3QE4 | pdb_00003qe4

An evolved aminoacyl-tRNA Synthetase with atypical polysubstrate specificity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.309 (Depositor), 0.327 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

An Evolved Aminoacyl-tRNA Synthetase with Atypical Polysubstrate Specificity .

Young, D.D.Young, T.S.Jahnz, M.Ahmad, I.Spraggon, G.Schultz, P.G.

(2011) Biochemistry 50: 1894-1900

  • DOI: https://doi.org/10.1021/bi101929e
  • Primary Citation Related Structures: 
    3QE4

  • PubMed Abstract: 

    We have employed a rapid fluorescence-based screen to assess the polyspecificity of several aminoacyl-tRNA synthetases (aaRSs) against an array of unnatural amino acids. We discovered that a p-cyanophenylalanine specific aminoacyl-tRNA synthetase (pCNF-RS) has high substrate permissivity for unnatural amino acids, while maintaining its ability to discriminate against the 20 canonical amino acids. This orthogonal pCNF-RS, together with its cognate amber nonsense suppressor tRNA, is able to selectively incorporate 18 unnatural amino acids into proteins, including trifluoroketone-, alkynyl-, and halogen-substituted amino acids. In an attempt to improve our understanding of this polyspecificity, the X-ray crystal structure of the aaRS-p-cyanophenylalanine complex was determined. A comparison of this structure with those of other mutant aaRSs showed that both binding site size and other more subtle features control substrate polyspecificity.


  • Organizational Affiliation
    • Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

Macromolecule Content 

  • Total Structure Weight: 71.91 kDa 
  • Atom Count: 5,114 
  • Modeled Residue Count: 613 
  • Deposited Residue Count: 624 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosyl-tRNA synthetase
A, B
312Methanocaldococcus jannaschiiMutation(s): 6 
Gene Names: MJ0389TyrRStyrS
EC: 6.1.1.1
UniProt
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57834 
Go to UniProtKB:  Q57834
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57834
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.309 (Depositor), 0.327 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.524α = 90
b = 68.937β = 90.6
c = 82.089γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection