3T1G

Engineering of organophosphate hydrolase by computational design and directed evolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Khare, S.D.Kipnis, Y.Greisen, P.J.Takeuchi, R.Ashani, Y.Goldsmith, M.Song, Y.Gallaher, J.L.Silman, I.Leader, H.Sussman, J.L.Stoddard, B.L.Tawfik, D.S.Baker, D.

(2012) Nat.Chem.Biol. 8: 294-300

  • DOI: 10.1038/nchembio.777

  • PubMed Abstract: 
  • The ability to redesign enzymes to catalyze noncognate chemical transformations would have wide-ranging applications. We developed a computational method for repurposing the reactivity of metalloenzyme active site functional groups to catalyze new re ...

    The ability to redesign enzymes to catalyze noncognate chemical transformations would have wide-ranging applications. We developed a computational method for repurposing the reactivity of metalloenzyme active site functional groups to catalyze new reactions. Using this method, we engineered a zinc-containing mouse adenosine deaminase to catalyze the hydrolysis of a model organophosphate with a catalytic efficiency (k(cat)/K(m)) of ~10(4) M(-1) s(-1) after directed evolution. In the high-resolution crystal structure of the enzyme, all but one of the designed residues adopt the designed conformation. The designed enzyme efficiently catalyzes the hydrolysis of the R(P) isomer of a coumarinyl analog of the nerve agent cyclosarin, and it shows marked substrate selectivity for coumarinyl leaving groups. Computational redesign of native enzyme active sites complements directed evolution methods and offers a general approach for exploring their untapped catalytic potential for new reactivities.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, Washington, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
organophosphate hydrolase
A
353Mus musculusMutation(s): 9 
Gene Names: Ada
EC: 3.5.4.4
Find proteins for P03958 (Mus musculus)
Go to UniProtKB:  P03958
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
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: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.189 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.391α = 90.00
b = 77.592β = 90.00
c = 94.972γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Database references