1UE0

Isoleucyl-tRNA synthetase editing domain complexed with L-Valine

1UE0 の概要

• エントリーDOI: 10.2210/pdb1ue0/pdb
• 関連するPDBエントリー: 1UDZ
• 分子名称: Isoleucyl-tRNA synthetase, VALINE (3 entities in total)
• 機能のキーワード: aminoacyl-trna synthetase, cp1, editing, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, ligase
• 由来する生物種: Thermus thermophilus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 40503.33

構造登録者

Fukunaga, R.,Fukai, S.,Ishitani, R.,Nureki, O.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2003-05-08, 公開日: 2004-03-23, 最終更新日: 2024-04-03)

主引用文献

Fukunaga, R.,Fukai, S.,Ishitani, R.,Nureki, O.,Yokoyama, S.
Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine.
J.Biol.Chem., 279:8396-8402, 2004

PubMed Abstract: Isoleucyl-tRNA synthetase (IleRS) links tRNA(Ile) with not only its cognate isoleucine but also the nearly cognate valine. The CP1 domain of IleRS deacylates, or edits, the mischarged Val-tRNA(Ile). We determined the crystal structures of the Thermus thermophilus IleRS CP1 domain alone, and in its complex with valine at 1.8- and 2.0-A resolutions, respectively. In the complex structure, the Asp(328) residue, which was shown to be critical for the editing reaction against Val-tRNA(Ile) by a previous mutational analysis, recognizes the valine NH(3)(+) group. The valine side chain binding pocket is only large enough to accommodate valine, and the placement of an isoleucine model in this location revealed that the additional methylene group of isoleucine would clash with His(319). The H319A mutant of Escherichia coli IleRS reportedly deacylates the cognate Ile-tRNA(Ile) in addition to Val-tRNA(Ile), indicating that the valine-binding mode found in this study represents that in the Val-tRNA(Ile) editing reaction. Analyses of the Val-tRNA(Ile) editing activities of T. thermophilus IleRS mutants revealed the importance of Thr(228), Thr(229), Thr(230), and Asp(328), which are coordinated with water molecules in the present structure. The structural model for the Val-adenosine moiety of Val-tRNA(Ile) bound in the IleRS editing site revealed some interesting differences in the substrate binding and recognizing mechanisms between IleRS and T. thermophilus leucyl-tRNA synthetase. For example, the carbonyl oxygens of the amino acids are located opposite to each other, relative to the adenosine ribose ring, and are differently recognized.

PubMed: 14672940
DOI: 10.1074/jbc.M312830200

実験手法

X-RAY DIFFRACTION (2 Å)