Sandbox Reserved 704: Difference between revisions

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=== Crystal structure of leucyl-tRNA synthetase and tRNA (leucine) complex ===

Aminoacyl-tRNA synthetases (aaRSs) are ligases which exclusively attach a particular amino acid to the 3’ 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 of the accuracy of this reaction.

Aminoacyl-tRNA synthetases (aaRSs) are ligases which exclusively attach a particular amino acid to the 3’ 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 of the accuracy of this reaction <ref name="Zhou">PMID:20482517</ref>.

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The structure can be divided into nine domains:

The structure can be divided into nine domains <ref name="Fukunaga">PMID:15663927</ref> :

1) The class I-characterizing Rossmann-fold aminoacylation catalytic domain. It contains the HIGH motif. It is located at the beginning of the long α-helix found below the Rossmann-fold core β-sheet.

Other the Rossmann fold domain, there are other fused and inserted domains.

2) CP (Connective Peptide)-core and 3) CP1 hairpin consist of antiparallel β-sheets, but only the CP core is fixed on the aminoacylation domain. There is a “joint” formed by the junction of the CP-core and the CP1 hairpin (Ala180 and His462 residues) which is essential for accommodating the tRNA.

2) CP (Connective Peptide)-core and 3) CP1 hairpin consist of antiparallel β-sheets, but only the CP core is fixed on the aminoacylation domain. There is a “joint” formed by the junction of the CP-core and the CP1 hairpin (Ala180 and His462 residues) which is essential for accommodating the tRNA <ref name="Fukunaga">PMID:16155584</ref>.

4) CP1 editing domain is located in the middle of the CP1 hairpin. It is the editing domain, that means that this region is responsible for the hydrolysis of the incorrectly synthesized products. Because LeuRS have a specific editing activity that hydrolyzes misactivated aminoacyl-adenylates (pre-transfer editing) and mischarged aminoacyl-tRNAs (post-transfer editing) or both when they have misformed with noncognate amino acids.The residue Asp 332 is necessary for post-transfer editing.

4) CP1 editing domain is located in the middle of the CP1 hairpin. It is the editing domain, that means that this region is responsible for the hydrolysis of the incorrectly synthesized products. Because LeuRS have a specific editing activity that hydrolyzes misactivated aminoacyl-adenylates (pre-transfer editing) and mischarged aminoacyl-tRNAs (post-transfer editing) or both when they have misformed with noncognate amino acids.The residue Asp 332 is necessary for post-transfer editing <ref name="Fukunaga">PMID:15663927</ref>.

5) CP2 is inserted between the second and third β-sheets of the CP core. It is composed of a pair of antiparallel α-helices and a connecting β-sheet and is necessary for the amino acid activation and post-transfer editing.

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6) C-terminal domain and 7) α-helix bundle domain are essential for the tRNA binding throughout the tRNA Leu charging reaction. The C-terminal domain is important for the second step of the reaction, the transfer of the leucyl from the leucyl-adenylate to the 3’end of tRNA Leu. The α-helix bundle is found at the bottom of the enzyme and consists of five long α-helices.

8) LSD (Leucine-specific domain) 1 and LSD2 have been described in Archaeal LeuRs, inserted between the two helices in Rossmann-fol domain. They vary in size. LSD1 is a small domain which includes two antiparallel α-helices. The crystal structure of the apo enzyme suggests that LSD1 may have the potential to regulate the KMSKS loop opening and closing. This loop is highly dynamic and flexible during amino acid activation. LSD2 is a large domain (5 bundle α-helices) located on the opposite site of the enzyme relative to the aminoacylation active site.

8) LSD (Leucine-specific domain) 1 and LSD2 have been described in Archaeal LeuRs, inserted between the two helices in Rossmann-fol domain. They vary in size. LSD1 is a small domain which includes two antiparallel α-helices. The crystal structure of the apo enzyme suggests that LSD1 may have the potential to regulate the KMSKS loop opening and closing. This loop is highly dynamic and flexible during amino acid activation. LSD2 is a large domain (5 bundle α-helices) located on the opposite site of the enzyme relative to the aminoacylation active site <ref name="Zhou">PMID:20482517</ref>.

9) SC-fold domain follows the Rossmann-fold domain. His β-α-α-β-α topology is characteristic. It contains the KMSKS motif, which is located on the loop between the first β-sheet and the first α-helix of its topology.

9) SC-fold domain follows the Rossmann-fold domain. His β-α-α-β-α topology is characteristic. It contains the KMSKS motif, which is located on the loop between the first β-sheet and the first α-helix of its topology <ref name="Fukunaga">PMID:15663927</ref>.

