3DQZ

Structure of the hydroxynitrile lyase from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.504 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Hydroxynitrile lyases with alpha / beta-hydrolase fold: two enzymes with almost identical 3D structures but opposite enantioselectivities and different reaction mechanisms

Andexer, J.N.Staunig, N.Eggert, T.Kratky, C.Pohl, M.Gruber, K.

(2012) Chembiochem 13: 1932-1939

  • DOI: 10.1002/cbic.201200239

  • PubMed Abstract: 
  • Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins to yield hydrocyanic acid (HCN) and the respective carbonyl compound and are key enzymes in the process of cyanogenesis in plants. In organic syntheses, HNLs are used as biocatalysts ...

    Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins to yield hydrocyanic acid (HCN) and the respective carbonyl compound and are key enzymes in the process of cyanogenesis in plants. In organic syntheses, HNLs are used as biocatalysts for the formation of enantiopure cyanohydrins. We determined the structure of the recently identified, R-selective HNL from Arabidopsis thaliana (AtHNL) at a crystallographic resolution of 2.5 Å. The structure exhibits an α/β-hydrolase fold, very similar to the homologous, but S-selective, HNL from Hevea brasiliensis (HbHNL). The similarities also extend to the active sites of these enzymes, with a Ser-His-Asp catalytic triad present in all three cases. In order to elucidate the mode of substrate binding and to understand the unexpected opposite enantioselectivity of AtHNL, complexes of the enzyme with both (R)- and (S)-mandelonitrile were modeled using molecular docking simulations. Compared to the complex of HbHNL with (S)-mandelonitrile, the calculations produced an approximate mirror image binding mode of the substrate with the phenyl rings located at very similar positions, but with the cyano groups pointing in opposite directions. A catalytic mechanism for AtHNL is proposed, in which His236 from the catalytic triad acts as a general base and the emerging negative charge on the cyano group is stabilized by main-chain amide groups and an α-helix dipole very similar to α/β-hydrolases. This mechanistic proposal is additionally supported by mutagenesis studies.


    Organizational Affiliation

    Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstrasse 25, Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-hydroxynitrile lyase-like protein
A, B, C, D
258Arabidopsis thalianaMutation(s): 0 
Gene Names: HNL (MES5)
EC: 4.1.2.10
Find proteins for Q9LFT6 (Arabidopsis thaliana)
Go to UniProtKB:  Q9LFT6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.504 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.248α = 90.00
b = 223.313β = 101.47
c = 50.201γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-14
    Type: Other
  • Version 1.3: 2012-04-25
    Type: Other
  • Version 1.4: 2013-10-23
    Type: Database references
  • Version 1.5: 2017-10-25
    Type: Refinement description