4OUD

Engineered tyrosyl-tRNA synthetase with the nonstandard amino acid L-4,4-biphenylalanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biocontainment of genetically modified organisms by synthetic protein design.

Mandell, D.J.Lajoie, M.J.Mee, M.T.Takeuchi, R.Kuznetsov, G.Norville, J.E.Gregg, C.J.Stoddard, B.L.Church, G.M.

(2015) Nature 518: 55-60

  • DOI: 10.1038/nature14121

  • PubMed Abstract: 
  • Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods ...

    Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.


    Organizational Affiliation

    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-tRNA synthetase
A
425Escherichia coli str. K-12 substr. MC4100Mutation(s): 7 
Gene Names: tyrS
EC: 6.1.1.1
Find proteins for A0A0H2UKY9 (Escherichia coli str. K-12 substr. MC4100)
Go to UniProtKB:  A0A0H2UKY9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-tRNA synthetase
B
394Escherichia coli str. K-12 substr. MC4100Mutation(s): 7 
Gene Names: tyrS
EC: 6.1.1.1
Find proteins for A0A0H2UKZ0 (Escherichia coli str. K-12 substr. MC4100)
Go to UniProtKB:  A0A0H2UKZ0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

Download SDF File 
Download CCD File 
A
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
B
L-PEPTIDE LINKINGC4 H9 N O2

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BIF
Query on BIF
A, B
L-PEPTIDE LINKINGC15 H15 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.340α = 90.00
b = 67.205β = 102.65
c = 90.682γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-18
    Type: Database references