6WRQ

Crystal structure of Mj 3-nitro-tyrosine tRNA synthetase (5B) S158C variant bound to 3-nitro-tyrosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase.

Beyer, J.N.Hosseinzadeh, P.Gottfried-Lee, I.Van Fossen, E.M.Zhu, P.Bednar, R.M.Karplus, P.A.Mehl, R.A.Cooley, R.B.

(2020) J Mol Biol 432: 4690-4704

  • DOI: 10.1016/j.jmb.2020.06.014
  • Primary Citation of Related Structures:  
    6WRK, 6WRN, 6WRQ, 6WRT

  • PubMed Abstract: 
  • Genetic Code Expansion (GCE) technologies incorporate non-canonical amino acids (ncAAs) into proteins at amber stop codons. To avoid unwanted truncated protein and improve ncAA-protein yields, genomically recoded strains of E. coli lacking Release Fa ...

    Genetic Code Expansion (GCE) technologies incorporate non-canonical amino acids (ncAAs) into proteins at amber stop codons. To avoid unwanted truncated protein and improve ncAA-protein yields, genomically recoded strains of E. coli lacking Release Factor 1 (RF1) are becoming increasingly popular expression hosts for GCE applications. In the absence of RF1, however, endogenous near-cognate amber suppressing tRNAs can lead to contaminating protein forms with natural amino acids in place of the ncAA. Here, we show that a 2 nd -generation amino-acyl tRNA synthetase (aaRS)/tRNA CUA pair for site-specific incorporation of 3-nitro-tyrosine could not outcompete near-cognate suppression in an RF1-deficient expression host and therefore could not produce homogenously nitrated protein. To resolve this, we used Rosetta to target positions in the nitroTyr aaRS active site for improved substrate binding, and then constructed of a small library of variants to subject to standard selection protocols. The top selected variant had an ~2-fold greater efficiency, and remarkably this relatively small improvement enabled homogeneous incorporation of nitroTyr in an RF1-deficient expression host and thus eliminates truncation issues associated with typical RF1-containing expression hosts. Structural and biochemical data suggest the aaRS efficiency improvement is based on higher affinity substrate binding. Taken together, the modest improvement in aaRS efficiency provides a large practical impact and expands our ability to study the role protein nitration plays in disease development through producing homogenous, truncation-free nitroTyr-containing protein. This work establishes Rosetta-guided design and incremental aaRS improvement as a viable and accessible path to improve GCE systems challenged by truncation and/or near-cognate suppression issues.


    Organizational Affiliation

    Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331. Electronic address: rick.cooley@oregonstate.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine--tRNA ligaseA314Methanocaldococcus jannaschii DSM 2661Mutation(s): 5 
Gene Names: tyrSMJ0389
EC: 6.1.1.1
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57834 
Go to UniProtKB:  Q57834
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NIY
Query on NIY

Download CCD File 
A
META-NITRO-TYROSINE
C9 H10 N2 O5
FBTSQILOGYXGMD-LURJTMIESA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102α = 90
b = 102β = 90
c = 71.66γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
PHENIXphasing
XSCALEdata scaling
XDSdata processing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM114653-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM131168-02
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States3F32GM120791-01S1

Revision History 

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references, Derived calculations