3TEH

Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with L-dopa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bacterial and Eukaryotic Phenylalanyl-tRNA Synthetases Catalyze Misaminoacylation of tRNA(Phe) with 3,4-Dihydroxy-L-Phenylalanine.

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

(2011) Chem Biol 18: 1221-1229

  • DOI: 10.1016/j.chembiol.2011.08.008
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases exert control over the accuracy of translation by selective pairing the correct amino acids with their cognate tRNAs, and proofreading the misacylated products. Here we show that three existing, structurally different pheny ...

    Aminoacyl-tRNA synthetases exert control over the accuracy of translation by selective pairing the correct amino acids with their cognate tRNAs, and proofreading the misacylated products. Here we show that three existing, structurally different phenylalanyl-tRNA synthetases-human mitochondrial (HsmtPheRS), human cytoplasmic (HsctPheRS), and eubacterial from Thermus thermophilus (TtPheRS), catalyze mischarging of tRNA(Phe) with an oxidized analog of tyrosine-L-dopa. The lowest level of L-dopa discrimination over the cognate amino acid, exhibited by HsmtPheRS, is comparable to that of tyrosyl-tRNA synthetase. HsmtPheRS and TtPheRS complexes with L-dopa revealed in the active sites an electron density shaping this ligand. HsctPheRS and TtPheRS possessing editing activity are capable of hydrolyzing the exogenous L-dopa-tRNA(Phe) as efficiently as Tyr-tRNA(Phe). However, editing activity of PheRS does not guarantee reduction of the aminoacylation error rate to escape misincorporation of L-dopa into polypeptide chains.


    Organizational Affiliation

    Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase alpha chainA350Thermus thermophilusMutation(s): 0 
Gene Names: pheS
EC: 6.1.1.20
Find proteins for P27001 (Thermus thermophilus)
Explore P27001 
Go to UniProtKB:  P27001
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phenylalanyl-tRNA synthetase beta chainB785Thermus thermophilusMutation(s): 0 
Gene Names: pheT
EC: 6.1.1.20
Find proteins for P27002 (Thermus thermophilus)
Explore P27002 
Go to UniProtKB:  P27002
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAH
Query on DAH

Download CCD File 
A, B
3,4-DIHYDROXYPHENYLALANINE
C9 H11 N O4
WTDRDQBEARUVNC-LURJTMIESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.316α = 90
b = 173.316β = 90
c = 139.162γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Structure summary