1riq: Difference between revisions

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-{{Seed}}
-[[Image:1riq.png|left|200px]]
-<!--
+==The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase==
-The line below this paragraph, containing "STRUCTURE_1riq", creates the "Structure Box" on the page.
+<StructureSection load='1riq' size='340' side='right'caption='[[1riq]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1riq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RIQ FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.14&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_1riq|  PDB=1riq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1riq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1riq OCA], [https://pdbe.org/1riq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1riq RCSB], [https://www.ebi.ac.uk/pdbsum/1riq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1riq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYA_AQUAE SYA_AQUAE] 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). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain (By similarity).[HAMAP-Rule:MF_00036]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/1riq_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1riq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Early work on aminoacylation of alanine-specific tRNA (tRNA(Ala)) by alanyl-tRNA synthetase (AlaRS) gave rise to the concept of an early "second genetic code" imbedded in the acceptor stems of tRNAs. A single conserved and position-specific G:U base pair in the tRNA acceptor stem is the key identity determinant. Further understanding has been limited due to lack of a crystal structure of the enzyme. We determined a 2.14 A crystal structure of the 453 amino acid catalytic fragment of Aquifex aeolicus AlaRS. It contains the catalytic domain characteristic of class II synthetases, a helical domain with a hairpin motif critical for acceptor-stem recognition, and a C-terminal domain of a mixed alpha/beta fold. Docking of tRNA(Ala) on AlaRS shows critical contacts with the three domains, consistent with previous mutagenesis and functional data. It also suggests conformational flexibility within the C domain, which might allow for the positional variation of the key G:U base pair seen in some tRNA(Ala)s.
-===The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase===
+Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition.,Swairjo MA, Otero FJ, Yang XL, Lovato MA, Skene RJ, McRee DE, Ribas de Pouplana L, Schimmel P Mol Cell. 2004 Mar 26;13(6):829-41. PMID:15053876<ref>PMID:15053876</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1riq" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15053876}}, adds the Publication Abstract to the page
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15053876 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15053876}}
+__TOC__
+</StructureSection>
-==About this Structure==
-RIQ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIQ OCA].
-==Reference==
-<ref group="xtra">PMID:15053876</ref><references group="xtra"/>
-[[Category: Alanine--tRNA ligase]]
 [[Category: Aquifex aeolicus]]
-[[Category: Lovato, M A.]]
+[[Category: Large Structures]]
-[[Category: McRee, D E.]]
+[[Category: Lovato MA]]
-[[Category: Otero, F J.]]
+[[Category: McRee DE]]
-[[Category: Pouplana, L Ribas de.]]
+[[Category: Otero FJ]]
-[[Category: Schimmel, P.]]
+[[Category: Ribas de Pouplana L]]
-[[Category: Skene, R J.]]
+[[Category: Schimmel P]]
-[[Category: Swairjo, M A.]]
+[[Category: Skene RJ]]
-[[Category: Yang, X L.]]
+[[Category: Swairjo MA]]
-[[Category: Beta sheet and flanking helice]]
+[[Category: Yang X-L]]
-[[Category: Class ii aminoacyl-trna synthetase]]
-[[Category: Helix-loop-helix motif]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:44:24 2009''