Open AccessCrystal structure of peptidyl‐tRNA hydrolase from a Gram‐positive bacterium, Streptococcus pyogenes at 2.19 Å resolution shows the closed structure of the substrate‐binding cleft
Author(s) -
Singh Avinash,
Gautam Lovely,
Sinha Mau,
Bhushan Asha,
Kaur Punit,
Sharma Sujata,
Singh T.P.
Publication year - 2014
Publication title -
febs open bio
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.718
H-Index - 31
ISSN - 2211-5463
DOI - 10.1016/j.fob.2014.10.010
Subject(s) - hydrolase , transfer rna , stereochemistry , crystal structure , chemistry , molecule , substrate (aquarium) , streptococcus pyogenes , peptide , crystallography , bacteria , resolution (logic) , active site , enzyme , biochemistry , biology , rna , ecology , genetics , organic chemistry , artificial intelligence , computer science , gene , staphylococcus aureus
Peptidyl‐tRNA hydrolase (Pth) catalyses the release of tRNA and peptide components from peptidyl‐tRNA molecules. Pth from a Gram‐positive bacterium Streptococcus pyogenes ( Sp Pth) was cloned, expressed, purified and crystallised. Three‐dimensional structure of Sp Pth was determined by X‐ray crystallography at 2.19 Å resolution. Structure determination showed that the asymmetric unit of the unit cell contained two crystallographically independent molecules, designated A and B. The superimposition of C α traces of molecules A and B showed an r.m.s. shift of 0.4 Å, indicating that the structures of two crystallographically independent molecules were identical. The polypeptide chain of Sp Pth adopted an overall α/β conformation. The substrate‐binding cleft in Sp Pth is formed with three loops: the gate loop, Ile91–Leu102; the base loop, Gly108–Gly115; and the lid loop, Gly136–Gly150. Unlike in the structures of Pth from Gram‐negative bacteria, the entry to the cleft in the structure of Sp Pth appeared to be virtually closed. However, the conformations of the active site residues were found to be similar.