1riq: Difference between revisions
From Proteopedia
Jump to navigationJump to search
New page: left|200px<br /><applet load="1riq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1riq, resolution 2.14Å" /> '''The crystal structur... |
No edit summary |
||
| (16 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
== | ==The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase== | ||
Early work on aminoacylation of alanine-specific tRNA (tRNA(Ala)) by | <StructureSection load='1riq' size='340' side='right'caption='[[1riq]], [[Resolution|resolution]] 2.14Å' scene=''> | ||
== Structural highlights == | |||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.14Å</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> | |||
<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. | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[ | <div class="pdbe-citations 1riq" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Lovato | [[Category: Lovato MA]] | ||
[[Category: McRee | [[Category: McRee DE]] | ||
[[Category: Otero | [[Category: Otero FJ]] | ||
[[Category: Pouplana | [[Category: Ribas de Pouplana L]] | ||
[[Category: Schimmel | [[Category: Schimmel P]] | ||
[[Category: Skene | [[Category: Skene RJ]] | ||
[[Category: Swairjo | [[Category: Swairjo MA]] | ||
[[Category: Yang | [[Category: Yang X-L]] | ||
Latest revision as of 07:19, 30 October 2024
The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase
| ||||||||||||
