Sandbox Reserved 704: Difference between revisions

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;The crystal structure of leucyl-tRNA synthetase and tRNA (leucine) complex
;The crystal structure of the archaeal leucyl-tRNA synthetase and tRNA (leucine) complex


Aminoacyl-tRNA synthetases (aaRSs) are ligases which exclusively attach a particular amino acid to the 3'-end of  its set of cognate tRNAs isoacceptors. It is a two-step reaction : first, an activated intermediate called aminoacyladenylate is synthesized from the amino acid and ATP. Then, the activated amino acid is transferred to the 3’-end of the tRNA. It leads to the formation of the aminoacyl-tRNA. The fidelity of protein synthesis depends on the accuracy of this reaction <ref name="Zhou">PMID:20482517</ref>.
Aminoacyl-tRNA synthetases (aaRSs) are ligases which exclusively attach a particular amino acid to the 3'-end of  its set of cognate tRNAs isoacceptors. It is a two-step reaction : first, an activated intermediate called aminoacyl-adenylate is synthesized from the amino acid and ATP. Then, the activated amino acid is transferred to the 3’-end of the tRNA. It leads to the formation of the aminoacyl-tRNA. The fidelity of protein synthesis depends on the accuracy of this reaction <ref name="Zhou">PMID:20482517</ref>.




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Leucyl-tRNA synthetase from the Archaeon ''Pyrococcus horikoshii'' is large (967 residues - 113kDa) and monomeric <ref name="Fukunaga">PMID:15663927</ref>. LeuRS catalyses the esterification of tRNAs Leu with Leucine. There are two classes of aaRSs. Leucyl-tRNA synthetase (LeuRS) belongs to the class I and more precisely to the class Ia. The class I enzymes have the Rossmann-fold domain (parallel β-sheet and α-helices) and the two characteristic motifs, with the consensus sequences of His-Ile-Gly-His (HIGH) and Lys-Met-Ser-Lys-Ser (KMSKS). This family is divided into prokaryotic and eukaryal/archaeal groups but we will focus on the second group.
Leucyl-tRNA synthetase from the Archaeon ''Pyrococcus horikoshii'' is large (967 residues - 113kDa) and monomeric <ref name="Fukunaga">PMID:15663927</ref>. LeuRS catalyses the esterification of tRNAs Leu with Leucine. There are two classes of aaRSs. Leucyl-tRNA synthetase (LeuRS) belongs to the class I and more precisely to the class Ia. The class I enzymes have the Rossmann-fold domain (parallel β-sheet and α-helices) and the two characteristic motifs, with the consensus sequences of His-Ile-Gly-His (HIGH) and Lys-Met-Ser-Lys-Ser (KMSKS). This family is divided into prokaryotic and eukaryal/archaeal groups but we will focus on the second group.


<Structure load='1wkb' size='350' frame='true' align='right' caption='1wkb: Crystal Structure of Leucyl-tRNA Synthetase from the Archaeon Pyrococcus horikoshii [[resolution 2.05Å]] ' scene='Insert optional scene name here' />
<Structure load='1wkb' size='340' frame='true' align='right' caption='Crystal Structure of Leucyl-tRNA Synthetase from the Archaeon Pyrococcus horikoshii [[resolution 2.05Å]] (PDB entry : [[1wkb]]) ' scene='Insert optional scene name here' />




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== Identity elements involved in complex formation ==
== Identity elements involved in complex formation ==


<StructureSection load='1wz2' size='300' frame='true' align='left' side='right' caption='(PDB entry [[1wz2]])' scene=''/>
<StructureSection load='1wz2' size='400' frame='true' align='left' side='right' caption='The crystal structure of Leucyl-tRNA synthetase and tRNA(leucine) complex(PDB entry [[1wz2]])' scene=''/>


