Hydroxynitrile lyase from the fern Davallia tyermanii in complex with (R)-mandelonitrile / benzaldehyde

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

Starting Model: experimental
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Enzyme discovery beyond homology: a unique hydroxynitrile lyase in the Bet v1 superfamily.

Lanfranchi, E.Pavkov-Keller, T.Koehler, E.M.Diepold, M.Steiner, K.Darnhofer, B.Hartler, J.Van Den Bergh, T.Joosten, H.J.Gruber-Khadjawi, M.Thallinger, G.G.Birner-Gruenberger, R.Gruber, K.Winkler, M.Glieder, A.

(2017) Sci Rep 7: 46738-46738

  • DOI: https://doi.org/10.1038/srep46738
  • Primary Citation of Related Structures:  
    5E46, 5E4B, 5E4D, 5E4M

  • PubMed Abstract: 

    Homology and similarity based approaches are most widely used for the identification of new enzymes for biocatalysis. However, they are not suitable to find truly novel scaffolds with a desired function and this averts options and diversity. Hydroxynitrile lyases (HNLs) are an example of non-homologous isofunctional enzymes for the synthesis of chiral cyanohydrins. Due to their convergent evolution, finding new representatives is challenging. Here we show the discovery of unique HNL enzymes from the fern Davallia tyermannii by coalescence of transcriptomics, proteomics and enzymatic screening. It is the first protein with a Bet v1-like protein fold exhibiting HNL activity, and has a new catalytic center, as shown by protein crystallography. Biochemical properties of D. tyermannii HNLs open perspectives for the development of a complementary class of biocatalysts for the stereoselective synthesis of cyanohydrins. This work shows that systematic integration of -omics data facilitates discovery of enzymes with unpredictable sequences and helps to extend our knowledge about enzyme diversity.

  • Organizational Affiliation

    Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxynitrile lyase
A, B
209Davallia tyermaniiMutation(s): 0 
Find proteins for A0A1C9V3S9 (Davallia tyermanii)
Explore A0A1C9V3S9 
Go to UniProtKB:  A0A1C9V3S9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C9V3S9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.362α = 90
b = 94.135β = 90
c = 116.143γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description