1SC9

Hydroxynitrile Lyase from Hevea brasiliensis in complex with the natural substrate acetone cyanohydrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 20501-20510

  • DOI: 10.1074/jbc.M401575200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The hydroxynitrile lyases (HNLs) from Hevea brasiliensis (HbHNL) and from Manihot esculenta (MeHNL) are both members of the alpha/beta-hydrolase superfamily. Mechanistic proposals have been put forward in the past for both enzymes; they differed with ...

    The hydroxynitrile lyases (HNLs) from Hevea brasiliensis (HbHNL) and from Manihot esculenta (MeHNL) are both members of the alpha/beta-hydrolase superfamily. Mechanistic proposals have been put forward in the past for both enzymes; they differed with respect to the role of the active-site lysine residue for which a catalytic function was claimed for the Hevea enzyme but denied for the Manihot enzyme. We applied a freeze-quench method to prepare crystals of the complex of HbHNL with the biological substrate acetone cyanohydrin and determined its three-dimensional structure. Site-directed mutagenesis was used to prepare the mutant K236L, which is inactive although its three-dimensional structure is similar to the wild-type enzyme. However, the structure of the K236L-acetone cyanohydrin complex shows the substrate in a different orientation from the wild-type complex. Finite difference Poisson-Boltzmann calculations show that in the absence of Lys(236) the catalytic base His(235) would be protonated at neutral pH. All of this suggests that Lys(236) is instrumental for catalysis in several ways, i.e. by correctly positioning the substrate, by stabilizing the negatively charged reaction product CN(-), and by modulating the basicity of the catalytic base. These data complete the elucidation of the reaction mechanism of alpha/beta-hydrolase HNLs, in which the catalytic triad acts as a general base rather than as a nucleophile; proton abstraction from the substrate is performed by the serine, and reprotonation of the product cyanide is performed by the histidine residues. Together with a threonine side chain, the active-site serine and lysine are also involved in substrate binding.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Institut für Chemie, Physikalische Chemie, Karl-Franzens Universitaät Heinrichstrasse 28, A-8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
(S)-acetone-cyanohydrin lyase
A
257Hevea 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
CNH
Query on CNH

Download SDF File 
Download CCD File 
A
2-HYDROXY-2-METHYLPROPANENITRILE
ACETONE CYANOHYDRIN
C4 H7 N O
MWFMGBPGAXYFAR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 47.393α = 90.00
b = 106.455β = 90.00
c = 127.988γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
MAR345data collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-29
    Type: Initial release
  • Version 1.1: 2008-04-29
    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