8IFJ

Crystal structure of pyrrolysyl-tRNA synthetase from methanogenic archaeon ISO4-G1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids.

Yanagisawa, T.Seki, E.Tanabe, H.Fujii, Y.Sakamoto, K.Yokoyama, S.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24076256
  • Primary Citation of Related Structures:  
    8IFJ

  • PubMed Abstract: 

    Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNA Pyl from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). Previously, we achieved full productivity of cell-free protein synthesis for bulky non-canonical amino acids, including N ε -(((( E )-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys), by using Methanomethylophilus alvus PylRS with structure-based mutations in and around the amino acid binding pocket (first-layer and second-layer mutations, respectively). Recently, the PylRS·tRNA Pyl pair from a methanogenic archaeon ISO4-G1 was used for genetic code expansion. In the present study, we determined the crystal structure of the methanogenic archaeon ISO4-G1 PylRS (ISO4-G1 PylRS) and compared it with those of structure-known PylRSs. Based on the ISO4-G1 PylRS structure, we attempted the site-specific incorporation of N ε -( p -ethynylbenzyloxycarbonyl)-L-lysine ( p EtZLys) into proteins, but it was much less efficient than that of TCO*Lys with M. alvus PylRS mutants. Thus, the first-layer mutations (Y125A and M128L) of ISO4-G1 PylRS, with no additional second-layer mutations, increased the protein productivity with p EtZLys up to 57 ± 8% of that with TCO*Lys at high enzyme concentrations in the cell-free protein synthesis.


  • Organizational Affiliation

    RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrrolysyl-tRNA synthetase PylS
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
276methanogenic archaeon mixed culture ISO4-G1Mutation(s): 0 
Gene Names: AUP07_0651
UniProt
Find proteins for A0A126QV54 (methanogenic archaeon mixed culture ISO4-G1)
Explore A0A126QV54 
Go to UniProtKB:  A0A126QV54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A126QV54
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.51α = 90
b = 102.68β = 90
c = 349.86γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP17am0101081
Japan Agency for Medical Research and Development (AMED)JapanJP19gm0010001
Japan Society for the Promotion of Science (JSPS)Japan16K05859
Japan Society for the Promotion of Science (JSPS)Japan24550203

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection