5N5U

Structure of p-boronophenylalanyl tRNA synthetase in complex with p-boronophenylalanine and adenosine monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Specific Cotranslational Incorporation of p-Boronophenylalanine into Biosynthetic Proteins.

Schiefner, A.Nastle, L.Landgraf, M.Reichert, A.J.Skerra, A.

(2018) Biochemistry 57: 2597-2600

  • DOI: 10.1021/acs.biochem.8b00171
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The site-specific incorporation of the non-natural amino acid p-boronophenylalanine (Bpa) into recombinant proteins enables the development of novel carbohydrate-binding functions as well as bioorthogonal chemical modification. To this end, Bpa is ge ...

    The site-specific incorporation of the non-natural amino acid p-boronophenylalanine (Bpa) into recombinant proteins enables the development of novel carbohydrate-binding functions as well as bioorthogonal chemical modification. To this end, Bpa is genetically encoded by an amber stop codon and cotranslationally inserted into the recombinant polypeptide chain at the ribosome by means of an artificial aminoacyl-tRNA synthetase (aaRS) in combination with a compatible suppressor tRNA. We describe the crystal structure of an aaRS specific for Bpa, which had been engineered on the basis of the TyrRS from Methanocaldococcus jannaschii, in complex with both Bpa and AMP. The substrates are bound in an orientation resembling the aminoacyl-AMP mixed anhydride intermediate and engaged in a network of four hydrogen bonds that allows specific recognition of the boronate moiety by the aaRS. The key determinant of this interaction is the coplanar alignment of its Glu162 carboxylate group with Bpa, which results in a double hydrogen bond with the boronic acid substituent. Our structural study elucidates how a small set of five side chain exchanges within the TyrRS active site can switch its substrate specificity to the hydrophilic amino acid Bpa, thus stimulating the reprogramming of other aaRS to recruit useful non-natural amino acids for next-generation protein engineering.


    Organizational Affiliation

    Lehrstuhl für Biologische Chemie , Technische Universität München , 85354 Freising (Weihenstephan) , Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine--tRNA ligase
A
314Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 7 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7N8
Query on 7N8

Download SDF File 
Download CCD File 
A
4-Borono-L-phenylalanine
C9 H12 B N O4
NFIVJOSXJDORSP-QMMMGPOBSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 52.582α = 90.00
b = 38.735β = 90.28
c = 82.034γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references