High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus

被引:3
|
作者
Matsumoto, Ami [1 ]
Uehara, Yuji [1 ]
Shimizu, Yoshihiro [2 ,3 ]
Ueda, Takuya [2 ]
Uchiumi, Toshio [1 ]
Ito, Kosuke [1 ]
机构
[1] Niigata Univ, Dept Biol, Fac Sci, Niigata, Japan
[2] Univ Tokyo, Grad Sch Frontier Sci, Dept Med Genome Sci, Chiba, Japan
[3] RIKEN Ctr Biosyst Dynam Res, Lab Cell Free Prot Synth, Osaka, Japan
基金
日本学术振兴会;
关键词
atomic resolution; dynamics; peptidyl-tRNA hydrolase; thermostability; translation; X-ray crystallography; X-RAY ANALYSIS; CRYSTALLOGRAPHIC STRUCTURE DETERMINATION; ESCHERICHIA-COLI; ANGSTROM RESOLUTION; RECOMBINANT PRODUCTION; ENZYMATIC-HYDROLYSIS; SECONDARY-STRUCTURE; PROTEIN-SYNTHESIS; METABOLIC ROLE; SITE;
D O I
10.1002/prot.25643
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are the products of defective translation, to recycle the tRNA for further rounds of protein synthesis. Pth is ubiquitous in nature, and its activity is essential for bacterial viability. Here, we have determined the crystal structure of Pth from Thermus thermophilus (TtPth) at 1.00 angstrom resolution. This is the first structure of a Pth from a thermophilic bacterium and the highest resolution Pth structure reported so far. The present atomic resolution data enabled the calculation of anisotropic displacement parameters for all atoms, which revealed the directionality of the fluctuations of key regions for the substrate recognition. Comparisons between TtPth and mesophilic bacterial Pths revealed that their structures are similar overall. However, the structures of the N- and C-terminal, loop-helix alpha 4, and helix alpha 6 regions are different. In addition, the helix alpha 1 to strand beta 4 region of TtPth is remarkably different from those of the mesophilic bacterial Pths, because this region is 9 or 10 amino acid residues shorter than those of the mesophilic bacterial Pths. This shortening seems to contribute to the thermostability of TtPth. To further understand the determinants for the thermostability of TtPth, we compared various structural factors of TtPth with those of mesophilic bacterial Pths. The data suggest that the decreases in accessible surface area and thermolabile amino acid residues, and the increases in ion pairs, hydrogen bonds, and proline residues cooperatively contribute to the thermostability of TtPth.
引用
收藏
页码:226 / 235
页数:10
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