Most aaRSs interact with the tRNA anticodon loop in order to form aminoacyl-tRNA <scene name='Sandbox_Reserved_704/Trna_enzyme_complex/1'>complex</scene>. But in the case of archaeal LeuRSs, none of them use this recognition mode. In fact, LeuRSs use two identity elements: the discriminator A73 and the long variable arm <ref name="Fukunaga">PMID:15663927</ref>.
Most aaRSs interact with the tRNA anticodon loop in order to form aminoacyl-tRNA <scene name='Sandbox_Reserved_704/Trna_enzyme_complex/1'>complex</scene>. But in the case of archaeal LeuRSs, none of them use this recognition mode. In fact, LeuRSs use two identity elements: the discriminator A73 and the long variable arm <ref name="Fukunaga">PMID:15663927</ref>.
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The C-terminal region of LeuRS is composed of β-sheet surrounded by α-helices and an additional region (a structure with α- α - α topology), specific to this enzyme. At the tip of the long variable arm of tRNA Leu, there are four nucleotides: G47a, U47b, A47c and G47d which formed a loop. Some of these nucleotides interact with C-terminal residues through Van der Waals interactions and hydrogen bonds.  
The C-terminal region of LeuRS is composed of β-sheet surrounded by α-helices and an additional region (a structure with α- α - α topology), specific to this enzyme. At the tip of the long variable arm of tRNA Leu, there are four nucleotides: G47a, U47b, A47c and G47d which formed a loop. Some of these nucleotides interact with C-terminal residues through Van der Waals interactions and hydrogen bonds.  
First, A47c and G47d which are turned outward of the loop interact with <scene name='Sandbox_Reserved_704/Pro962/2'>Pro962</scene> and <scene name='Sandbox_Reserved_704/Glu_967/1'>Glu967</scene>.  
First, A47c and G47d which are turned outward of the loop interact with <scene name='Sandbox_Reserved_704/Pro962/2'>Pro962</scene> and <scene name='Sandbox_Reserved_704/Glu_967/1'>Glu967</scene>.  
Then, A47c interacts specifically with <scene name='Sandbox_Reserved_704/Ile849_ile966_glu967/1'>3_residues</scene>: Ile849, Ile966 and Glu967. And G47d interacts with <scene name='Sandbox_Reserved_704/4_residues/1'>4 residues</scene>: Ile 849, Ile964, Asp845 and Pro962.
Then, A47c interacts specifically with <scene name='Sandbox_Reserved_704/Ile849_ile966_glu967/1'>3 residues</scene>: Ile849, Ile966 and Glu967. And G47d interacts with <scene name='Sandbox_Reserved_704/4_residues/1'>4 residues</scene>: Ile 849, Ile964, Asp845 and Pro962.
Both A47c and G47d recognition by C-terminal region of the enzyme are important for recognition of the variable arm and a correct translation process <ref name="">PMID:16155584</ref>.
Both A47c and G47d recognition by C-terminal region of the enzyme are important for recognition of the variable arm and a correct translation process <ref name="">PMID:16155584</ref>.


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The translocation between these two states seems to be allowed thanks to the flexibility of the CCA end. It is able to go towards either the aminoacylation site either the editing site whereas the rest of the tRNA remains bound to the enzyme core. These two conformation states involved two modes of A73 recognition and also of C74, C75 and A73, residues of the 3’-terminal region <ref name="">PMID:16155584</ref>.
The translocation between these two states seems to be allowed thanks to the flexibility of the CCA end. It is able to go towards either the aminoacylation site either the editing site whereas the rest of the tRNA remains bound to the enzyme core. These two conformation states involved two modes of A73 recognition and also of C74, C75 and A73, residues of the 3’-terminal region <ref name="">PMID:16155584</ref>.


==== 1) Interactions with A73 and C74 ====
==== Interactions with A73 and C74 ====


{| class="wikitable centre"
{| class="wikitable centre"
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==== 2) Interactions with C75 and A76 ====
==== Interactions with C75 and A76 ====


{| class="wikitable centre"
{| class="wikitable centre"
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<references/>
<references/>
== Contributors ==
Marion Vandeputte, Perrine Faiderbe
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