OCA at 12:13, 1 February 2024

2024-02-01T12:13:18Z

←Older revision		Revision as of 12:13, 1 February 2024
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	==Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA==		==Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA==
-	<StructureSection load='7ap1' size='340' side='right'caption='[[7ap1]]' scene=''>	+	<StructureSection load='7ap1' size='340' side='right'caption='[[7ap1]], [[Resolution\|resolution]] 2.18Å' 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=7AP1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7AP1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ap1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AP1 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7ap1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ap1 OCA], [~~http~~://pdbe.org/7ap1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7ap1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7ap1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7ap1 ProSAT]</span></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]] 2.18Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=RUZ:[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate'>RUZ</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=7ap1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ap1 OCA], [https://pdbe.org/7ap1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ap1 RCSB], [https://www.ebi.ac.uk/pdbsum/7ap1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ap1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SYS_KLEP7 SYS_KLEP7] 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).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aminoacyl-tRNA synthetases (aaRSs) have become viable targets for the development of antimicrobial agents due to their crucial role in protein translation. A series of six amino acids were coupled to the purine-like 7-amino-5-hydroxymethylbenzimidazole nucleoside analogue following an optimized synthetic pathway. These compounds were designed as aaRS inhibitors and can be considered as 1,3-dideazaadenine analogues carrying a 2-hydroxymethyl substituent. Despite our intentions to obtain N(1)-glycosylated 4-aminobenzimidazole congeners, resembling the natural purine nucleosides glycosylated at the N(9)-position, we obtained the N(3)-glycosylated benzimidazole derivatives as the major products, resembling the respective purine N(7)-glycosylated nucleosides. A series of X-ray crystal structures of class I and II aaRSs in complex with newly synthesized compounds revealed interesting interactions of these "base-flipped" analogues with their targets. While the exocyclic amine of the flipped base mimics the reciprocal interaction of the N(3)-purine atom of aminoacyl-sulfamoyl adenosine (aaSA) congeners, the hydroxymethyl substituent of the flipped base apparently loses part of the standard interactions of the adenine N(1) and the N(6)-amine as seen with aaSA analogues. Upon the evaluation of the inhibitory potency of the newly obtained analogues, nanomolar inhibitory activities were noted for the leucine and isoleucine analogues targeting class I aaRS enzymes, while rather weak inhibitory activity against the corresponding class II aaRSs was observed. This class bias could be further explained by detailed structural analysis.
		+
		+	Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors.,Zhang B, Pang L, Nautiyal M, De Graef S, Gadakh B, Lescrinier E, Rozenski J, Strelkov SV, Weeks SD, Van Aerschot A Molecules. 2020 Oct 16;25(20). pii: molecules25204751. doi:, 10.3390/molecules25204751. PMID:33081246<ref>PMID:33081246</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ap1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: De Graef S]]		[[Category: De Graef S]]

OCA at 08:02, 11 November 2020

2020-11-11T08:02:06Z

←Older revision		Revision as of 08:02, 11 November 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7ap1 ~~is ON HOLD~~	+	==Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA==
-		+	<StructureSection load='7ap1' size='340' side='right'caption='[[7ap1]]' scene=''>
-	~~Authors~~: ~~Pang~~, L., ~~De Graef~~, S., ~~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=7AP1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7AP1 FirstGlance]. <br>
-	~~Description: Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7ap1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ap1 OCA], [http://pdbe.org/7ap1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7ap1 RCSB], [http://www.ebi.ac.uk/pdbsum/7ap1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7ap1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Weeks,~~ S.D]]	+	__TOC__
-	[[Category: ~~De Graef, S~~]]	+	</StructureSection>
-	[[Category: Strelkov~~, S.V~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Pang, L~~]]	+	[[Category: De Graef S]]
		+	[[Category: Pang L]]
		+	[[Category: Strelkov SV]]
		+	[[Category: Weeks SD]]

OCA: Protected "7ap1" [edit=sysop:move=sysop]

2020-10-21T06:40:36Z

Protected "7ap1" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:40, 21 October 2020

OCA: New page: '''Unreleased structure''' The entry 7ap1 is ON HOLD Authors: Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D. Description: Klebsiella pneumoniae Seryl-tRNA synthetase in Complex wi...

2020-10-21T06:40:35Z

New page: '''Unreleased structure''' The entry 7ap1 is ON HOLD Authors: Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D. Description: Klebsiella pneumoniae Seryl-tRNA synthetase in Complex wi...

New page

'''Unreleased structure'''

The entry 7ap1 is ON HOLD

Authors: Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D.

Description: Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA
[[Category: Unreleased Structures]]
[[Category: Weeks, S.D]]
[[Category: De Graef, S]]
[[Category: Strelkov, S.V]]
[[Category: Pang, L]]

7ap1 - Revision history

OCA at 12:13, 1 February 2024

OCA at 08:02, 11 November 2020

OCA: Protected "7ap1" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7ap1 is ON HOLD Authors: Pang, L., De Graef, S., Strelkov, S.V., Weeks, S.D. Description: Klebsiella pneumoniae Seryl-tRNA synthetase in Complex wi...