4S0J

Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: 11BIF, 42F, 79S, and 123V mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Transition states. Trapping a transition state in a computationally designed protein bottle.

Pearson, A.D.Mills, J.H.Song, Y.Nasertorabi, F.Han, G.W.Baker, D.Stevens, R.C.Schultz, P.G.

(2015) Science 347: 863-867

  • DOI: https://doi.org/10.1126/science.aaa2424
  • Primary Citation of Related Structures:  
    4S02, 4S03, 4S0I, 4S0J, 4S0K, 4S0L

  • PubMed Abstract: 

    The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here, we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl. This latter moiety was introduced biosynthetically as the side chain of the noncanonical amino acid p-biphenylalanine. Through iterative rounds of computational design and structural analysis, we identified a protein in which the side chain of p-biphenylalanine is trapped in the energetically disfavored, coplanar conformation of the TS of the bond rotation reaction.


  • Organizational Affiliation

    Department of Chemistry, and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Threonine--tRNA ligase151Pyrococcus abyssi GE5Mutation(s): 6 
Gene Names: PAB1490PYRAB13430thrS
EC: 6.1.1.3
UniProt
Find proteins for Q9UZ14 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9UZ14 
Go to UniProtKB:  Q9UZ14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UZ14
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
BIF
Query on BIF
A
L-PEPTIDE LINKINGC15 H15 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.285α = 90
b = 78.963β = 90
c = 90.558γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description