5B12 | pdb_00005b12

Crystal structure of the B-type halohydrin hydrogen-halide-lyase mutant F71W/Q125T/D199H from Corynebacterium sp. N-1074


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Improvement of enantioselectivity of the B-type halohydrin hydrogen-halide-lyase from Corynebacterium sp. N-1074

Watanabe, F.Yu, F.Ohtaki, A.Yamanaka, Y.Noguchi, K.Odaka, M.Yohda, M.

(2016) J Biosci Bioeng 122: 270-275

  • DOI: https://doi.org/10.1016/j.jbiosc.2016.02.003
  • Primary Citation Related Structures: 
    5B12

  • PubMed Abstract: 

    Halohydrin hydrogen-halide-lyase (H-Lyase) is a bacterial enzyme involved in the degradation of halohydrins. This enzyme catalyzes the intramolecular nucleophilic displacement of a halogen by a vicinal hydroxyl group in halohydrins, producing the corresponding epoxides. The H-Lyases have been classified into A, B and C subtypes based on amino acid sequence similarities. These enzymes have attracted much attention as industrial catalysts in the synthesis of chiral chemicals from prochiral halohydrins. In the present study, we constructed mutants of B-type H-Lyase from Corynebacterium sp. N-1074 (HheB) displaying higher enantioselectivity by structure-based site-directed mutagenesis and random mutagenesis. A triple mutant of HheB exhibited 98.5% enantioselectivity, the highest ever reported, toward (R)-4-chloro-3-hydroxy-butyronitrile production, with the yield reaching approximately two-fold that of the wild-type enzyme. We discuss the structural basis of the high enantioselectivity and productivity of the mutant by comparing the crystal structures of the mutant HheB and the wild-type enzyme in complex with or without the substrate analogue.


  • Organizational Affiliation
    • Yokohama Research Laboratories, Mitsubishi Rayon Co. Ltd., Yokohama, Kanagawa 230-0053, Japan.

Macromolecule Content 

  • Total Structure Weight: 152.36 kDa 
  • Atom Count: 12,157 
  • Modeled Residue Count: 1,346 
  • Deposited Residue Count: 1,362 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Halohydrin epoxidase B
A, B, C, D, E
A, B, C, D, E, F
227Corynebacterium sp.Mutation(s): 3 
Gene Names: hheB
UniProt
Find proteins for A0ACD6B934 (Corynebacterium sp)
Explore A0ACD6B934 
Go to UniProtKB:  A0ACD6B934
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B934
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.913α = 90
b = 215.005β = 90
c = 104.864γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2017-02-15
    Changes: Other
  • Version 1.3: 2020-02-26
    Changes: Data collection
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references