6G82

Serum paraoxonase-1 by directed evolution with the L69S/H115W/F222S mutations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.401 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Enzyme neo- versus re-functionalization - an epistatic ratchet versus a smooth reversible transition.

Ben-David, M.Soskine, M.Dubovetskyi, A.Cherukuri, K.P.Dym, O.Sussman, J.L.Liao, Q.Szeler, K.Kamerlin, S.C.L.Tawfik, D.S.

(2019) Mol.Biol.Evol. --: --

  • DOI: 10.1093/molbev/msz298
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Evolutionary trajectories are deemed largely irreversible. In a newly diverged protein, reversion of mutations that led to the functional switch typically results in loss of both the new and ancestral functions. Nonetheless, evolutionary transitions ...

    Evolutionary trajectories are deemed largely irreversible. In a newly diverged protein, reversion of mutations that led to the functional switch typically results in loss of both the new and ancestral functions. Nonetheless, evolutionary transitions where reversions are viable have also been described. The structural and mechanistic causes of reversion compatibility versus incompatibility therefore remain unclear. We examined two laboratory evolution trajectories of mammalian paraoxonase-1 (PON1), a lactonase with promiscuous organophosphate hydrolase (OPH) activity. Both trajectories began with the same active-site mutant, His115Trp, which lost the native lactonase activity and acquired higher OPH activity. A neo-functionalization trajectory amplified the promiscuous OPH activity, while the re-functionalization trajectory restored the native activity, thus generating a new lactonase that lacks His115. The His115 revertants of these trajectories indicated opposite trends. Revertants of the neo-functionalization trajectory lost both the evolved OPH and the original lactonase activity. Revertants of the trajectory that restored the original lactonase function were, however, fully active. Crystal structures and molecular simulations show that in the newly diverged OPH, the reverted His115 and other catalytic residues are displaced, thus causing loss of both the original and new activity. In contrast, in the re-functionalization trajectory, reversion compatibility of the original lactonase activity derives from mechanistic versatility whereby multiple residues can fulfill the same task. This versatility enables unique sequence-reversible compositions that are inaccessible when the active site was repurposed toward a new function.


    Organizational Affiliation

    Department of Biomolecular Sciences, and Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden.,Weizmann Institute of Science, Rehovot, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serum paraoxonase-1 by directed evolution with the L69S/H115W/F222S mutations
A
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.401 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.135α = 90.00
b = 98.135β = 90.00
c = 139.189γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2020-02-05
    Type: Database references