4YLY

Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium, staphylococcus aureus at 2.25 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

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Literature

Crystal structure of Staphylococcus aureus peptidyl-tRNA hydrolase at a 2.25 angstrom resolution.

Zhang, F.Song, Y.Niu, L.Teng, M.Li, X.

(2015) Acta Biochim Biophys Sin (Shanghai) 47: 1005-1010

  • DOI: https://doi.org/10.1093/abbs/gmv114
  • Primary Citation of Related Structures:  
    4YLY

  • PubMed Abstract: 

    Peptidyl-tRNA hydrolase (Pth) catalyzes the release of tRNA to relieve peptidyl-tRNA accumulation. Because Pth activity is essential for the viability of bacteria, Pth is regarded as a promising target for the discovery of new antimicrobial agents. Here, the structure of Pth from the Gram-positive bacterium Staphylococcus aureus (SaPth) was solved by X-ray crystallography at a 2.25 Å resolution. The SaPth structure exhibits significant structural similarity with other members of the Pth superfamily, with a conserved α/β/α sandwich fold. A molecular phylogenetic analysis and a structure database search indicated that SaPth is most similar to its homolog in Streptococcus pyogenes, but it has a different substrate-binding cleft state.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei 230026, China Key Laboratory of Structural Biology, Hefei Science Center, Chinese Academy of Science, Hefei 230026, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase
A, B
198Staphylococcus aureusMutation(s): 0 
Gene Names: pth
EC: 3.1.1.29
UniProt
Find proteins for Q6YP15 (Staphylococcus aureus)
Explore Q6YP15 
Go to UniProtKB:  Q6YP15
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6YP15
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.752α = 90
b = 70.604β = 90
c = 128.751γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Chinese Ministry of Science and TechnologyChina2012CB917200 and 2009CB825500
the Chinese National Natural Science FoundationChina31270014, 31130018, 30900224 and 10979039

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description