Crystal 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

Avinash Singh; Lovely Gautam; Mau Sinha; Asha Bhushan; Punit Kaur; Sujata Sharma; T P Singh

doi:10.1016/j.fob.2014.10.010

Crystal 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

FEBS Open Bio. 2014 Oct 22:4:915-22. doi: 10.1016/j.fob.2014.10.010. eCollection 2014.

Authors

Avinash Singh¹, Lovely Gautam¹, Mau Sinha¹, Asha Bhushan¹, Punit Kaur¹, Sujata Sharma¹, T P Singh¹

Affiliation

¹ Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.

Abstract

Peptidyl-tRNA hydrolase (Pth) catalyses the release of tRNA and peptide components from peptidyl-tRNA molecules. Pth from a Gram-positive bacterium Streptococcus pyogenes (SpPth) was cloned, expressed, purified and crystallised. Three-dimensional structure of SpPth 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 SpPth adopted an overall α/β conformation. The substrate-binding cleft in SpPth 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 SpPth appeared to be virtually closed. However, the conformations of the active site residues were found to be similar.

Keywords: Ab, Acinetobacter baumannii; Bt, Burkholderia thailandensis; Closed conformation; Crystal structure; Ec, Escherichia coli; Ft, Francisella tularensis; Ms, Mycobacterium smegmatis; Mt, Mycobacterium tuberculosis; Pa, Pseudomonas aeruginosa; Peptidyl-tRNA hydrolase; Pth, peptidyl-tRNA hydrolase; Sp, Streptococcus pyogenes; Streptococcus pyogenes; Substrate binding cleft.