2e89
From Proteopedia
(Difference between revisions)
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<StructureSection load='2e89' size='340' side='right'caption='[[2e89]], [[Resolution|resolution]] 2.50Å' scene=''> | <StructureSection load='2e89' size='340' side='right'caption='[[2e89]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2e89]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[2e89]] is a 4 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=2E89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E89 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2e89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e89 OCA], [https://pdbe.org/2e89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e89 RCSB], [https://www.ebi.ac.uk/pdbsum/2e89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e89 ProSAT], [https://www.topsan.org/Proteins/RSGI/2e89 TOPSAN]</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=2e89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e89 OCA], [https://pdbe.org/2e89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e89 RCSB], [https://www.ebi.ac.uk/pdbsum/2e89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e89 ProSAT], [https://www.topsan.org/Proteins/RSGI/2e89 TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/TILS_AQUAE TILS_AQUAE] Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine (By similarity). | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=2e89 ConSurf]. | </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=2e89 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | In the bacterial genetic-code system, the codon AUA is decoded as isoleucine by tRNA(Ile)(2) with the lysidine residue at the wobble position. Lysidine is derived from cytidine, with ATP and L-lysine, by tRNA(Ile) lysidine synthetase (TilS), which is an N-type ATP pyrophosphatase. In this study, we determined the crystal structure of Aquifex aeolicus TilS, complexed with ATP, Mg2+, and L-lysine, at 2.5 A resolution. The presence of the TilS-specific subdomain causes the active site to have two separate gateways, a large hole and a narrow tunnel on the opposite side. ATP is bound inside the hole, and L-lysine is bound at the entrance of the tunnel. The conserved Asp36 in the PP-motif coordinates Mg2+. In these initial binding modes, the ATP, Mg2+, and L-lysine are held far apart from each other, but they seem to be brought together for the reaction upon cytidine binding, with putative structural changes of the complex. | ||
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| + | Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine.,Kuratani M, Yoshikawa Y, Bessho Y, Higashijima K, Ishii T, Shibata R, Takahashi S, Yutani K, Yokoyama S Structure. 2007 Dec;15(12):1642-53. PMID:18073113<ref>PMID:18073113</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2e89" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Aquifex aeolicus | + | [[Category: Aquifex aeolicus]] |
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Kuratani | + | [[Category: Kuratani M]] |
| - | + | [[Category: Takahashi S]] | |
| - | [[Category: Takahashi | + | [[Category: Yokoyama S]] |
| - | [[Category: Yokoyama | + | [[Category: Yoshikawa Y]] |
| - | [[Category: Yoshikawa | + | |
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Revision as of 08:36, 25 October 2023
Crystal structure of Aquifex aeolicus TilS in a complex with ATP, Magnesium ion, and L-lysine
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