4E3T

Round 18 Arylesterase Variant of Phosphotriesterase with Bound Transition State Analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

Tokuriki, N.Jackson, C.J.Afriat-Jurnou, L.Wyganowski, K.T.Tang, R.Tawfik, D.S.

(2012) Nat Commun 3: 1257-1257

  • DOI: 10.1038/ncomms2246
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Optimization processes, such as evolution, are constrained by diminishing returns-the closer the optimum, the smaller the benefit per mutation, and by tradeoffs-improvement of one property at the cost of others. However, the magnitude and molecular b ...

    Optimization processes, such as evolution, are constrained by diminishing returns-the closer the optimum, the smaller the benefit per mutation, and by tradeoffs-improvement of one property at the cost of others. However, the magnitude and molecular basis of these parameters, and their effect on evolutionary transitions, remain unknown. Here we pursue a complete functional transition of an enzyme with a >10(9)-fold change in the enzyme's selectivity using laboratory evolution. We observed strong diminishing returns, with the initial mutations conferring >25-fold higher improvements than later ones, and asymmetric tradeoffs whereby the gain/loss ratio of the new/old activity decreased 400-fold from the beginning of the trajectory to its end. We describe the molecular basis for these phenomena and suggest they have an important role in shaping natural proteins. These findings also suggest that the catalytic efficiency and specificity of many natural enzymes may be far from their optimum.


    Organizational Affiliation

    Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4. tokuriki@msl.ubc.ca




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphotriesterase
A, B
333Brevundimonas diminutaMutation(s): 0 
Gene Names: opd
EC: 3.1.8.1
Find proteins for P0A434 (Brevundimonas diminuta)
Go to UniProtKB:  P0A434
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HLN
Query on HLN

Download SDF File 
Download CCD File 
B
hexyl(naphthalen-2-yloxy)phosphinic acid
C16 H21 O3 P
UBECMGZHZQOIIW-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.771α = 90.00
b = 85.975β = 90.00
c = 88.727γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
DNAdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release