4QT4

Crystal structure of Peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 Angstrom resolution shows the Closed Structure of the Substrate Binding Cleft

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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Literature

Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 angstrom resolution shows the closed structure of the substrate-binding cleft.

Singh, A., Gautam, L., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

(2014) FEBS Open Bio 4: 915-922

  • DOI: 10.1016/j.fob.2014.10.010
  • Primary Citation of Related Structures:  
    4QT4

  • PubMed 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolaseA, B189Streptococcus pyogenes NZ131Mutation(s): 0 
Gene Names: pth, Spy49_0005
EC: 3.1.1.29
UniProt
Find proteins for B5XIP6 (Streptococcus pyogenes serotype M49 (strain NZ131))
Explore B5XIP6 
Go to UniProtKB:  B5XIP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5XIP6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.024α = 90.33
b = 43.028β = 105.78
c = 65.1γ = 112.51
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references