1YB7

Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-dimethyl-2-hydroxy-butyronitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis

Gartler, G.Kratky, C.Gruber, K.

(2007) J.Biotechnol. 129: 87-97

  • DOI: 10.1016/j.jbiotec.2006.12.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis (HbHNL) is utilized as a biocatalyst in stereospecific syntheses of alpha-hydroxynitriles from aldehydes and methyl-ketones. The catalyzed reaction represents one of the few in ...

    The hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis (HbHNL) is utilized as a biocatalyst in stereospecific syntheses of alpha-hydroxynitriles from aldehydes and methyl-ketones. The catalyzed reaction represents one of the few industrially relevant examples of enzyme mediated C-C coupling reactions. In this work, we determined the X-ray crystal structures (at 1.54 and 1.76 Angstroms resolution) of HbHNL complexes with two chiral substrates -- mandelonitrile and 2,3-dimethyl-2-hydroxy-butyronitrile -- by soaking and rapid freeze quenching techniques. This is the first structural observation of the complex between a HNL and chiral substrates. Consistent with the known selectivity of the enzyme, only the S-enantiomers of the two substrates were observed in the active site. The binding modes of the chiral substrates were identical to that observed for the biological substrate acetone cyanohydrin. This indicates that the transformation of these non-natural substrates follows the same mechanism. A large hydrophobic pocket was identified in the active site of HbHNL which accommodates the more voluminous substituents of the two substrates. A three-point binding mode of the substrates -- hydrophobic pocket, hydrogen bonds between the hydroxyl group and Ser80 and Thr11, electrostatic interaction of the cyano group with Lys236 -- offers a likely structural explanation for the enantioselectivity of the enzyme. The structural data rationalize the observed (S)-enantioselectivity and form the basis for modifying the stereospecificity through rational design. The structures also revealed the necessity of considerable flexibility of the sidechain of Trp128 in order to bind and transform larger substrates.


    Related Citations: 
    • Mechanism of Cyanogenesis: The Crystal Structure of Hydroxynitrile Lyase from Hevea Brasiliensis
      Wagner, U.G.,Hasslacher, M.,Griengl, H.,Schwab, H.,Kratky, C.
      (1996) Structure 4: 811
    • Atomic Resolution Crystal Structure of Hydroxynitrile Lyase from Hevea Brasiliensis
      Gruber, K.,Gugganig, M.,Wagner, U.G.,Kratky, C.
      (1999) Biol.Chem. 380: 993
    • Three-Dimensional Structures of Enzyme-Substrate Complexes of the Hydroxynitrile Lyase from Hevea Brasiliensis
      Zuegg, J.,Gruber, K.,Gugganig, M.,Wagner, U.G.,Kratky, C.
      (1999) Protein Sci. 8: 1990
    • Reaction Mechanism of Hydroxynitrile Lyases of the Alpha/Beta-Hydrolase Superfamily: The Three-Dimensional Structure of the Transient Enzyme-Substrate Complex Certifies the Crucial Role of Lys236
      Gruber, K.,Gartler, G.,Krammer, B.,Schwab, H.,Kratky, C.
      (2004) J.Biol.Chem. 279: 20501


    Organizational Affiliation

    Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
(S)-acetone-cyanohydrin lyase
A
256Hevea brasiliensisMutation(s): 0 
Gene Names: HNL
EC: 4.1.2.47
Find proteins for P52704 (Hevea brasiliensis)
Go to UniProtKB:  P52704
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ICN
Query on ICN

Download SDF File 
Download CCD File 
A
(S)-2-HYDROXY-2,3-DIMETHYLBUTANENITRILE
C6 H11 N O
QCKRFEBWZBKGTR-ZCFIWIBFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 47.155α = 90.00
b = 106.553β = 90.00
c = 128.284γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description