2e21: Difference between revisions
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<StructureSection load='2e21' size='340' side='right'caption='[[2e21]], [[Resolution|resolution]] 2.70Å' scene=''> | <StructureSection load='2e21' size='340' side='right'caption='[[2e21]], [[Resolution|resolution]] 2.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2e21]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[2e21]] 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=2E21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E21 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</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=2e21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e21 OCA], [https://pdbe.org/2e21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e21 RCSB], [https://www.ebi.ac.uk/pdbsum/2e21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e21 ProSAT], [https://www.topsan.org/Proteins/RSGI/2e21 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=2e21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e21 OCA], [https://pdbe.org/2e21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e21 RCSB], [https://www.ebi.ac.uk/pdbsum/2e21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e21 ProSAT], [https://www.topsan.org/Proteins/RSGI/2e21 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=2e21 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=2e21 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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2e21" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Aquifex aeolicus | [[Category: Aquifex aeolicus]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bessho | [[Category: Bessho Y]] | ||
[[Category: Ishii | [[Category: Ishii T]] | ||
[[Category: Kuratani | [[Category: Kuratani M]] | ||
[[Category: Sekine S]] | |||
[[Category: Sekine | [[Category: Shibata R]] | ||
[[Category: Shibata | [[Category: Yokoyama S]] | ||
[[Category: Yokoyama | [[Category: Yoshikawa Y]] | ||
[[Category: Yoshikawa | |||
Latest revision as of 11:33, 25 October 2023
Crystal structure of TilS in a complex with AMPPNP from Aquifex aeolicus.Crystal structure of TilS in a complex with AMPPNP from Aquifex aeolicus.
Structural highlights
FunctionTILS_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 Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedIn 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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