6kid - Revision history

OCA at 10:33, 22 November 2023

OCA — Wed, 22 Nov 2023 10:33:47 GMT

←Older revision		Revision as of 10:33, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6kid' size='340' side='right'caption='[[6kid]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='6kid' size='340' side='right'caption='[[6kid]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kid]] is a 1 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=6KID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KID FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kid]] is a 1 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=6KID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KID FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ATP:ADENOSINE~~-~~5-TRIPHOSPHATE'>ATP</scene>~~, ~~<scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 3.15Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~LARS, KIAA1352 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=9606 HUMAN])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Leucine--tRNA_ligase Leucine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.4 6.1.1.4]~~ </~~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=6kid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kid OCA], [https://pdbe.org/6kid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kid RCSB], [https://www.ebi.ac.uk/pdbsum/6kid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kid 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=6kid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kid OCA], [https://pdbe.org/6kid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kid RCSB], [https://www.ebi.ac.uk/pdbsum/6kid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kid ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/SYLC_HUMAN SYLC_HUMAN]] Acute infantile liver failure-multisystemic involvement syndrome. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/SYLC_HUMAN SYLC_HUMAN] Acute infantile liver failure-multisystemic involvement syndrome. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SYLC_HUMAN SYLC_HUMAN]] Catalyzes the specific attachment of an amino acid to its cognate tRNA in a two step reaction: the amino acid (AA) is first activated by ATP to form AA-AMP and then transferred to the acceptor end of the tRNA. Exhibits a post-transfer editing activity to hydrolyze mischarged tRNAs.<ref>PMID:19426743</ref>	+	[https://www.uniprot.org/uniprot/SYLC_HUMAN SYLC_HUMAN] Catalyzes the specific attachment of an amino acid to its cognate tRNA in a two step reaction: the amino acid (AA) is first activated by ATP to form AA-AMP and then transferred to the acceptor end of the tRNA. Exhibits a post-transfer editing activity to hydrolyze mischarged tRNAs.<ref>PMID:19426743</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Leucine--tRNA ligase]]~~	+	[[Category: Hwang KY]]
-	[[Category: Hwang~~, K Y~~]]	+	[[Category: Kim S]]
-	[[Category: Kim, S]]	+	[[Category: Son J]]
-	[[Category: Son, J]]	+
-	~~[[Category: Atp-bound structure]]~~	+
-	~~[[Category: Leucyl-trna synthetase]]~~	+
-	~~[[Category: Ligase~~]]	+

OCA at 06:11, 11 August 2021

OCA — Wed, 11 Aug 2021 06:11:17 GMT

←Older revision		Revision as of 06:11, 11 August 2021
Line 1:		Line 1:

	==Crystal structure of human leucyl-tRNA synthetase, ATP-bound form==		==Crystal structure of human leucyl-tRNA synthetase, ATP-bound form==
-	<StructureSection load='6kid' size='340' side='right'caption='[[6kid]]' scene=''>	+	<StructureSection load='6kid' size='340' side='right'caption='[[6kid]], [[Resolution\|resolution]] 3.15Å' 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=6KID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KID FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kid]] is a 1 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=6KID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KID 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=6kid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kid OCA], [https://pdbe.org/6kid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kid RCSB], [https://www.ebi.ac.uk/pdbsum/6kid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kid 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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LARS, KIAA1352 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Leucine--tRNA_ligase Leucine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.4 6.1.1.4] </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=6kid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kid OCA], [https://pdbe.org/6kid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kid RCSB], [https://www.ebi.ac.uk/pdbsum/6kid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kid ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[[https://www.uniprot.org/uniprot/SYLC_HUMAN SYLC_HUMAN]] Acute infantile liver failure-multisystemic involvement syndrome. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/SYLC_HUMAN SYLC_HUMAN]] Catalyzes the specific attachment of an amino acid to its cognate tRNA in a two step reaction: the amino acid (AA) is first activated by ATP to form AA-AMP and then transferred to the acceptor end of the tRNA. Exhibits a post-transfer editing activity to hydrolyze mischarged tRNAs.<ref>PMID:19426743</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Leucyl-tRNA synthetase 1 (LARS1) mediates activation of leucine-dependent mechanistic target of rapamycin complex 1 (mTORC1) as well as ligation of leucine to its cognate tRNAs, yet its mechanism of leucine sensing is poorly understood. Here we describe leucine binding-induced conformational changes of LARS1. We determine different crystal structures of LARS1 complexed with leucine, ATP, and a reaction intermediate analog, leucyl-sulfamoyl-adenylate (Leu-AMS), and find two distinct functional states of LARS1 for mTORC1 activation. Upon leucine binding to the synthetic site, H251 and R517 in the connective polypeptide and (50)FPYPY(54) in the catalytic domain change the hydrogen bond network, leading to conformational change in the C-terminal domain, correlating with RagD association. Leucine binding to LARS1 is increased in the presence of ATP, further augmenting leucine-dependent interaction of LARS1 and RagD. Thus, this work unveils the structural basis for leucine-dependent long-range communication between the catalytic and RagD-binding domains of LARS1 for mTORC1 activation.
		+
		+	Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation.,Kim S, Yoon I, Son J, Park J, Kim K, Lee JH, Park SY, Kang BS, Han JM, Hwang KY, Kim S Cell Rep. 2021 Apr 27;35(4):109031. doi: 10.1016/j.celrep.2021.109031. PMID:33910001<ref>PMID:33910001</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kid" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hwang KY]]	+	[[Category: Leucine--tRNA ligase]]
-	[[Category: Kim S]]	+	[[Category: Hwang, K Y]]
-	[[Category: Son J]]	+	[[Category: Kim, S]]
		+	[[Category: Son, J]]
		+	[[Category: Atp-bound structure]]
		+	[[Category: Leucyl-trna synthetase]]
		+	[[Category: Ligase]]

