3wqy: Difference between revisions

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<StructureSection load='3wqy' size='340' side='right'caption='[[3wqy]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
<StructureSection load='3wqy' size='340' side='right'caption='[[3wqy]], [[Resolution|resolution]] 3.30&Aring;' 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]] 3.3&#8491;</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, G3*U70, mainly on the kcat level. Here we report the crystal structures of an archaeal AlaRS in complex with tRNA(Ala) with G3*U70 and its A3*U70 variant. AlaRS interacts with both the minor- and the major-groove sides of G3*U70, widening the major groove. The geometry difference between G3*U70 and A3*U70 is transmitted along the acceptor stem to the 3'-CCA region. Thus, the 3'-CCA region of tRNA(Ala) with G3*U70 is oriented to the reactive route that reaches the active site, whereas that of the A3*U70 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&reg;/PubMed&reg;, 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==
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__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]]

Latest revision as of 11:46, 20 March 2024

Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70

Structural highlights

3wqy is a 3 chain structure with sequence from Archaeoglobus fulgidus DSM 4304. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

See Also

References

  1. ↑ Naganuma M, Sekine S, Fukunaga R, Yokoyama S. Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization. Proc Natl Acad Sci U S A. 2009 May 26;106(21):8489-94. Epub 2009 May 7. PMID:19423669

3wqy, resolution 3.30Å

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