3a2k

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of TilS complexed with tRNA

Structural highlights

3a2k is a 4 chain structure with sequence from Bacillus subtilis and Geobacillus kaustophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.65Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3a2k"

@@ Line 3: / Line 3: @@
 <StructureSection load='3a2k' size='340' side='right'caption='[[3a2k]], [[Resolution|resolution]] 3.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3a2k]] is a 4 chain structure with sequence from [https://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=3A2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A2K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3a2k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A2K FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GK0060, tilS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</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]] 3.65&#8491;</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=3a2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2k OCA], [https://pdbe.org/3a2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a2k RCSB], [https://www.ebi.ac.uk/pdbsum/3a2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2k ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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).
+[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a2/3a2k_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 35: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus kaustophilus prickett 1928]]
+[[Category: Bacillus subtilis]]
+[[Category: Geobacillus kaustophilus]]
 [[Category: Large Structures]]
-[[Category: Bonnefond, L]]
+[[Category: Bonnefond L]]
-[[Category: Ishitani, R]]
+[[Category: Ishitani R]]
-[[Category: Nakanishi, K]]
+[[Category: Nakanishi K]]
-[[Category: Nureki, O]]
+[[Category: Nureki O]]
-[[Category: Ligase]]
-[[Category: Ligase-rna complex]]
-[[Category: Pseudo-knot]]
-[[Category: Rna]]

3a2k

From Proteopedia

Current revision

Crystal structure of TilS complexed with tRNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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