Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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This is version 1.3 of the entry. See complete history


Crystal structure at 1.2 A resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase.

Schmitt, E.Mechulam, Y.Fromant, M.Plateau, P.Blanquet, S.

(1997) EMBO J 16: 4760-4769

  • DOI: https://doi.org/10.1093/emboj/16.15.4760
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Peptidyl-tRNA hydrolase activity from Escherichia coli ensures the recycling of peptidyl-tRNAs produced through abortion of translation. This activity, which is essential for cell viability, is carried out by a monomeric protein of 193 residues. The structure of crystalline peptidyl-tRNA hydrolase could be solved at 1.2 A resolution. It indicates a single alpha/beta globular domain built around a twisted mixed beta-sheet, similar to the central core of an aminopeptidase from Aeromonas proteolytica. This similarity allowed the characterization by site-directed mutagenesis of several residues of the active site of peptidyl-tRNA hydrolase. These residues, strictly conserved among the known peptidyl-tRNA hydrolase sequences, delineate a channel which, in the crystal, is occupied by the C-end of a neighbouring peptidyl-tRNA hydrolase molecule. Hence, several main chain atoms of three residues belonging to one peptidyl-tRNA hydrolase polypeptide establish contacts inside the active site of another peptidyl-tRNA hydrolase molecule. Such an interaction is assumed to represent the formation of a complex between the enzyme and one product of the catalysed reaction.

  • Organizational Affiliation

    Laboratoire de Biochimie, Unit'e de Recherche Associ'ee No. 1970 du Centre National de la Recherche Scientifique, Ecole Polytechnique, Palaiseau, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDYL-TRNA HYDROLASE193Escherichia coli K-12Mutation(s): 0 
Gene Names: PTH
Find proteins for P0A7D1 (Escherichia coli (strain K12))
Explore P0A7D1 
Go to UniProtKB:  P0A7D1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7D1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.24α = 90
b = 63.59β = 90
c = 62.57γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-25
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Other