1J7G

Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase

1J7G の概要

• エントリーDOI: 10.2210/pdb1j7g/pdb
• 分子名称: D-tyrosyl-tRNA(Tyr) deacylase (2 entities in total)
• 機能のキーワード: d-tyr-trna(tyr) deacylase, structural genomics, hypothetical protein, structure 2 function project, s2f, hydrolase
• 由来する生物種: Haemophilus influenzae Rd KW20
• 細胞内の位置: Cytoplasm (Probable): P44814
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 15879.17

構造登録者

Lim, K.,Herzberg, O.,Structure 2 Function Project (S2F) (登録日: 2001-05-16, 公開日: 2003-04-22, 最終更新日: 2024-02-07)

主引用文献

Lim, K.,Tempczyk, A.,Bonander, N.,Toedt, J.,Howard, A.,Einsenstein, E.,Herzberg, O.
A Catalytic Mechanism for D-Tyr-tRNATyr Deacylase Based on the Crystal Structure of Hemophilus influenzae HI0670
J.Biol.Chem., 278:13496-13502, 2003

PubMed Abstract: D-Tyr-tRNA(Tyr) deacylase is an editing enzyme that removes d-tyrosine and other d-amino acids from charged tRNAs, thereby preventing incorrect incorporation of d-amino acids into proteins. A model for the catalytic mechanism of this enzyme is proposed based on the crystal structure of the enzyme from Haemophilus influenzae determined at a 1.64-A resolution. Structural comparison of this dimeric enzyme with the very similar structure of the enzyme from Escherichia coli together with sequence analyses indicate that the active site is located in the dimer interface within a depression that includes an invariant threonine residue, Thr-80. The active site contains an oxyanion hole formed by the main chain nitrogen atoms of Thr-80 and Phe-79 and the side chain amide group of the invariant Gln-78. The Michaelis complex between the enzyme and D-Tyr-tRNA was modeled assuming a nucleophilic attack on the carbonyl carbon of D-Tyr by the Thr-80 O(gamma) atom and a role for the oxyanion hole in stabilizing the negatively charged tetrahedral transition states. The model is consistent with all of the available data on substrate specificity. Based on this model, we propose a substrate-assisted acylation/deacylation-catalytic mechanism in which the amino group of the D-Tyr is deprotonated and serves as the general base.

PubMed: 12571243
DOI: 10.1074/jbc.M213150200

実験手法

X-RAY DIFFRACTION (1.64 Å)