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 
  • R-Value Observed: 0.226 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/nature14121
  • Primary Citation of Related Structures:  
    4OUD

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosyl-tRNA synthetase425Escherichia coli str. K-12 substr. MC4100Mutation(s): 7 
Gene Names: tyrSBN896_1452
EC: 6.1.1.1
UniProt
Find proteins for A0A0H2UKY9 (Escherichia coli str. K-12 substr. MC4100)
Explore A0A0H2UKY9 
Go to UniProtKB:  A0A0H2UKY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2UKY9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosyl-tRNA synthetase394Escherichia coli str. K-12 substr. MC4100Mutation(s): 7 
Gene Names: tyrSBN896_1452
EC: 6.1.1.1
UniProt
Find proteins for A0A0H2UKZ0 (Escherichia coli str. K-12 substr. MC4100)
Explore A0A0H2UKZ0 
Go to UniProtKB:  A0A0H2UKZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2UKZ0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

Download Ideal Coordinates CCD File 
C [auth A]TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
BIF
Query on BIF
A
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 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.34α = 90
b = 67.205β = 102.65
c = 90.682γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description