5KVC

Thermostable mutant of halohydrin dehalogenase (HheC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.501 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A robust cosolvent-compatible halohydrin dehalogenase by computational library design.

Arabnejad, H.Dal Lago, M.Jekel, P.A.Floor, R.J.Thunnissen, A.W.H.Terwisscha van Scheltinga, A.C.Wijma, H.J.Janssen, D.B.

(2017) Protein Eng. Des. Sel. 30: 173-187

  • DOI: 10.1093/protein/gzw068
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To improve the applicability of halohydrin dehalogenase as a catalyst for reactions in the presence of organic cosolvents, we explored a computational library design strategy (Framework for Rapid Enzyme Stabilization by Computational libraries) that ...

    To improve the applicability of halohydrin dehalogenase as a catalyst for reactions in the presence of organic cosolvents, we explored a computational library design strategy (Framework for Rapid Enzyme Stabilization by Computational libraries) that involves discovery and in silico evaluation of stabilizing mutations. Energy calculations, disulfide bond predictions and molecular dynamics simulations identified 218 point mutations and 35 disulfide bonds with predicted stabilizing effects. Experiments confirmed 29 stabilizing point mutations, most of which were located in two distinct regions, whereas introduction of disulfide bonds was not effective. Combining the best mutations resulted in a 12-fold mutant (HheC-H12) with a 28°C higher apparent melting temperature and a remarkable increase in resistance to cosolvents. This variant also showed a higher optimum temperature for catalysis while activity at low temperature was preserved. Mutant H12 was used as a template for the introduction of mutations that enhance enantioselectivity or activity. Crystal structures showed that the structural changes in the H12 mutant mostly agreed with the computational predictions and that the enhanced stability was mainly due to mutations that redistributed surface charges and improved interactions between subunits, the latter including better interactions of water molecules at the subunit interfaces.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Halohydrin dehalogenase
A, B
254Rhizobium radiobacterMutation(s): 12 
Gene Names: hheC
Find proteins for Q93D82 (Rhizobium radiobacter)
Go to UniProtKB:  Q93D82
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
A, B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.501 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.171 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.839α = 90.00
b = 81.839β = 90.00
c = 155.609γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references