7wpi - Revision history

OCA at 17:43, 29 November 2023

2023-11-29T17:43:13Z

←Older revision		Revision as of 17:43, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7wpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WPI FirstGlance]. <br>		<table><tr><td colspan='2'>[[7wpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WPI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1V7:2-(4-bromanyl-3-oxidanyl-phenyl)-1-[(1R)-2-[2-(2-tert-butylphenoxy)ethanoylamino]-1-(3,4-dimethoxyphenyl)ethyl]-N-methyl-benzimidazole-5-carboxamide'>1V7</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.92Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1V7:2-(4-bromanyl-3-oxidanyl-phenyl)-1-[(1R)-2-[2-(2-tert-butylphenoxy)ethanoylamino]-1-(3,4-dimethoxyphenyl)ethyl]-N-methyl-benzimidazole-5-carboxamide'>1V7</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=7wpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wpi OCA], [https://pdbe.org/7wpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wpi RCSB], [https://www.ebi.ac.uk/pdbsum/7wpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wpi 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=7wpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wpi OCA], [https://pdbe.org/7wpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wpi RCSB], [https://www.ebi.ac.uk/pdbsum/7wpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wpi ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:26, 24 November 2022

2022-11-24T10:26:56Z

←Older revision		Revision as of 10:26, 24 November 2022
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	<StructureSection load='7wpi' size='340' side='right'caption='[[7wpi]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='7wpi' size='340' side='right'caption='[[7wpi]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7wpi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WPI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7wpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WPI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1V7:2-(4-bromanyl-3-oxidanyl-phenyl)-1-[(1R)-2-[2-(2-tert-butylphenoxy)ethanoylamino]-1-(3,4-dimethoxyphenyl)ethyl]-N-methyl-benzimidazole-5-carboxamide'>1V7</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1V7:2-(4-bromanyl-3-oxidanyl-phenyl)-1-[(1R)-2-[2-(2-tert-butylphenoxy)ethanoylamino]-1-(3,4-dimethoxyphenyl)ethyl]-N-methyl-benzimidazole-5-carboxamide'>1V7</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methionine--tRNA_ligase Methionine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.10 6.1.1.10] </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=7wpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wpi OCA], [https://pdbe.org/7wpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wpi RCSB], [https://www.ebi.ac.uk/pdbsum/7wpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wpi 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=7wpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wpi OCA], [https://pdbe.org/7wpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wpi RCSB], [https://www.ebi.ac.uk/pdbsum/7wpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wpi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SYM_STAAC SYM_STAAC]] Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.	+	[https://www.uniprot.org/uniprot/SYM_STAAC SYM_STAAC] Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.
	<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 7wpi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7wpi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Methionine--tRNA ligase~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: Cai, Z]]	+	[[Category: Cai Z]]
-	[[Category: Chen, B]]	+	[[Category: Chen B]]
-	[[Category: Gu, Q]]	+	[[Category: Gu Q]]
-	[[Category: Lu, F]]	+	[[Category: Lu F]]
-	[[Category: Luo, Z]]	+	[[Category: Luo Z]]
-	[[Category: Qiu, H]]	+	[[Category: Qiu H]]
-	[[Category: Xu, J]]	+	[[Category: Xu J]]
-	[[Category: Yi, J]]	+	[[Category: Yi J]]
-	[[Category: Zhou, H]]	+	[[Category: Zhou H]]
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Ligase-inhibitor complex~~]]	+

OCA at 10:29, 18 May 2022

2022-05-18T10:29:19Z

←Older revision		Revision as of 10:29, 18 May 2022
Line 1:		Line 1:

