3HFZ

Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with m-tyrosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Eukaryotic cytosolic and mitochondrial phenylalanyl-tRNA synthetases catalyze the charging of tRNA with the meta-tyrosine

Klipcan, L.Moor, N.Kessler, N.Safro, M.G.

(2009) Proc Natl Acad Sci U S A 106: 11045-11048

  • DOI: https://doi.org/10.1073/pnas.0905212106
  • Primary Citation of Related Structures:  
    3HFV, 3HFZ

  • PubMed Abstract: 

    The accumulation of proteins damaged by reactive oxygen species (ROS), conventionally regarded as having pathological potentials, is associated with age-related diseases such as Alzheimer's, atherosclerosis, and cataractogenesis. Exposure of the aromatic amino acid phenylalanine to ROS-generating systems produces multiple isomers of tyrosine: m-tyrosine (m-Tyr), o-tyrosine (o-Tyr), and the standard p-tyrosine (Tyr). Previously it was demonstrated that exogenously supplied, oxidized amino acids could be incorporated into bacterial and eukaryotic proteins. It is, therefore, likely that in many cases, in vivo-damaged amino acids are available for de novo synthesis of proteins. Although the involvement of aminoacyl-tRNA synthetases in this process has been hypothesized, the specific pathway by which ROS-damaged amino acids are incorporated into proteins remains unclear. We provide herein evidence that mitochondrial and cytoplasmic phenylalanyl-tRNA synthetases (HsmtPheRS and HsctPheRS, respectively) catalyze direct attachment of m-Tyr to tRNA(Phe), thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into eukaryotic proteins. Crystal complexes of mitochondrial and bacterial PheRSs with m-Tyr reveal the net of highly specific interactions within the synthetic and editing sites.


  • Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase alpha chain350Thermus thermophilusMutation(s): 0 
EC: 6.1.1.20
UniProt
Find proteins for Q5SGX2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SGX2 
Go to UniProtKB:  Q5SGX2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SGX2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase beta chain785Thermus thermophilusMutation(s): 0 
EC: 6.1.1.20
UniProt
Find proteins for Q5SGX1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SGX1 
Go to UniProtKB:  Q5SGX1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SGX1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
MTY PDBBind:  3HFZ Ki: 1.30e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.181α = 90
b = 173.181β = 90
c = 138.852γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Atomic model
  • Version 1.3: 2016-12-14
    Changes: Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description