3ziu - Revision history

OCA at 11:02, 20 December 2023

OCA — Wed, 20 Dec 2023 11:02:43 GMT

←Older revision		Revision as of 11:02, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='3ziu' size='340' side='right'caption='[[3ziu]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='3ziu' size='340' side='right'caption='[[3ziu]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ziu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43663 Atcc 43663~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZIU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZIU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ziu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesomycoplasma_mobile Mesomycoplasma mobile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZIU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZIU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=LSS:5-O-(L-LEUCYLSULFAMOYL)ADENOSINE'>LSS</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]] 2.07Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LSS:5-O-(L-LEUCYLSULFAMOYL)ADENOSINE'>LSS</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=3ziu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ziu OCA], [https://pdbe.org/3ziu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ziu RCSB], [https://www.ebi.ac.uk/pdbsum/3ziu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ziu 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=3ziu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ziu OCA], [https://pdbe.org/3ziu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ziu RCSB], [https://www.ebi.ac.uk/pdbsum/3ziu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ziu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6KHA5_MYCMO Q6KHA5_MYCMO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43663]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Leucine--tRNA ligase~~]]	+	[[Category: Mesomycoplasma mobile]]
-	[[Category: Boniecki~~, M T~~]]	+	[[Category: Boniecki MT]]
-	[[Category: Cusack, S]]	+	[[Category: Cusack S]]
-	[[Category: Li, L]]	+	[[Category: Li L]]
-	[[Category: Li, Z]]	+	[[Category: Li Z]]
-	[[Category: Lukk, T]]	+	[[Category: Lukk T]]
-	[[Category: Luthey-Schulten~~, Z A~~]]	+	[[Category: Luthey-Schulten ZA]]
-	[[Category: Martinis~~, S A~~]]	+	[[Category: Martinis SA]]
-	[[Category: Palencia, A]]	+	[[Category: Palencia A]]
-	~~[[Category: Ligase~~]]	+

OCA at 05:47, 10 August 2022

OCA — Wed, 10 Aug 2022 05:47:56 GMT

←Older revision		Revision as of 05:47, 10 August 2022
Line 1:		Line 1:

	==Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site==		==Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site==
-	<StructureSection load='3ziu' size='340' side='right' caption='[[3ziu]], [[Resolution\|resolution]] 2.07Å' scene=''>	+	<StructureSection load='3ziu' size='340' side='right'caption='[[3ziu]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ziu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43663 Atcc 43663]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZIU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ZIU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ziu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43663 Atcc 43663]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZIU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZIU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LSS:5-O-(L-LEUCYLSULFAMOYL)ADENOSINE'>LSS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LSS:5-O-(L-LEUCYLSULFAMOYL)ADENOSINE'>LSS</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Leucine--tRNA_ligase Leucine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.4 6.1.1.4] </span></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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ziu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ziu OCA], [~~http~~://pdbe.org/3ziu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ziu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ziu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ziu 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=3ziu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ziu OCA], [https://pdbe.org/3ziu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ziu RCSB], [https://www.ebi.ac.uk/pdbsum/3ziu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ziu ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 3ziu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ziu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43663]]		[[Category: Atcc 43663]]
		+	[[Category: Large Structures]]
	[[Category: Leucine--tRNA ligase]]		[[Category: Leucine--tRNA ligase]]
	[[Category: Boniecki, M T]]		[[Category: Boniecki, M T]]

OCA at 20:06, 11 August 2016

OCA — Thu, 11 Aug 2016 20:06:31 GMT

←Older revision		Revision as of 20:06, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site==		==Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site==
	<StructureSection load='3ziu' size='340' side='right' caption='[[3ziu]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='3ziu' size='340' side='right' caption='[[3ziu]], [[Resolution\|resolution]] 2.07Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LSS:5-O-(L-LEUCYLSULFAMOYL)ADENOSINE'>LSS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LSS:5-O-(L-LEUCYLSULFAMOYL)ADENOSINE'>LSS</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Leucine--tRNA_ligase Leucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.4 6.1.1.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Leucine--tRNA_ligase Leucine--tRNA ligase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ziu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ziu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ziu RCSB], [http://www.ebi.ac.uk/pdbsum/3ziu PDBsum]</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=3ziu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ziu OCA], [http://pdbe.org/3ziu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ziu RCSB], [http://www.ebi.ac.uk/pdbsum/3ziu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ziu ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3ziu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:49, 4 January 2015

OCA — Sun, 04 Jan 2015 09:49:37 GMT

←Older revision		Revision as of 09:49, 4 January 2015
Line 1:		Line 1:
-	[[~~Image:~~3ziu.~~jpg~~\|~~left\|200px~~]]	+	==Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site==
		+	<StructureSection load='3ziu' size='340' side='right' caption='[[3ziu]], [[Resolution\|resolution]] 2.07Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ziu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43663 Atcc 43663]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZIU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZIU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LSS:5-O-(L-LEUCYLSULFAMOYL)ADENOSINE'>LSS</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Leucine--tRNA_ligase Leucine--tRNA ligase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ziu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ziu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ziu RCSB], [http://www.ebi.ac.uk/pdbsum/3ziu PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mycoplasma leucyl-tRNA synthetases (LeuRSs) have been identified in which the connective polypeptide 1 (CP1) amino acid editing domain that clears mischarged tRNAs are missing (Mycoplasma mobile) or highly degenerate (Mycoplasma synoviae). Thus, these enzymes rely on a clearance pathway called pretransfer editing, which hydrolyzes misactivated aminoacyl-adenylate intermediate via a nebulous mechanism that has been controversial for decades. Even as the sole fidelity pathway for clearing amino acid selection errors in the pathogenic M. mobile, pretransfer editing is not robust enough to completely block mischarging of tRNA, resulting in codon ambiguity and statistical proteins. A high-resolution X-ray crystal structure shows that M. mobile LeuRS structurally overlaps with other LeuRS cores. However, when CP1 domains from different aminoacyl-tRNA synthetases and origins were fused to this common LeuRS core, surprisingly, pretransfer editing was enhanced. It is hypothesized that the CP1 domain evolved as a molecular rheostat to balance multiple functions. These include distal control of specificity and enzyme activity in the ancient canonical core, as well as providing a separate hydrolytic active site for clearing mischarged tRNA.

