1YGB

Crystal Structure of the catalytic fragment of alanyl-tRNA synthetase in complex with L-serine

1YGB の概要

• エントリーDOI: 10.2210/pdb1ygb/pdb
• 関連するPDBエントリー: 1RIQ 1YFR 1YFS 1YFT
• 分子名称: Alanyl-tRNA synthetase, SERINE (3 entities in total)
• 機能のキーワード: helix-turn-helix motif, alpha-beta fold, amino acid binding, ligase
• 由来する生物種: Aquifex aeolicus
• 細胞内の位置: Cytoplasm: O67323
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 53877.34

構造登録者

Swairjo, M.A.,Schimmel, P.R. (登録日: 2005-01-04, 公開日: 2005-01-25, 最終更新日: 2023-08-23)

主引用文献

Swairjo, M.A.,Schimmel, P.R.
Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase.
Proc.Natl.Acad.Sci.USA, 102:988-993, 2005

PubMed Abstract: The genetic code is fixed in aminoacylation reactions catalyzed by aminoacyl-tRNA synthetases. Amino acid discrimination occurs at two sites: one for amino acid activation and aminoacylation and one for editing misactivated amino acids. Although the active site sieves out bulkier amino acids, misactivation occurs with substrates whose side chains are smaller than the cognate one. Paradoxically, although alanyl-tRNA synthetase activates glycine as well as alanine, the sterically larger (than alanine) serine is also misactivated. Here, we report crystal structures of an active fragment of Aquifex aeolicus alanyl-tRNA synthetase complexed, separately, with Mg2+-ATP, alanine, glycine, and serine. Ala and Gly are bound in similar orientations in a side-chain-accommodating pocket, where alpha-amino and carboxyl groups are stabilized by salt bridges, and the carboxyl by an H-bond from the side chain NH2 of Asn-194. In contrast, whereas the same two salt bridges stabilize bound Ser, H-bonding of the highly conserved (among class II tRNA synthetases) Asn-194 side chain NH2 to the Ser OH, instead of to the carboxyl, forces pocket expansion. Significantly, in the Mg2+-ATP complex, Asn-194 coordinates a Mg2+-alpha-phosphate bridge. Thus, the sieve for Ser exclusion is broken because of selective pressure to retain Asn-194 for Mg2+-ATP and Ala binding.

PubMed: 15657145
DOI: 10.1073/pnas.0409024102

実験手法

X-RAY DIFFRACTION (2.48 Å)