OT3 FirstGlance]. <br>
-	</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=7ot3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ot3 OCA], [https://pdbe.org/7ot3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ot3 RCSB], [https://www.ebi.ac.uk/pdbsum/7ot3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ot3 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0W4:~{N}-[(2-chlorophenyl)methyl]-3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide'>0W4</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7ot2\|7ot2]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=7ot3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ot3 OCA], [https://pdbe.org/7ot3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ot3 RCSB], [https://www.ebi.ac.uk/pdbsum/7ot3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ot3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/SYEP_HUMAN SYEP_HUMAN]] Catalyzes the attachment of the cognate amino acid to the corresponding tRNA in a two-step reaction: the amino acid is first activated by ATP to form a covalent intermediate with AMP and is then transferred to the acceptor end of the cognate tRNA. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation and subsequent phosphorylation dissociates from the multisynthetase complex and assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation.<ref>PMID:1756734</ref> <ref>PMID:15479637</ref> <ref>PMID:23071094</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human cytosolic prolyl-tRNA synthetase (HcProRS) catalyses the formation of the prolyl-tRNA(Pro), playing an important role in protein synthesis. Inhibition of HcProRS activity has been shown to have potential benefits in the treatment of fibrosis, autoimmune diseases and cancer. Recently, potent pyrazinamide-based inhibitors were identified by a high-throughput screening (HTS) method, but no further elaboration was reported. The pyrazinamide core is a bioactive fragment found in numerous clinically validated drugs and has been subjected to various modifications. Therefore, we applied a virtual screening protocol to our in-house library of pyrazinamide-containing small molecules, searching for potential novel HcProRS inhibitors. We identified a series of 3-benzylaminopyrazine-2-carboxamide derivatives as positive hits. Five of them were confirmed by a thermal shift assay (TSA) with the best compounds 3b and 3c showing EC50 values of 3.77 and 7.34 microM, respectively, in the presence of 1 mM of proline (Pro) and 3.45 microM enzyme concentration. Co-crystal structures of HcProRS in complex with these compounds and Pro confirmed the initial docking studies and show how the Pro facilitates binding of the ligands that compete with ATP substrate. Modelling 3b into other human class II aminoacyl-tRNA synthetases (aaRSs) indicated that the subtle differences in the ATP binding site of these enzymes likely contribute to its potential selective binding of HcProRS. Taken together, this study successfully identified novel HcProRS binders from our anti-tuberculosis in-house compound library, displaying opportunities for repurposing old drug candidates for new applications such as therapeutics in HcProRS-related diseases.
		+
		+	Towards Novel 3-Aminopyrazinamide-Based Prolyl-tRNA Synthetase Inhibitors: In Silico Modelling, Thermal Shift Assay and Structural Studies.,Pang L, Weeks SD, Juhas M, Strelkov SV, Zitko J, Van Aerschot A Int J Mol Sci. 2021 Jul 21;22(15). pii: ijms22157793. doi: 10.3390/ijms22157793. PMID:34360555<ref>PMID:34360555</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ot3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pang L]]	+	[[Category: Pang, L]]
-	[[Category: Strelkov SV]]	+	[[Category: Strelkov, S V]]
-	[[Category: Weeks SD]]	+	[[Category: Weeks, S D]]
-	[[Category: Zitko J]]	+	[[Category: Zitko, J]]
		+	[[Category: Beta barrel]]
		+	[[Category: Ligase]]
		+	[[Category: Protein-inhibitor complex]]
		+	[[Category: Trna synthetase]]

OCA at 10:36, 28 July 2021

OCA — Wed, 28 Jul 2021 10:36:15 GMT

←Older revision		Revision as of 10:36, 28 July 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7ot3 ~~is ON HOLD until Paper Publication~~	+	==Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 3b==
-		+	<StructureSection load='7ot3' size='340' side='right'caption='[[7ot3]]' scene=''>
-	~~Authors~~: ~~Pang~~, L., ~~Zitko~~, J., ~~Strelkov, S~~.V., ~~Weeks, S~~.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OT3 FirstGlance]. <br>
-	~~Description: Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 3b~~	+	</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=7ot3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ot3 OCA], [https://pdbe.org/7ot3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ot3 RCSB], [https://www.ebi.ac.uk/pdbsum/7ot3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ot3 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Pang, L]]	+	__TOC__
-	[[Category: Strelkov~~, S.V~~]]	+	</StructureSection>
-	[[Category: Weeks~~, S.D~~]]	+	[[Category: Large Structures]]
-	[[Category: Zitko, J]]	+	[[Category: Pang L]]
		+	[[Category: Strelkov SV]]
		+	[[Category: Weeks SD]]
		+	[[Category: Zitko J]]

OCA: Protected "7ot3" [edit=sysop:move=sysop]

OCA — Thu, 17 Jun 2021 13:53:05 GMT

Protected "7ot3" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:53, 17 June 2021

OCA: New page: '''Unreleased structure''' The entry 7ot3 is ON HOLD until Paper Publication Authors: Pang, L., Zitko, J., Strelkov, S.V., Weeks, S.D. Description: Human Prolyl-tRNA Synthetase in Comp...

OCA — Thu, 17 Jun 2021 13:53:04 GMT

New page: '''Unreleased structure''' The entry 7ot3 is ON HOLD until Paper Publication Authors: Pang, L., Zitko, J., Strelkov, S.V., Weeks, S.D. Description: Human Prolyl-tRNA Synthetase in Comp...

New page

'''Unreleased structure'''

The entry 7ot3 is ON HOLD until Paper Publication

Authors: Pang, L., Zitko, J., Strelkov, S.V., Weeks, S.D.

Description: Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 3b
[[Category: Unreleased Structures]]
[[Category: Pang, L]]
[[Category: Strelkov, S.V]]
[[Category: Weeks, S.D]]
[[Category: Zitko, J]]