3N2Y

Crystal structure of tyrosyl-tRNA synthetase complexed with p-(2-tetrazolyl)-phenylalanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A biosynthetic route to photoclick chemistry on proteins

Wang, J.Zhang, W.Song, W.Wang, Y.Yu, Z.Li, J.Wu, M.Wang, L.Zang, J.Lin, Q.

(2010) J.Am.Chem.Soc. 132: 14812-14818

  • DOI: 10.1021/ja104350y

  • PubMed Abstract: 
  • Light-induced chemical reactions exist in nature, regulating many important cellular and organismal functions, e.g., photosensing in prokaryotes and vision formation in mammals. Here, we report the genetic incorporation of a photoreactive unnatural a ...

    Light-induced chemical reactions exist in nature, regulating many important cellular and organismal functions, e.g., photosensing in prokaryotes and vision formation in mammals. Here, we report the genetic incorporation of a photoreactive unnatural amino acid, p-(2-tetrazole)phenylalanine (p-Tpa), into myoglobin site-specifically in E. coli by evolving an orthogonal tRNA/aminoacyl-tRNA synthetase pair and the use of p-Tpa as a bioorthogonal chemical "handle" for fluorescent labeling of p-Tpa-encoded myoglobin via the photoclick reaction. Moreover, we elucidated the structural basis for the biosynthetic incorporation of p-Tpa into proteins by solving the X-ray structure of p-Tpa-specific aminoacyl-tRNA synthetase in complex with p-Tpa. The genetic encoding of this photoreactive amino acid should make it possible in the future to photoregulate protein function in living systems.


    Organizational Affiliation

    National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. jwang@ibp.ac.cn




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-tRNA synthetase
A, B
314Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 6 
Gene Names: tyrS
EC: 6.1.1.1
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q57834
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEF
Query on TEF

Download SDF File 
Download CCD File 
A, B
4-(2H-tetrazol-2-yl)-L-phenylalanine
p-(2-tetrazolyl)-phenylalanine
C10 H11 N5 O2
KHTQUIIGXJUWFB-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.242 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 101.115α = 90.00
b = 101.115β = 90.00
c = 71.418γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
MAR345dtbdata collection
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-05-19 
  • Released Date: 2010-11-03 
  • Deposition Author(s): Wu, M., Li, J., Zang, J.

Revision History 

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description