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:  
    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 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: 
    • 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
    • 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: 

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



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HydroxynitrilaseA257Hevea brasiliensisMutation(s): 0 
Gene Names: HNL
EC: 4.1.2.37 (PDB Primary Data), 4.1.2.47 (UniProt)
Find proteins for P52704 (Hevea brasiliensis)
Explore P52704 
Go to UniProtKB:  P52704
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
SCN
Query on SCN
Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M		 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
b = 106.344β = 90
c = 128.312γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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View more in-depth experimental data

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
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description