3HFZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.USA 106: 11045-11048

  • DOI: 10.1073/pnas.0905212106
  • Primary Citation of Related Structures:  

  • 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 arom ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase alpha chain
A
350Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: pheS
EC: 6.1.1.20
Find proteins for Q5SGX2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SGX2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase beta chain
B
785Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: pheT
EC: 6.1.1.20
Find proteins for Q5SGX1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SGX1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTY
Query on MTY

Download SDF File 
Download CCD File 
A, B
META-TYROSINE
C9 H11 N O3
JZKXXXDKRQWDET-QMMMGPOBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTYKi: 13000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.269 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 173.181α = 90.00
b = 173.181β = 90.00
c = 138.852γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-16
    Type: Atomic model
  • Version 1.3: 2016-12-14
    Type: Structure summary