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TitleCryo-EM and directed evolution reveal how nitrilase specificity is influenced by its quaternary structure.
Journal, issue, pagesCommun Biol, Vol. 2, Page 260, Year 2019
Publish dateJul 17, 2019
AuthorsAndani E Mulelu / Angela M Kirykowicz / Jeremy D Woodward /
PubMed AbstractNitrilases 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 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 . 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.
External linksCommun Biol / PubMed:31341959 / PubMed Central
MethodsEM (helical sym.)
Resolution3.4 - 20.0 Å
Structure data

0320

6i00

EMDB-0320, PDB-6i00:
Cryo-EM informed directed evolution of Nitrilase 4 leads to a change in quaternary structure.
Method: EM (helical sym.) / Resolution: 3.4 Å

EMDB-4406:
Cryo-EM informed directed evolution of Nitrilase 4 leads to a change in quaternary structure.
Method: EM (helical sym.) / Resolution: 20.0 Å

EMDB-4407:
Cryo-EM informed directed evolution of Nitrilase 4 leads to a change in quaternary structure.
Method: EM (helical sym.) / Resolution: 20.0 Å

EMDB-4804:
Cryo-EM informed directed evolution of Nitrilase 4 leads to a change in quaternary structure.
Method: EM (helical sym.) / Resolution: 20.0 Å

Source
  • arabidopsis thaliana (thale cress)
  • Synechocystis sp. PCC 6803 (bacteria)
KeywordsHYDROLASE / NITRILASE / Cyanide detoxification / Beta-cyano-L-alanine hydrolase / Helical filament

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