	==Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a phenylbenzimidazole inhibitor==		==Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a phenylbenzimidazole inhibitor==
-	<StructureSection load='7wpi' size='340' side='right'caption='[[7wpi]]' scene=''>	+	<StructureSection load='7wpi' size='340' side='right'caption='[[7wpi]], [[Resolution\|resolution]] 1.92Å' 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=7WPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WPI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7wpi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WPI 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=7wpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wpi OCA], [https://pdbe.org/7wpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wpi RCSB], [https://www.ebi.ac.uk/pdbsum/7wpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wpi 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=1V7:2-(4-bromanyl-3-oxidanyl-phenyl)-1-[(1R)-2-[2-(2-tert-butylphenoxy)ethanoylamino]-1-(3,4-dimethoxyphenyl)ethyl]-N-methyl-benzimidazole-5-carboxamide'>1V7</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methionine--tRNA_ligase Methionine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.10 6.1.1.10] </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=7wpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wpi OCA], [https://pdbe.org/7wpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wpi RCSB], [https://www.ebi.ac.uk/pdbsum/7wpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wpi ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/SYM_STAAC SYM_STAAC]] Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methionyl-tRNA synthetase (MetRS) charges tRNAMet with l-methionine (L-Met) to decode the ATG codon for protein translation, making it indispensable for all cellular lives. Many gram-positive bacteria use a type 1 MetRS (MetRS1), which is considered a promising antimicrobial drug target due to its low sequence identity with human cytosolic MetRS (HcMetRS, which belongs to MetRS2). Here, we report crystal structures of a representative MetRS1 from Staphylococcus aureus (SaMetRS) in its apo and substrate-binding forms. The connecting peptide (CP) domain of SaMetRS differs from HcMetRS in structural organization and dynamic movement. We screened 1049 chemical fragments against SaMetRS preincubated with or without substrate ATP, and ten hits were identified. Four cocrystal structures revealed that the fragments bound to either the L-Met binding site or an auxiliary pocket near the tRNA CCA end binding site of SaMetRS. Interestingly, fragment binding was enhanced by ATP in most cases, suggesting a potential ATP-assisted ligand binding mechanism in MetRS1. Moreover, co-binding with ATP was also observed in our cocrystal structure of SaMetRS with a class of newly reported inhibitors that simultaneously occupied the auxiliary pocket, tRNA site and L-Met site. Our findings will inspire the development of new MetRS1 inhibitors for fighting microbial infections.
		+
		+	Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase.,Yi J, Cai Z, Qiu H, Lu F, Luo Z, Chen B, Gu Q, Xu J, Zhou H Nucleic Acids Res. 2022 Apr 26. pii: 6574669. doi: 10.1093/nar/gkac285. PMID:35474479<ref>PMID:35474479</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7wpi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cai Z]]	+	[[Category: Methionine--tRNA ligase]]
-	[[Category: Chen B]]	+	[[Category: Cai, Z]]
-	[[Category: Gu Q]]	+	[[Category: Chen, B]]
-	[[Category: Lu F]]	+	[[Category: Gu, Q]]
-	[[Category: Luo Z]]	+	[[Category: Lu, F]]
-	[[Category: Qiu H]]	+	[[Category: Luo, Z]]
-	[[Category: Xu J]]	+	[[Category: Qiu, H]]
-	[[Category: Yi J]]	+	[[Category: Xu, J]]
-	[[Category: Zhou H]]	+	[[Category: Yi, J]]
		+	[[Category: Zhou, H]]
		+	[[Category: Inhibitor]]
		+	[[Category: Ligase]]
		+	[[Category: Ligase-inhibitor complex]]

OCA at 11:40, 27 April 2022

2022-04-27T11:40:31Z

←Older revision		Revision as of 11:40, 27 April 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7wpi is ~~ON HOLD until Paper Publication~~	+	==Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a phenylbenzimidazole inhibitor==
-		+	<StructureSection load='7wpi' size='340' side='right'caption='[[7wpi]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WPI FirstGlance]. <br>
-	~~Description~~:	+	</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=7wpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wpi OCA], [https://pdbe.org/7wpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wpi RCSB], [https://www.ebi.ac.uk/pdbsum/7wpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wpi ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cai Z]]
		+	[[Category: Chen B]]
		+	[[Category: Gu Q]]
		+	[[Category: Lu F]]
		+	[[Category: Luo Z]]
		+	[[Category: Qiu H]]
		+	[[Category: Xu J]]
		+	[[Category: Yi J]]
		+	[[Category: Zhou H]]

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

2022-02-02T05:48:48Z

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

←Older revision

Revision as of 05:48, 2 February 2022

OCA: New page: '''Unreleased structure''' The entry 7wpi is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2022-02-02T05:48:47Z

New page: '''Unreleased structure''' The entry 7wpi is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7wpi is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]