3wqy - Revision history

OCA at 08:46, 20 March 2024

OCA — Wed, 20 Mar 2024 08:46:36 GMT

←Older revision		Revision as of 08:46, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3wqy' size='340' side='right'caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3wqy' size='340' side='right'caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wqy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arcfu Arcfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wqy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WQY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=A5A:5~~-~~O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE'>A5A</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3wqz\|3wqz]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5A:5-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE'>A5A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>AF_2255, alaS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~224325 ARCFU])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7]~~ </~~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=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [https://pdbe.org/3wqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [https://www.ebi.ac.uk/pdbsum/3wqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wqy 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=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [https://pdbe.org/3wqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [https://www.ebi.ac.uk/pdbsum/3wqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wqy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SYA_ARCFU SYA_ARCFU]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Incorrectly charged aminoacyl-tRNA(Ala) is also edited in situ by the editing domain.<ref>PMID:19423669</ref>	+	[https://www.uniprot.org/uniprot/SYA_ARCFU SYA_ARCFU] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Incorrectly charged aminoacyl-tRNA(Ala) is also edited in situ by the editing domain.<ref>PMID:19423669</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Ligation of tRNAs with their cognate amino acids, by aminoacyl-tRNA synthetases, establishes the genetic code. Throughout evolution, tRNA(Ala) selection by alanyl-tRNA synthetase (AlaRS) has depended predominantly on a single wobble base pair in the acceptor stem, G3U70, mainly on the kcat level. Here we report the crystal structures of an archaeal AlaRS in complex with tRNA(Ala) with G3U70 and its A3U70 variant. AlaRS interacts with both the minor- and the major-groove sides of G3U70, widening the major groove. The geometry difference between G3U70 and A3U70 is transmitted along the acceptor stem to the 3'-CCA region. Thus, the 3'-CCA region of tRNA(Ala) with G3U70 is oriented to the reactive route that reaches the active site, whereas that of the A3U70 variant is folded back into the non-reactive route. This novel mechanism enables the single wobble pair to dominantly determine the specificity of tRNA selection, by an approximate 100-fold difference in kcat.	+
-		+
-	The selective tRNA aminoacylation mechanism based on a single G*U pair.,Naganuma M, Sekine S, Chong YE, Guo M, Yang XL, Gamper H, Hou YM, Schimmel P, Yokoyama S Nature. 2014 Jun 26;510(7506):507-11. doi: 10.1038/nature13440. Epub 2014 Jun 11. PMID:24919148<ref>PMID:24919148</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3wqy" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 29:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alanine--tRNA ligase]]~~	+	[[Category: Archaeoglobus fulgidus DSM 4304]]
-	~~[[Category: Arcfu~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Naganuma, M]]	+	[[Category: Naganuma M]]
-	[[Category: Sekine, S]]	+	[[Category: Sekine S]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Alanyladenylate analogue]]~~	+
-	~~[[Category: Aminoacyl-trna synthetase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Ligase-rna complex]]~~	+
-	~~[[Category: Protein-rna complex~~]]	+

OCA at 05:46, 3 August 2022

OCA — Wed, 03 Aug 2022 05:46:47 GMT

←Older revision		Revision as of 05:46, 3 August 2022
Line 1:		Line 1:

	==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70==		==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70==
-	<StructureSection load='3wqy' size='340' side='right' caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='3wqy' size='340' side='right'caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wqy]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wqy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WQY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5A:5-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE'>A5A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5A:5-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE'>A5A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wqz\|3wqz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wqz\|3wqz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </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=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [~~http~~://pdbe.org/3wqy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wqy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wqy 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=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [https://pdbe.org/3wqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [https://www.ebi.ac.uk/pdbsum/3wqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wqy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SYA_ARCFU SYA_ARCFU]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Incorrectly charged aminoacyl-tRNA(Ala) is also edited in situ by the editing domain.<ref>PMID:19423669</ref>	+	[[https://www.uniprot.org/uniprot/SYA_ARCFU SYA_ARCFU]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Incorrectly charged aminoacyl-tRNA(Ala) is also edited in situ by the editing domain.<ref>PMID:19423669</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]		*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
	== References ==		== References ==
Line 30:		Line 31:
	[[Category: Alanine--tRNA ligase]]		[[Category: Alanine--tRNA ligase]]
	[[Category: Arcfu]]		[[Category: Arcfu]]
		+	[[Category: Large Structures]]
	[[Category: Naganuma, M]]		[[Category: Naganuma, M]]
	[[Category: Sekine, S]]		[[Category: Sekine, S]]

