6JP2

Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fully Productive Cell-Free Genetic Code Expansion by Structure-Based Engineering ofMethanomethylophilus alvusPyrrolysyl-tRNA Synthetase.

Seki, E.Yanagisawa, T.Kuratani, M.Sakamoto, K.Yokoyama, S.

(2020) ACS Synth Biol 9: 718-732

  • DOI: 10.1021/acssynbio.9b00288
  • Primary Citation of Related Structures:  
    6JP2

  • PubMed Abstract: 
  • Pyrrolysyl-tRNA synthetase (PylRS)/tRNA Pyl pairs from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). ...

    Pyrrolysyl-tRNA synthetase (PylRS)/tRNA Pyl pairs from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). In this study, we achieved the full productivity of cell-free protein synthesis for difficult, bulky non-canonical amino acids, such as N ε -(((( E )-cyclooct-2-en-1-yl)oxy)carbonyl)-l-lysine (TCO*Lys), by using Methanomethylophilus alvus PylRS. First, based on the crystal structure of M. alvus PylRS, the productivities for various non-canonical amino acids were greatly increased by rational engineering of the amino acid-binding pocket. The productivities were further enhanced by using a much higher concentration of PylRS over that of M. mazei PylRS, or by mutating the outer layer of the amino acid-binding pocket. Thus, we achieved full productivity even for TCO*Lys. The quantity and quality of the cell-free-produced antibody fragment containing TCO*Lys were drastically improved. These results demonstrate the importance of full productivity for the expanded genetic code.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA. daniel.southworth@ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrrolysyl-tRNA synthetaseABCD278Candidatus Methanomethylophilus alvusMutation(s): 0 
EC: 6.1.1.26
Find proteins for M9SC49 (Methanomethylophilus alvus (strain Mx1201))
Explore M9SC49 
Go to UniProtKB:  M9SC49
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.38α = 90
b = 112.78β = 114.21
c = 107.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan24550203
Japan Agency for Medical Research and Development (AMED)JapanJP17am0101081

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references