3C70

HNL from Hevea brasiliensis to atomic resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

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: 10.1074/jbc.M801056200
  • Primary Citation of Related Structures:  

  • 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 hydroxynitr ...

    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.

    Related Citations: 
    • 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

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydroxynitrilase
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
SCN
Query on SCN
Download SDF File 
Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 47.276α = 90.00
b = 106.344β = 90.00
c = 128.312γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SHELXmodel building
SCALEPACKdata scaling
REFMACphasing
SHELXL-97refinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2008-02-06 
  • Released Date: 2008-06-03 
  • Deposition Author(s): Schmidt, A.

Revision History 

  • Version 1.0: 2008-06-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description