OCA at 09:16, 21 February 2019

OCA — Thu, 21 Feb 2019 09:16:33 GMT

←Older revision		Revision as of 09:16, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='3wqy' size='340' side='right' caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3wqy' size='340' side='right' caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wqy]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wqy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WQY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5A:5-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE'>A5A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5A:5-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE'>A5A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wqz\|3wqz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wqz\|3wqz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </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=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [http://pdbe.org/3wqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [http://www.ebi.ac.uk/pdbsum/3wqy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wqy ProSAT]</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=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [http://pdbe.org/3wqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [http://www.ebi.ac.uk/pdbsum/3wqy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wqy ProSAT]</span></td></tr>
Line 22:		Line 23:

	==See Also==		==See Also==
-	*[[~~TRNA~~\|~~TRNA~~]]	+	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Alanine--tRNA ligase]]		[[Category: Alanine--tRNA ligase]]
		+	[[Category: Arcfu]]
	[[Category: Naganuma, M]]		[[Category: Naganuma, M]]
	[[Category: Sekine, S]]		[[Category: Sekine, S]]

OCA at 10:07, 4 August 2016

OCA — Thu, 04 Aug 2016 10:07:26 GMT

←Older revision		Revision as of 10:07, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70==		==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70==
	<StructureSection load='3wqy' size='340' side='right' caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3wqy' size='340' side='right' caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wqz\|3wqz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wqz\|3wqz]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </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=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [http://www.ebi.ac.uk/pdbsum/3wqy 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=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [http://pdbe.org/3wqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [http://www.ebi.ac.uk/pdbsum/3wqy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wqy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 3wqy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRNA\|TRNA]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:11, 25 December 2014

OCA — Thu, 25 Dec 2014 08:11:50 GMT

←Older revision		Revision as of 08:11, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wqy]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WQY FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wqy]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WQY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5A:5-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE'>A5A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5A:5-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE'>A5A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wqz\|3wqz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wqz\|3wqz]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [http://www.ebi.ac.uk/pdbsum/3wqy 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=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [http://www.ebi.ac.uk/pdbsum/3wqy PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYA_ARCFU SYA_ARCFU]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Incorrectly charged aminoacyl-tRNA(Ala) is also edited in situ by the editing domain.<ref>PMID:19423669</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Alanine--tRNA ligase]]		[[Category: Alanine--tRNA ligase]]
-	[[Category: Naganuma, M.]]	+	[[Category: Naganuma, M]]
-	[[Category: Sekine, S.]]	+	[[Category: Sekine, S]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Alanyladenylate analogue]]		[[Category: Alanyladenylate analogue]]
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]