-	~~{{STRUCTURE_3ziu\| PDB=3ziu \| SCENE= }}~~	+	Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in Mycoplasma pathogens.,Li L, Palencia A, Lukk T, Li Z, Luthey-Schulten ZA, Cusack S, Martinis SA, Boniecki MT Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3817-22. doi:, 10.1073/pnas.1218374110. Epub 2013 Feb 19. PMID:23431144<ref>PMID:23431144</ref>

-	~~===Crystal structure~~ of ~~Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in~~ the ~~active site===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	==~~About this Structure~~==	+	<references/>
-	~~[[3ziu]] is a 2 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Mycoplasma_mobile Mycoplasma mobile]. Full crystallographic information is available from~~ [~~http~~:~~//oca.weizmann.ac.il/oca-bin/ocashort?id=3ZIU OCA~~].	+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc 43663]]
	[[Category: Leucine--tRNA ligase]]		[[Category: Leucine--tRNA ligase]]
-	~~[[Category: Mycoplasma mobile]]~~	+	[[Category: Boniecki, M T]]
-	[[Category: Boniecki, M T.]]	+	[[Category: Cusack, S]]
-	[[Category: Cusack, S.]]	+	[[Category: Li, L]]
-	[[Category: Li, L.]]	+	[[Category: Li, Z]]
-	[[Category: Li, Z.]]	+	[[Category: Lukk, T]]
-	[[Category: Lukk, T.]]	+	[[Category: Luthey-Schulten, Z A]]
-	[[Category: Luthey-Schulten, Z A.]]	+	[[Category: Martinis, S A]]
-	[[Category: Martinis, S A.]]	+	[[Category: Palencia, A]]
-	[[Category: Palencia, A.]]	+
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 14:51, 27 February 2013

OCA — Wed, 27 Feb 2013 14:51:26 GMT

←Older revision		Revision as of 14:51, 27 February 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3ziu.jpg\|left\|200px]]

-	~~The entry~~ 3ziu ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3ziu\| PDB=3ziu \| SCENE= }}

-	~~Authors: Li, L., Palencia, A., Lukk, T., Li, Z., Luthey~~-~~Schulten, Z.A., Cusack, S., Martinis, S.A., Boniecki, M.T.~~	+	===Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site===

-	~~Description: Crystal~~ structure of Mycoplasma mobile ~~Leucyl~~-tRNA ~~Synthetase with Leu~~-~~AMS in the active site~~	+
		+	==About this Structure==
		+	[[3ziu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycoplasma_mobile Mycoplasma mobile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZIU OCA].
		+	[[Category: Leucine--tRNA ligase]]
		+	[[Category: Mycoplasma mobile]]
		+	[[Category: Boniecki, M T.]]
		+	[[Category: Cusack, S.]]
		+	[[Category: Li, L.]]
		+	[[Category: Li, Z.]]
		+	[[Category: Lukk, T.]]
		+	[[Category: Luthey-Schulten, Z A.]]
		+	[[Category: Martinis, S A.]]
		+	[[Category: Palencia, A.]]
		+	[[Category: Ligase]]

OCA at 10:57, 23 January 2013

OCA — Wed, 23 Jan 2013 10:57:20 GMT

←Older revision		Revision as of 10:57, 23 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3ziu is ON HOLD	+	The entry 3ziu is ON HOLD until Paper Publication

	Authors: Li, L., Palencia, A., Lukk, T., Li, Z., Luthey-Schulten, Z.A., Cusack, S., Martinis, S.A., Boniecki, M.T.		Authors: Li, L., Palencia, A., Lukk, T., Li, Z., Luthey-Schulten, Z.A., Cusack, S., Martinis, S.A., Boniecki, M.T.

	Description: Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site		Description: Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site

OCA: Protected "3ziu" [edit=sysop:move=sysop]

OCA — Wed, 16 Jan 2013 08:12:32 GMT

Protected "3ziu" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:12, 16 January 2013

OCA: New page: '''Unreleased structure''' The entry 3ziu is ON HOLD Authors: Li, L., Palencia, A., Lukk, T., Li, Z., Luthey-Schulten, Z.A., Cusack, S., Martinis, S.A., Boniecki, M.T. Description: Cry...

OCA — Wed, 16 Jan 2013 08:12:31 GMT

New page: '''Unreleased structure''' The entry 3ziu is ON HOLD Authors: Li, L., Palencia, A., Lukk, T., Li, Z., Luthey-Schulten, Z.A., Cusack, S., Martinis, S.A., Boniecki, M.T. Description: Cry...

New page

'''Unreleased structure'''

The entry 3ziu is ON HOLD

Authors: Li, L., Palencia, A., Lukk, T., Li, Z., Luthey-Schulten, Z.A., Cusack, S., Martinis, S.A., Boniecki, M.T.

Description: Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site