6I00

Cryo-EM informed directed evolution of Nitrilase 4 leads to a change in quaternary structure.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM and directed evolution reveal howArabidopsisnitrilase specificity is influenced by its quaternary structure.

Mulelu, A.E.Kirykowicz, A.M.Woodward, J.D.

(2019) Commun Biol 2: 260-260

  • DOI: 10.1038/s42003-019-0505-4

  • PubMed Abstract: 
  • Nitrilases are helical enzymes that convert nitriles to acids and/or amides. All plants have a nitrilase 4 homolog specific for ß-cyanoalanine, while in some plants neofunctionalization has produced nitrilases with altered specificity. Plant nitrilas ...

    Nitrilases are helical enzymes that convert nitriles to acids and/or amides. All plants have a nitrilase 4 homolog specific for ß-cyanoalanine, while in some plants neofunctionalization has produced nitrilases with altered specificity. Plant nitrilase substrate size and specificity correlate with helical twist, but molecular details of this relationship are lacking. Here we determine, to our knowledge, the first close-to-atomic resolution (3.4 Å) cryo-EM structure of an active helical nitrilase, the nitrilase 4 from Arabidopsis thaliana . We apply site-saturation mutagenesis directed evolution to three residues (R95, S224, and L169) and generate a mutant with an altered helical twist that accepts substrates not catalyzed by known plant nitrilases. We reveal that a loop between α2 and α3 limits the length of the binding pocket and propose that it shifts position as a function of helical twist. These insights will allow us to start designing nitrilases for chemoenzymatic synthesis.


    Organizational Affiliation

    1Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa.,2Structural Biology Research Unit, University of Cape Town, Cape Town, 7925 South Africa.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional nitrilase/nitrile hydratase NIT4
J, I, H, G, F, E, D, C, B, A, L, K
361Arabidopsis thalianaMutation(s): 0 
Gene Names: NIT4
EC: 3.5.5.1, 3.5.5.4, 4.2.1.65
Find proteins for P46011 (Arabidopsis thaliana)
Go to UniProtKB:  P46011
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation in South AfricaSouth AfricaResearch Career Advancement Fellowship
Global Challenges Research FundUnited KingdomStart: Synchrotron Techniques for African Research and Technology, ST/R002754/1

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-07
    Type: Data collection, Database references
  • Version 1.2: 2019-11-06
    Type: Data collection, Refinement description