Sandbox Reserved 704: Difference between revisions

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Most aaRSs interact with the tRNA anticodon loop in order to form aminoacyl-tRNA complex. 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.

Most aaRSs interact with the tRNA anticodon loop in order to form aminoacyl-tRNA complex. 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>.

==== Recognition of the long variable arm ====

The first identity element in the complex is the recognition between the long variable arm of tRNA Leu and C-terminal residues of LeuRS. These residues recognize nucleotides localized at the tip of the arm but not at the stem region of the arm. This characteristic avoids interactions of tRNA Leu with SerRS and TyrRS, which also recognize tRNA with a long variable arm. It is not a direct interaction but a pocket is formed for a tip of the variable arm.

The first identity element in the complex is the recognition between the long variable arm of tRNA Leu and C-terminal residues of LeuRS <ref name="Fukunaga">PMID:15663927</ref>. These residues recognize nucleotides localized at the tip of the arm but not at the stem region of the arm. This characteristic avoids interactions of tRNA Leu with SerRS and TyrRS, which also recognize tRNA with a long variable arm. It is not a direct interaction but a pocket is formed for a tip of the variable arm <ref name="">PMID:16155584</ref>.

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 Pro962 and Glu967.

Then, A47c interacts specifically with 3 residues: Ile849, Ile966 and Glu967. And G47d interacts with four residues: 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.

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>.

==== Interactions with the discriminator, A73 ====

LeuRS employs the discriminator A73 as second identity element. A73 is localized in the tRNA 3’ region which has two conformations: the canonical ‘aminoacylation state’ and the ‘intermediate state’. Consequently, there is two recognition modes of A73, depending on complex structure.

LeuRS employs the discriminator A73 as second identity element <ref name="Fukunaga">PMID:15663927</ref>. A73 is localized in the tRNA 3’ region which has two conformations: the canonical ‘aminoacylation state’ and the ‘intermediate state’. Consequently, there is two recognition modes of A73, depending on complex structure.

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The second structure, the intermediate complex, is observed when the CCA end is relocated toward the editing active site.

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.

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 ====

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| Hydrogen bond between 2’OH of C74 and the positively charged Lys506 in the side chain

Hydrogen bond between N3 of C74 and NH of Ala507 in the main chain

|}

|} <ref name="">PMID:16155584</ref>

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|-

|Hydrogen bond between 3’OH of A76 and His81 in the side chain

|}

|} <ref name="">PMID:16155584</ref>

Sandbox Reserved 704: Difference between revisions

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@@ Line 39: / Line 39: @@
 <StructureSection load='1wz2' size='300' frame='true' align='left' side='right' caption='(PDB entry [[1wz2]])' scene=''/>
-Most aaRSs interact with the tRNA anticodon loop in order to form aminoacyl-tRNA complex. 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.
+Most aaRSs interact with the tRNA anticodon loop in order to form aminoacyl-tRNA complex. 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>.
 ==== Recognition of the long variable arm ====
-The first identity element in the complex is the recognition between the long variable arm of tRNA Leu and C-terminal residues of LeuRS. These residues recognize nucleotides localized at the tip of the arm but not at the stem region of the arm. This characteristic avoids interactions of tRNA Leu with SerRS and TyrRS, which also recognize tRNA with a long variable arm. It is not a direct interaction but a pocket is formed for a tip of the variable arm.
+The first identity element in the complex is the recognition between the long variable arm of tRNA Leu and C-terminal residues of LeuRS  <ref name="Fukunaga">PMID:15663927</ref>. These residues recognize nucleotides localized at the tip of the arm but not at the stem region of the arm. This characteristic avoids interactions of tRNA Leu with SerRS and TyrRS, which also recognize tRNA with a long variable arm. It is not a direct interaction but a pocket is formed for a tip of the variable arm <ref name="">PMID:16155584</ref>.
 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 Pro962 and Glu967.
 Then, A47c interacts specifically with 3 residues: Ile849, Ile966 and Glu967. And G47d interacts with four residues: 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.
+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>.
 ==== Interactions with the discriminator, A73 ====
-LeuRS employs the discriminator A73 as second identity element. A73 is localized in the tRNA 3’ region which has two conformations: the canonical ‘aminoacylation state’ and the ‘intermediate state’. Consequently, there is two recognition modes of A73, depending on complex structure.
+LeuRS employs the discriminator A73 as second identity element <ref name="Fukunaga">PMID:15663927</ref>. A73 is localized in the tRNA 3’ region which has two conformations: the canonical ‘aminoacylation state’ and the ‘intermediate state’. Consequently, there is two recognition modes of A73, depending on complex structure.
@@ Line 62: / Line 62: @@
 The second structure, the intermediate complex, is observed when the CCA end is relocated toward the editing active site.
-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.
+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 ====
@@ Line 86: / Line 86: @@
   | 	Hydrogen bond between 2’OH of C74 and the positively charged Lys506 in the side chain
 	Hydrogen bond between N3 of C74 and NH of Ala507 in the main chain
-  |}
+  |} <ref name="">PMID:16155584</ref>
@@ Line 103: / Line 103: @@
   |-
   |Hydrogen bond between 3’OH of A76 and His81 in the side chain
-  |}
+  |} <ref name="">PMID:16155584</ref>