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| | ==Crystal structure of TILS C-terminal domain== | | ==Crystal structure of TILS C-terminal domain== |
| - | <StructureSection load='3hj7' size='340' side='right' caption='[[3hj7]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3hj7' size='340' side='right'caption='[[3hj7]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3hj7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HJ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HJ7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3hj7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HJ7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GK0060, tilS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hj7 OCA], [http://pdbe.org/3hj7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hj7 RCSB], [http://www.ebi.ac.uk/pdbsum/3hj7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hj7 ProSAT]</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=3hj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hj7 OCA], [https://pdbe.org/3hj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hj7 RCSB], [https://www.ebi.ac.uk/pdbsum/3hj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hj7 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TILS_GEOKA TILS_GEOKA]] 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). | + | [https://www.uniprot.org/uniprot/TILS_GEOKA TILS_GEOKA] 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]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hj/3hj7_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hj/3hj7_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> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus kaustophilus prickett 1928]] | + | [[Category: Geobacillus kaustophilus]] |
| - | [[Category: Bonnefond, L]] | + | [[Category: Large Structures]] |
| - | [[Category: Ishitani, R]] | + | [[Category: Bonnefond L]] |
| - | [[Category: Kimura, S]] | + | [[Category: Ishitani R]] |
| - | [[Category: Nakanishi, K]] | + | [[Category: Kimura S]] |
| - | [[Category: Nureki, O]] | + | [[Category: Nakanishi K]] |
| - | [[Category: Suzuki, T]] | + | [[Category: Nureki O]] |
| - | [[Category: Atp-binding]]
| + | [[Category: Suzuki T]] |
| - | [[Category: Helix-turn-helix]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Pseudo-knot]]
| + | |
| - | [[Category: Trna processing]]
| + | |
| Structural highlights
Function
TILS_GEOKA 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 PubMed
Maturation of precursor transfer RNA (pre-tRNA) includes excision of the 5' leader and 3' trailer sequences, removal of introns and addition of the CCA terminus. Nucleotide modifications are incorporated at different stages of tRNA processing, after the RNA molecule adopts the proper conformation. In bacteria, tRNA(Ile2) lysidine synthetase (TilS) modifies cytidine into lysidine (L; 2-lysyl-cytidine) at the first anticodon of tRNA(Ile2) (refs 4-9). This modification switches tRNA(Ile2) from a methionine-specific to an isoleucine-specific tRNA. However, the aminoacylation of tRNA(Ile2) by methionyl-tRNA synthetase (MetRS), before the modification by TilS, might lead to the misincorporation of methionine in response to isoleucine codons. The mechanism used by bacteria to avoid this pitfall is unknown. Here we show that the TilS enzyme specifically recognizes and modifies tRNA(Ile2) in its precursor form, thereby avoiding translation errors. We identified the lysidine modification in pre-tRNA(Ile2) isolated from RNase-E-deficient Escherichia coli and did not detect mature tRNA(Ile2) lacking this modification. Our kinetic analyses revealed that TilS can modify both types of RNA molecule with comparable efficiencies. X-ray crystallography and mutational analyses revealed that TilS specifically recognizes the entire L-shape structure in pre-tRNA(Ile2) through extensive interactions coupled with sequential domain movements. Our results demonstrate how TilS prevents the recognition of tRNA(Ile2) by MetRS and achieves high specificity for its substrate. These two key points form the basis for maintaining the fidelity of isoleucine codon translation in bacteria. Our findings also provide a rationale for the necessity of incorporating specific modifications at the precursor level during tRNA biogenesis.
Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.,Nakanishi K, Bonnefond L, Kimura S, Suzuki T, Ishitani R, Nureki O Nature. 2009 Oct 22;461(7267):1144-8. PMID:19847269[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nakanishi K, Bonnefond L, Kimura S, Suzuki T, Ishitani R, Nureki O. Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature. 2009 Oct 22;461(7267):1144-8. PMID:19847269 doi:10.1038/nature08474
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