3UFZ

Crystal structure of a Trp-less green fluorescent protein translated by the universal genetic code


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Simplification of the genetic code: restricted diversity of genetically encoded amino acids.

Kawahara-Kobayashi, A.Masuda, A.Araiso, Y.Sakai, Y.Kohda, A.Uchiyama, M.Asami, S.Matsuda, T.Ishitani, R.Dohmae, N.Yokoyama, S.Kigawa, T.Nureki, O.Kiga, D.

(2012) Nucleic Acids Res. 40: 10576-10584

  • DOI: 10.1093/nar/gks786
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • At earlier stages in the evolution of the universal genetic code, fewer than 20 amino acids were considered to be used. Although this notion is supported by a wide range of data, the actual existence and function of the genetic codes with a limited s ...

    At earlier stages in the evolution of the universal genetic code, fewer than 20 amino acids were considered to be used. Although this notion is supported by a wide range of data, the actual existence and function of the genetic codes with a limited set of canonical amino acids have not been addressed experimentally, in contrast to the successful development of the expanded codes. Here, we constructed artificial genetic codes involving a reduced alphabet. In one of the codes, a tRNAAla variant with the Trp anticodon reassigns alanine to an unassigned UGG codon in the Escherichia coli S30 cell-free translation system lacking tryptophan. We confirmed that the efficiency and accuracy of protein synthesis by this Trp-lacking code were comparable to those by the universal genetic code, by an amino acid composition analysis, green fluorescent protein fluorescence measurements and the crystal structure determination. We also showed that another code, in which UGU/UGC codons are assigned to Ser, synthesizes an active enzyme. This method will provide not only new insights into primordial genetic codes, but also an essential protein engineering tool for the assessment of the early stages of protein evolution and for the improvement of pharmaceuticals.


    Organizational Affiliation

    Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Midori-ku, Yokohama-shi, Kanagawa 226-8503, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
229Aequorea victoriaMutations: F97S, M151T, Q78R, T9A, V161A, Y198C, A204V, W57F, S203T
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO
A
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.844α = 90.00
b = 62.955β = 90.00
c = 67.369γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data scaling
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references