2zzg: Difference between revisions
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==Crystal structure of alanyl-tRNA synthetase in complex with 5''-O-(N-(L-alanyl)-sulfamyoxyl) adenine without oligomerization domain== | ==Crystal structure of alanyl-tRNA synthetase in complex with 5''-O-(N-(L-alanyl)-sulfamyoxyl) adenine without oligomerization domain== | ||
<StructureSection load='2zzg' size='340' side='right' caption='[[2zzg]], [[Resolution|resolution]] 3.10Å' scene=''> | <StructureSection load='2zzg' size='340' side='right'caption='[[2zzg]], [[Resolution|resolution]] 3.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2zzg]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2zzg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZZG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZZG FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</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><td class="sblockLbl"><b>[[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zzg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzg OCA], [https://pdbe.org/2zzg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zzg RCSB], [https://www.ebi.ac.uk/pdbsum/2zzg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zzg ProSAT]</span></td></tr> | ||
</table> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | == Function == | ||
<table> | [https://www.uniprot.org/uniprot/SYA_PYRHO SYA_PYRHO] 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). Edits incorrectly charged Ser-tRNA(Ala). Incorrectly charged amino acids occur because the of inherent physicochemical limitations on discrimination between closely related amino acids (Gly and Ser) in the charging step.<ref>PMID:16087889</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zz/2zzg_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zz/2zzg_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2zzg ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 27: | Line 28: | ||
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 2zzg" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Aminoacyl tRNA | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Pyrococcus horikoshii]] | [[Category: Pyrococcus horikoshii]] | ||
[[Category: Nakamura | [[Category: Nakamura A]] | ||
[[Category: Nureki | [[Category: Nureki O]] | ||
[[Category: Ose | [[Category: Ose T]] | ||
[[Category: Sokabe | [[Category: Sokabe M]] | ||
[[Category: Tanaka | [[Category: Tanaka I]] | ||
[[Category: Tokunaga | [[Category: Tokunaga K]] | ||
[[Category: Yao | [[Category: Yao M]] | ||
Latest revision as of 17:04, 1 November 2023
Crystal structure of alanyl-tRNA synthetase in complex with 5-O-(N-(L-alanyl)-sulfamyoxyl) adenine without oligomerization domainCrystal structure of alanyl-tRNA synthetase in complex with 5-O-(N-(L-alanyl)-sulfamyoxyl) adenine without oligomerization domain
Structural highlights
FunctionSYA_PYRHO 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). Edits incorrectly charged Ser-tRNA(Ala). Incorrectly charged amino acids occur because the of inherent physicochemical limitations on discrimination between closely related amino acids (Gly and Ser) in the charging step.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedAlanyl-tRNA synthetase (AlaRS) catalyzes synthesis of Ala-tRNA(Ala) and hydrolysis of mis-acylated Ser- and Gly-tRNA(Ala) at 2 different catalytic sites. Here, we describe the monomer structures of C-terminal truncated archaeal AlaRS, with both activation and editing domains in the apo form, in complex with an Ala-AMP analog, and in a high-resolution lysine-methylated form. The structures show docking of the editing domain to the activation domain opposite from the predicted tRNA-binding surface. Thus, the editing site is positioned >35 A from the activation site, prompting us to model 2 different tRNA complexes: one binding tRNA at the activation site, and the other binding tRNA at the editing site. Interestingly, a gel-shift assay also implies the presence of 2 types of tRNA complex with different mobility. These results suggest that tRNA translocation via a canonical CCA flipping is unlikely to occur in AlaRS. The structure also demonstrated the binding of zinc in the editing site, in which the specific coordination of zinc would be facilitated by a conserved GGQ motif, implying that the editing mechanism may not be the same as in ThrRS. As Asn-194 in eubacterial AlaRS important for Ser misactivation is replaced by Thr-213 in archaeal AlaRS, a different Ser accommodation mechanism is proposed. The structure of alanyl-tRNA synthetase with editing domain.,Sokabe M, Ose T, Nakamura A, Tokunaga K, Nureki O, Yao M, Tanaka I Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11028-33. Epub 2009 Jun 19. PMID:19549823[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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