OCA at 06:23, 2 July 2014

OCA — Wed, 02 Jul 2014 06:23:33 GMT

←Older revision		Revision as of 06:23, 2 July 2014
Line 1:		Line 1:
-	==Crystal structure of ~~aminoacyl~~-tRNA synthetase in complex with a tRNA==	+	==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70==
	<StructureSection load='3wqy' size='340' side='right' caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3wqy' size='340' side='right' caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 8:		Line 8:
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [http://www.ebi.ac.uk/pdbsum/3wqy PDBsum]</span></td></tr>		<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [http://www.ebi.ac.uk/pdbsum/3wqy PDBsum]</span></td></tr>
	<table>		<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ligation of tRNAs with their cognate amino acids, by aminoacyl-tRNA synthetases, establishes the genetic code. Throughout evolution, tRNA(Ala) selection by alanyl-tRNA synthetase (AlaRS) has depended predominantly on a single wobble base pair in the acceptor stem, G3U70, mainly on the kcat level. Here we report the crystal structures of an archaeal AlaRS in complex with tRNA(Ala) with G3U70 and its A3U70 variant. AlaRS interacts with both the minor- and the major-groove sides of G3U70, widening the major groove. The geometry difference between G3U70 and A3U70 is transmitted along the acceptor stem to the 3'-CCA region. Thus, the 3'-CCA region of tRNA(Ala) with G3U70 is oriented to the reactive route that reaches the active site, whereas that of the A3U70 variant is folded back into the non-reactive route. This novel mechanism enables the single wobble pair to dominantly determine the specificity of tRNA selection, by an approximate 100-fold difference in kcat.
		+
		+	The selective tRNA aminoacylation mechanism based on a single G*U pair.,Naganuma M, Sekine S, Chong YE, Guo M, Yang XL, Gamper H, Hou YM, Schimmel P, Yokoyama S Nature. 2014 Jun 26;510(7506):507-11. doi: 10.1038/nature13440. Epub 2014 Jun 11. PMID:24919148<ref>PMID:24919148</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:05, 18 June 2014

OCA — Wed, 18 Jun 2014 08:05:45 GMT

←Older revision		Revision as of 08:05, 18 June 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of aminoacyl-tRNA synthetase in complex with a tRNA==
-		+	<StructureSection load='3wqy' size='340' side='right' caption='[[3wqy]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~The entry~~ 3wqy is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3wqy]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WQY FirstGlance]. <br>
-	~~Authors~~: Naganuma, M., Sekine, S., Yokoyama, S.	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5A:5-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE'>A5A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wqz\|3wqz]]</td></tr>
-	~~Description~~: ~~Crystal structure of aminoacyl~~-~~tRNA~~ synthetase in complex ~~with a tRNA~~	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wqy RCSB], [http://www.ebi.ac.uk/pdbsum/3wqy PDBsum]</span></td></tr>
		+	<table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alanine--tRNA ligase]]
		+	[[Category: Naganuma, M.]]
		+	[[Category: Sekine, S.]]
		+	[[Category: Yokoyama, S.]]
		+	[[Category: Alanyladenylate analogue]]
		+	[[Category: Aminoacyl-trna synthetase]]
		+	[[Category: Ligase]]
		+	[[Category: Ligase-rna complex]]
		+	[[Category: Protein-rna complex]]

OCA at 04:48, 4 June 2014

OCA — Wed, 04 Jun 2014 04:48:06 GMT

←Older revision		Revision as of 04:48, 4 June 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Naganuma, M., Sekine, S., Yokoyama, S.		Authors: Naganuma, M., Sekine, S., Yokoyama, S.

	Description: Crystal structure of aminoacyl-tRNA synthetase in complex with a tRNA		Description: Crystal structure of aminoacyl-tRNA synthetase in complex with a tRNA

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

OCA — Thu, 13 Feb 2014 04:43:43 GMT

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

←Older revision

Revision as of 04:43, 13 February 2014

OCA: New page: '''Unreleased structure''' The entry 3wqy is ON HOLD Authors: Naganuma, M., Sekine, S., Yokoyama, S. Description: Crystal structure of aminoacyl-tRNA synthetase in complex with a tRNA

OCA — Thu, 13 Feb 2014 04:43:43 GMT

New page: '''Unreleased structure''' The entry 3wqy is ON HOLD Authors: Naganuma, M., Sekine, S., Yokoyama, S. Description: Crystal structure of aminoacyl-tRNA synthetase in complex with a tRNA

New page

'''Unreleased structure'''

The entry 3wqy is ON HOLD

Authors: Naganuma, M., Sekine, S., Yokoyama, S.

Description: Crystal structure of aminoacyl-tRNA synthetase in complex with a tRNA