HNL from Hevea brasiliensis to atomic resolution

Experimental Data Snapshot

  • Resolution: 1.05 Å

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This is version 1.3 of the entry. See complete history


Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis

Schmidt, A.Gruber, K.Kratky, C.Lamzin, V.S.

(2008) J Biol Chem 283: 21827-21836

  • DOI: https://doi.org/10.1074/jbc.M801056200
  • Primary Citation of Related Structures:  
    3C6X, 3C6Y, 3C6Z, 3C70

  • PubMed Abstract: 

    Hydroxynitrile lyases are versatile enzymes that enantiospecifically cope with cyanohydrins, important intermediates in the production of various agrochemicals or pharmaceuticals. We determined four atomic resolution crystal structures of hydroxynitrile lyase from Hevea brasiliensis: one native and three complexes with acetone, isopropyl alcohol, and thiocyanate. We observed distinct distance changes among the active site residues related to proton shifts upon substrate binding. The combined use of crystallography and ab initio quantum chemical calculations allowed the determination of the protonation states in the enzyme active site. We show that His(235) of the catalytic triad must be protonated in order for catalysis to proceed, and we could reproduce the cyanohydrin synthesis in ab initio calculations. We also found evidence for the considerable pK(a) shifts that had been hypothesized earlier. We envision that this knowledge can be used to enhance the catalytic properties and the stability of the enzyme for industrial production of enantiomerically pure cyanohydrins.

  • Organizational Affiliation

    EMBL Hamburg c/o Deutsches Elektronen Synchrotron, Notkestrasse 85, Hamburg, Germany. andrea@embl-hamburg.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxynitrilase257Hevea brasiliensisMutation(s): 0 
Gene Names: HNL
Find proteins for P52704 (Hevea brasiliensis)
Explore P52704 
Go to UniProtKB:  P52704
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52704
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.05 Å
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.276α = 90
b = 106.344β = 90
c = 128.312γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2008-06-03 
  • Deposition Author(s): Schmidt, A.

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description