5EHT

Indirect contributions of mutations underlie optimization of new enzyme function


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects.

Yang, G.Hong, N.Baier, F.Jackson, C.J.Tokuriki, N.

(2016) Biochemistry 55: 4583-4593

  • DOI: 10.1021/acs.biochem.6b00561
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • How remote mutations can lead to changes in enzyme function at a molecular level is a central question in evolutionary biochemistry and biophysics. Here, we combine laboratory evolution with biochemical, structural, genetic, and computational analysi ...

    How remote mutations can lead to changes in enzyme function at a molecular level is a central question in evolutionary biochemistry and biophysics. Here, we combine laboratory evolution with biochemical, structural, genetic, and computational analysis to dissect the molecular basis for the functional optimization of phosphotriesterase activity in a bacterial lactonase (AiiA) from the metallo-β-lactamase (MBL) superfamily. We show that a 1000-fold increase in phosphotriesterase activity is caused by a more favorable catalytic binding position of the paraoxon substrate in the evolved enzyme that resulted from conformational tinkering of the active site through peripheral mutations. A nonmutated active site residue, Phe68, was displaced by ∼3 Å through the indirect effects of two second-shell trajectory mutations, allowing molecular interactions between the residue and paraoxon. Comparative mutational scanning, i.e., examining the effects of alanine mutagenesis on different genetic backgrounds, revealed significant changes in the functional roles of Phe68 and other nonmutated active site residues caused by the indirect effects of trajectory mutations. Our work provides a quantitative measurement of the impact of second-shell mutations on the catalytic contributions of nonmutated residues and unveils the underlying intramolecular network of strong epistatic mutational relationships between active site residues and more remote residues. Defining these long-range conformational and functional epistatic relationships has allowed us to better understand the subtle, but cumulatively significant, role of second- and third-shell mutations in evolution.


    Organizational Affiliation

    Research School of Chemistry, Australian National University , Canberra, ACT 0200, Australia.,Michael Smith Laboratories, University of British Columbia , Vancouver, BC V6T 1Z4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acyl homoserine lactonase
A
253Bacillus thuringiensisMutation(s): 7 
Gene Names: aiiA
EC: 3.1.1.81
Find proteins for A3FJ64 (Bacillus thuringiensis)
Go to UniProtKB:  A3FJ64
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.126 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.638α = 90.00
b = 55.735β = 90.00
c = 79.878γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release