OCA at 07:52, 27 January 2021

OCA — Wed, 27 Jan 2021 07:52:00 GMT

←Older revision		Revision as of 07:52, 27 January 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kid ~~is ON HOLD until Jan 18 2022~~	+	==Crystal structure of human leucyl-tRNA synthetase, ATP-bound form==
-		+	<StructureSection load='6kid' size='340' side='right'caption='[[6kid]]' scene=''>
-	~~Authors~~: ~~Kim~~, S., ~~Son~~, J., ~~Kim, S~~., ~~Hwang, K~~.Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KID FirstGlance]. <br>
-	~~Description: Crystal structure of human leucyl-tRNA synthetase, ATP-bound form~~	+	</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=6kid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kid OCA], [https://pdbe.org/6kid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kid RCSB], [https://www.ebi.ac.uk/pdbsum/6kid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kid ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Kim, S~~]]	+	__TOC__
-	[[Category: ~~Hwang, K.Y~~]]	+	</StructureSection>
-	[[Category: Son, J]]	+	[[Category: Large Structures]]
		+	[[Category: Hwang KY]]
		+	[[Category: Kim S]]
		+	[[Category: Son J]]

OCA at 05:45, 22 July 2020

OCA — Wed, 22 Jul 2020 05:45:33 GMT

←Older revision		Revision as of 05:45, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kid is ON HOLD until ~~Paper Publication~~	+	The entry 6kid is ON HOLD until Jan 18 2022

	Authors: Kim, S., Son, J., Kim, S., Hwang, K.Y.		Authors: Kim, S., Son, J., Kim, S., Hwang, K.Y.

OCA at 06:33, 2 October 2019

OCA — Wed, 02 Oct 2019 06:33:04 GMT

←Older revision		Revision as of 06:33, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kim, S., Son, J., Kim, S., Hwang, K.Y.		Authors: Kim, S., Son, J., Kim, S., Hwang, K.Y.

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

OCA — Wed, 24 Jul 2019 04:17:17 GMT

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

←Older revision

Revision as of 04:17, 24 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kid is ON HOLD Authors: Kim, S., Son, J., Kim, S., Hwang, K.Y. Description: Crystal structure of human leucyl-tRNA synthetase, ATP-bound form [[Ca...

OCA — Wed, 24 Jul 2019 04:17:15 GMT

New page: '''Unreleased structure''' The entry 6kid is ON HOLD Authors: Kim, S., Son, J., Kim, S., Hwang, K.Y. Description: Crystal structure of human leucyl-tRNA synthetase, ATP-bound form [[Ca...

New page

'''Unreleased structure'''

The entry 6kid is ON HOLD

Authors: Kim, S., Son, J., Kim, S., Hwang, K.Y.

Description: Crystal structure of human leucyl-tRNA synthetase, ATP-bound form
[[Category: Unreleased Structures]]
[[Category: Kim, S]]
[[Category: Hwang, K.Y]]
[[Category: Son, J]]