3ZN2

protein engineering of halohydrin dehalogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Single Point Mutation Enhances Hydroxynitrile Synthesis by Halohydrin Dehalogenase.

Schallmey, M.Jekel, P.Tang, L.Majeric Elenkov, M.Hoffken, H.W.Hauer, B.Janssen, D.B.

(2015) Enzyme Microb Technol 70: 50

  • DOI: https://doi.org/10.1016/j.enzmictec.2014.12.009
  • Primary Citation of Related Structures:  
    3ZN2

  • PubMed Abstract: 

    The cyanide-mediated ring opening of epoxides catalyzed by halohydrin dehalogenases yields β-hydroxynitriles that are of high interest for synthetic chemistry. The best studied halohydrin dehalogenase to date is the enzyme from Agrobacterium radiobacter, but this enzyme (HheC) exhibits only low cyanolysis activities. Sequence comparison between a pair of related halohydrin dehalogenases from Corynebacterium and Mycobacterium suggested that substitution of a threonine that interacts with the active site might be responsible for the higher cyanolytic activity of the former enzyme. Here we report that a variant of HheC in which this substitution (T134A) is adopted displays an up to 11-fold higher activity in cyanide-mediated epoxide ring-opening. The mutation causes removal of the hydrogen bond between residue 134 and the side chain O of the active site serine 132, which donates a hydrogen bond to the substrate oxygen. The mutation also increases dehalogenase rates with various substrates. Structural analysis revealed that the anion-binding site of the mutant enzyme remained unaltered, showing that the enhanced activity is due to altered interactions with the substrate oxygen rather than changes in the nucleophile binding site.


  • Organizational Affiliation

    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HALOHYDRIN DEHALOGENASE
A, B
254Agrobacterium tumefaciensMutation(s): 3 
UniProt
Find proteins for Q93D82 (Rhizobium radiobacter)
Explore Q93D82 
Go to UniProtKB:  Q93D82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93D82
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG5
Query on PG5

Download Ideal Coordinates CCD File 
H [auth B]1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
C8 H18 O4
YFNKIDBQEZZDLK-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
K
Query on K

Download Ideal Coordinates CCD File 
J [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.33α = 90
b = 103.33β = 90
c = 118.43γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description