Sandbox Reserved 704: Difference between revisions

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@@ Line 5: / Line 5: @@
 === Crystal structure of leucyl-tRNA synthetase and tRNA (leucine) complex ===
-Aminoacyl-tRNA synthetases (aaRSs) are ligases which exclusively attach a particular amino acid to the 3’ 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 of the accuracy of this reaction.
+Aminoacyl-tRNA synthetases (aaRSs) are ligases which exclusively attach a particular amino acid to the 3’ 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 of the accuracy of this reaction <ref name="Zhou">PMID:20482517</ref>.
@@ Line 16: / Line 16: @@
-The structure can be divided into nine domains:
+The structure can be divided into nine domains <ref name="Fukunaga">PMID:15663927</ref> :
 ) The class I-characterizing Rossmann-fold aminoacylation catalytic domain. It contains the HIGH motif. It is located at the beginning of the long α-helix found below the Rossmann-fold core β-sheet.
 Other the Rossmann fold domain, there are other fused and inserted domains.
-) CP (Connective Peptide)-core and 3) CP1 hairpin consist of antiparallel β-sheets, but only the CP core is fixed on the aminoacylation domain. There is a “joint” formed by the junction of the CP-core and the CP1 hairpin (Ala180 and His462 residues) which is essential for accommodating the tRNA.
+) CP (Connective Peptide)-core and 3) CP1 hairpin consist of antiparallel β-sheets, but only the CP core is fixed on the aminoacylation domain. There is a “joint” formed by the junction of the CP-core and the CP1 hairpin (Ala180 and His462 residues) which is essential for accommodating the tRNA <ref name="Fukunaga">PMID:16155584</ref>.
-) CP1 editing domain is located in the middle of the CP1 hairpin. It is the editing domain, that means that this region is responsible for the hydrolysis of the incorrectly synthesized products. Because LeuRS have a specific editing activity that hydrolyzes misactivated aminoacyl-adenylates  (pre-transfer editing) and mischarged aminoacyl-tRNAs (post-transfer editing) or both when they have misformed with noncognate amino acids.The residue Asp 332 is necessary for post-transfer editing.
+) CP1 editing domain is located in the middle of the CP1 hairpin. It is the editing domain, that means that this region is responsible for the hydrolysis of the incorrectly synthesized products. Because LeuRS have a specific editing activity that hydrolyzes misactivated aminoacyl-adenylates  (pre-transfer editing) and mischarged aminoacyl-tRNAs (post-transfer editing) or both when they have misformed with noncognate amino acids.The residue Asp 332 is necessary for post-transfer editing <ref name="Fukunaga">PMID:15663927</ref>.
 ) CP2 is inserted between the second and third β-sheets of the CP core. It is composed of a pair of antiparallel α-helices and a connecting β-sheet and is necessary for the amino acid activation and post-transfer editing.
@@ Line 29: / Line 29: @@
 ) C-terminal domain and 7) α-helix bundle domain are essential for the tRNA binding throughout the tRNA Leu charging reaction. The C-terminal domain is important for the second step of the reaction, the transfer of the leucyl from the leucyl-adenylate to the 3’end of tRNA Leu. The α-helix bundle is found at the bottom of the enzyme and consists of five long α-helices.
-) LSD (Leucine-specific domain) 1 and LSD2 have been described in Archaeal LeuRs, inserted between the two helices in Rossmann-fol domain. They vary in size. LSD1 is a small domain which includes two antiparallel α-helices. The crystal structure of the apo enzyme suggests that LSD1 may have the potential to regulate the KMSKS loop opening and closing. This loop is highly dynamic and flexible during amino acid activation. LSD2 is a large domain (5 bundle α-helices) located on the opposite site of the enzyme relative to the aminoacylation active site.
+) LSD (Leucine-specific domain) 1 and LSD2 have been described in Archaeal LeuRs, inserted between the two helices in Rossmann-fol domain. They vary in size. LSD1 is a small domain which includes two antiparallel α-helices. The crystal structure of the apo enzyme suggests that LSD1 may have the potential to regulate the KMSKS loop opening and closing. This loop is highly dynamic and flexible during amino acid activation. LSD2 is a large domain (5 bundle α-helices) located on the opposite site of the enzyme relative to the aminoacylation active site <ref name="Zhou">PMID:20482517</ref>.
-) SC-fold domain follows the Rossmann-fold domain. His β-α-α-β-α  topology is characteristic. It contains the KMSKS motif, which is located on the loop between the first β-sheet and the first α-helix of its topology.
+) SC-fold domain follows the Rossmann-fold domain. His β-α-α-β-α  topology is characteristic. It contains the KMSKS motif, which is located on the loop between the first β-sheet and the first α-helix of its topology <ref name="Fukunaga">PMID:15663927</ref>.