4TQD

Crystal Structure of the C-terminal domain of IFRS bound with 3-iodo-L-Phe and ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1429 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.

Guo, L.T.Wang, Y.S.Nakamura, A.Eiler, D.Kavran, J.M.Wong, M.Kiessling, L.L.Steitz, T.A.O'Donoghue, P.Soll, D.

(2014) Proc.Natl.Acad.Sci.USA 111: 16724-16729

  • DOI: 10.1073/pnas.1419737111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA(Pyl) have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS vari ...

    Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA(Pyl) have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS variants were previously selected to acylate N(ε)-acetyl-Lys (AcK) onto tRNA(Pyl). Here, we examine an N(ε)-acetyl-lysyl-tRNA synthetase (AcKRS), which is polyspecific (i.e., active with a broad range of ncAAs) and 30-fold more efficient with Phe derivatives than it is with AcK. Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant [iodo-phenylalanyl-tRNA synthetase (IFRS)] that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs. IFRS, a product of directed evolution, has distinct binding modes for different ncAAs. These data indicate that in vivo selections do not produce optimally specific tRNA synthetases and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids.


    Organizational Affiliation

    Departments of Molecular Biophysics & Biochemistry and Chemistry, and Howard Hughes Medical Institute, Yale University, New Haven, CT 06510;,Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706; and.,Departments of Molecular Biophysics & Biochemistry and.,Departments of Molecular Biophysics & Biochemistry and Chemistry, and.,Departments of Molecular Biophysics & Biochemistry and Chemistry, and patrick.odonoghue@uwo.ca dieter.soll@yale.edu.,Departments of Biochemistry and Chemistry, The University of Western Ontario, London, ON, Canada N6A 5C1 patrick.odonoghue@uwo.ca dieter.soll@yale.edu.,Novartis Institutes of Biomedical Research, Cambridge, MA 02139;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrrolysine--tRNA ligase
A
291Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)Mutation(s): 2 
Gene Names: pylS
EC: 6.1.1.26
Find proteins for Q8PWY1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Go to UniProtKB:  Q8PWY1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
33S
Query on 33S

Download SDF File 
Download CCD File 
A
3-iodo-L-phenylalanine
C9 H10 I N O2
BABTYIKKTLTNRX-QMMMGPOBSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1429 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.155 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 104.700α = 90.00
b = 104.700β = 90.00
c = 70.660γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references
  • Version 1.2: 2014-12-03
    Type: Database references