Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.83 kDa 
• Atom Count: 1750 
• Modelled Residue Count: 194 
• Deposited Residue Count: 194 
• Unique protein chains: 1

4QAJ

Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa at 1.5 Angstrom resolution

• PDB DOI: 10.2210/pdb4QAJ/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-05 Released: 2014-05-28 
• Deposition Author(s): Singh, A., Kumar, A., Gautam, L., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Arora, A., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.220 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Structural and binding studies of peptidyl-tRNA hydrolase from Pseudomonas aeruginosa provide a platform for the structure-based inhibitor design against peptidyl-tRNA hydrolase

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

(2014) Biochem J 463: 329-337

• PubMed: 25101795 
• DOI: 10.1042/BJ20140631
• Primary Citation of Related Structures:  
  4FNO, 4JC4, 4QAJ, 4QBK, 4QD3


• PubMed Abstract: 
  

During the course of protein synthesis in the cell, the translation process is often terminated due to various reasons. As a result, peptidyl-tRNA molecules are released which are toxic to the cell as well reducing the availability of free amino acid and tRNA molecules for the required protein synthesis in the cell. Such a situation is corrected by an enzyme, Pth (peptidyl-tRNA hydrolase), which catalyses the release of free tRNA and peptide moieties from peptidyl-tRNAs. This means that the active Pth is essential for the survival of bacteria. In order to design inhibitors of PaPth (Pth from Pseudomonas aeruginosa), we determined the structures of PaPth in its native and bound states with compounds amino acylate-tRNA analogue and 5-azacytidine. The structure determination of the native protein revealed that the substrate-binding site was partially occupied by Glu161 from the neigh-bouring molecule. The structure of PaPth indicated that the substrate-binding site can be broadly divided into three distinct subsites. The structures of the two complexes showed that the amino acylate-tRNA analogue filled three subsites, whereas 5-azacytidine filled two subsites. The common sugar and the base moieties of the two compounds occupied identical positions in the cleft. Using surface plasmon resonance, the dissociation constants for the amino acylate-tRNA analogue and 5-azacytidine were found to be 3.53×10-8 M and 5.82×10-8 M respectively.

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Organizational Affiliation: 

*Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029 Delhi, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A	194	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA4672, pth EC: 3.1.1.29
UniProt
Find proteins for Q9HVC3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVC3  Go to UniProtKB:  Q9HVC3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.220 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.115	α = 90
b = 64.115	β = 90
c = 155.312	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-05 
• Released Date: 2014-05-28 
Deposition Author(s): Singh, A., Kumar, A., Gautam, L., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Arora, A., Singh, T.P.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Database references