4ZXP

Crystal structure of Peptidyl- tRNA Hydrolase from Vibrio cholerae

4ZXP の概要

• エントリーDOI: 10.2210/pdb4zxp/pdb
• 分子名称: Peptidyl-tRNA hydrolase, CITRATE ANION (3 entities in total)
• 機能のキーワード: hydrolase, peptidyl-trna
• 由来する生物種: Vibrio cholerae O1 biovar El Tor str. N16961
• 細胞内の位置: Cytoplasm : Q9KQ21
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 43709.44

構造登録者

Shahid, S.,Pal, R.K.,Kabra, A.,Yadav, R.,Kumar, A.,Arora, A. (登録日: 2015-05-20, 公開日: 2016-06-22, 最終更新日: 2024-11-06)

主引用文献

Kabra, A.,Shahid, S.,Pal, R.K.,Yadav, R.,Pulavarti, S.V.,Jain, A.,Tripathi, S.,Arora, A.
Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase.
RNA, 23:202-216, 2017

PubMed Abstract: Bacterial peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby prevents cell death by alleviating tRNA starvation. X-ray and NMR studies of Vibrio cholerae Pth (VcPth) and mutants of its key residues involved in catalysis show that the activity and selectivity of the protein depends on the stereochemistry and dynamics of residues H24, D97, N118, and N14. D97-H24 interaction is critical for activity because it increases the nucleophilicity of H24. The N118 and N14 have orthogonally competing interactions with H24, both of which reduce the nucleophilicity of H24 and are likely to be offset by positioning of a peptidyl-tRNA substrate. The region proximal to H24 and the lid region exhibit slow motions that may assist in accommodating the substrate. Helix α3 exhibits a slow wobble with intermediate time scale motions of its N-cap residue N118, which may work as a flypaper to position the scissile ester bond of the substrate. Overall, the dynamics of interactions between the side chains of N14, H24, D97, and N118, control the catalysis of substrate by this enzyme.

PubMed: 28096445
DOI: 10.1261/rna.057620.116

実験手法

X-RAY DIFFRACTION (1.63 Å)