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 1.1 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: 10.1126/science.aaa2424
  • Primary Citation of Related Structures:  
    4S0I, 4S0J, 4S0K, 4S0L, 4S02, 4S03

  • 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 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Threonine--tRNA ligaseA151Pyrococcus 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BIF
Query on BIF
AL-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