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

Experimental Data Snapshot

  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1038/s42003-019-0505-4
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional nitrilase/nitrile hydratase NIT4361Arabidopsis thalianaMutation(s): 0 
Gene Names: NIT4At5g22300MWD9.8
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Find proteins for P46011 (Arabidopsis thaliana)
Explore P46011 
Go to UniProtKB:  P46011
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46011
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-18
    Changes: Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references