3wqz: Difference between revisions

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 <StructureSection load='3wqz' size='340' side='right'caption='[[3wqz]], [[Resolution|resolution]] 3.49&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3wqz]] 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=3WQZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WQZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3wqz]] 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=3WQZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WQZ 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=ZN:ZINC+ION'>ZN</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]] 3.489&#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;'>[[3wqy|3wqy]]</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=ZN:ZINC+ION'>ZN</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=3wqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqz OCA], [https://pdbe.org/3wqz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wqz RCSB], [https://www.ebi.ac.uk/pdbsum/3wqz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wqz ProSAT]</span></td></tr>
 </table>
 == 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 3wqz" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 29: / Line 18: @@
 __TOC__
 </StructureSection>
-[[Category: Alanine--tRNA ligase]]
+[[Category: Archaeoglobus fulgidus DSM 4304]]
-[[Category: Arcfu]]
 [[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: Homodimer]]
-[[Category: Ligase]]
-[[Category: Ligase-rna complex]]
-[[Category: Protein-rna complex]]