User:Harry Gritsch/Sandbox 1
From Proteopedia
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Structural insights into ValRS come from a fluorine-19 NMR study on E.coli ValRS<ref>DOI: 10.1021/bi00220a031</ref> and a crystal structure of T. thermophilus ValRS complexed with tRNA(val) and a valine-AMP analog solved at 2.9Å<ref>DOI 10.1261/rna.2760703</ref>. The major structural elements of ValRS, like other class-Ia aminoacyl-tRNA synthetases, are a helical insertion into the N-terminal half of a Rossmann fold domain and an α-helix bundle domain near the C-terminus. Additionally, ValRS has a large editing domain important in the discrimination between valine and structurally similar amino acids. A positively charged <scene name='10/1078173/Sc-fold_domain/3'>stem-contact-fold</scene> (SC-fold) domain contacts the D-loop of tRNA(val), creating a space between the anticodon recognition and editing domains where the tRNA is "pinched" and held onto. This positive patch lines up with the negative backbone of the D-stem, with the Arg570 side chain contacting the oxygens of C11 and C25, the aromatic nitrogen of Trp571 forming weak bonds with the oxygens of U12, and the side chain of Arg566 hydrogen bonding with the backbone of C13. | Structural insights into ValRS come from a fluorine-19 NMR study on E.coli ValRS<ref>DOI: 10.1021/bi00220a031</ref> and a crystal structure of T. thermophilus ValRS complexed with tRNA(val) and a valine-AMP analog solved at 2.9Å<ref>DOI 10.1261/rna.2760703</ref>. The major structural elements of ValRS, like other class-Ia aminoacyl-tRNA synthetases, are a helical insertion into the N-terminal half of a Rossmann fold domain and an α-helix bundle domain near the C-terminus. Additionally, ValRS has a large editing domain important in the discrimination between valine and structurally similar amino acids. A positively charged <scene name='10/1078173/Sc-fold_domain/3'>stem-contact-fold</scene> (SC-fold) domain contacts the D-loop of tRNA(val), creating a space between the anticodon recognition and editing domains where the tRNA is "pinched" and held onto. This positive patch lines up with the negative backbone of the D-stem, with the Arg570 side chain contacting the oxygens of C11 and C25, the aromatic nitrogen of Trp571 forming weak bonds with the oxygens of U12, and the side chain of Arg566 hydrogen bonding with the backbone of C13. | ||
== tRNA(val) Recognition == | == tRNA(val) Recognition == | ||
| - | The anticodon of tRNA(val) is recognized and bound by a highly conserved α-helix bundle domain near the C-terminus. Upon binding to ValRS, the anitcodon loop of tRNA(val) becomes extensively unwound and deformed, leading to disordered anticodon. In this state, the first base of the anticodon (C34) is wound out towards the solvent and does not form any interactions with ValRS (which is likely important in wobble during translation). Instead, A35 and C36 become the primary identity elements of the tRNA(val) anticodon. A35 and C36 are spatially stabilized through stacking interactions which may be important in tRNA discrimination as both the A34-C35 and A36-C37 sequences are quite rare in natural tRNA species<ref>DOI: 10.1093/nar/26.1.148</ref>. | + | The anticodon of tRNA(val) is recognized and bound by a highly conserved α-helix bundle domain near the C-terminus. Upon binding to ValRS, the anitcodon loop of tRNA(val) becomes extensively unwound and deformed, leading to disordered anticodon. In this state, the first base of the anticodon (C34) is wound out towards the solvent and does not form any interactions with ValRS (which is likely important in wobble during translation). Instead, A35 and C36 become the primary identity elements of the tRNA(val) anticodon. A35 and C36 are spatially stabilized through stacking interactions which may be important in tRNA discrimination as both the A34-C35 and A36-C37 sequences are quite rare in natural tRNA species<ref>DOI: 10.1093/nar/26.1.148</ref>. A35 is recognized by van der Waals interactions with the side chains of Phe588 and Leu650 and hydrogen bonding between the 6-NH2 group and the side chains of Glu651/Arg587 and the backbone of Cys646. C36 is recognized by hydrogen bonding with the side chains of Lys581 and Asn584. |
== Amino Acid Discrimination == | == Amino Acid Discrimination == | ||
Revision as of 18:46, 25 April 2025
Valyl-tRNA Synthetase
Valyl-tRNA synthetase (ValRS, also known as valine tRNA ligase) is the enzyme responsible for charging tRNA(val) with valine. In humans, ValRS exists in a cytosolic and a mitochondrial form. The cytosolic form is a monomeric 140kDa protein encoded by VARS1 while the mitochondrial form is a slightly smaller monomeric 118kDa protein encoded by VARS2. ValRS is a member of the class-Ia subfamily of aminoacyl-tRNA synthetases, defined by a characteristic α helix bundle at the C-terminus used for tRNA recognition. Aminoacyl-tRNA synthetases are generally highly conserved, and ValRS exhibits high structural similarity to IleRS and LeuRS. Human disease related to mutations in ValRS are very rare but life-threatening. Biallelic mutations in ValRS are associated with neurological defects and global developmental delay, including epileptic encephalopathy, microcephaly and microphthalmia[1]. These phenotypes are thought to be due to a global lack of charged tRNA molecules which induces an amino acid starvation response and inhibits cell proliferation[2].
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