5LVA | pdb_00005lva

Crystal structure of thermophilic tryptophan halogenase (Th-Hal) enzyme from Streptomycin violaceusniger.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 
    0.238 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes.

Menon, B.R.Latham, J.Dunstan, M.S.Brandenburger, E.Klemstein, U.Leys, D.Karthikeyan, C.Greaney, M.F.Shepherd, S.A.Micklefield, J.

(2016) Org Biomol Chem 14: 9354-9361

  • DOI: https://doi.org/10.1039/c6ob01861k
  • Primary Citation Related Structures: 
    5LV9, 5LVA

  • PubMed Abstract: 

    Flavin-dependent halogenase (Fl-Hal) enzymes have been shown to halogenate a range of synthetic as well as natural aromatic compounds. The exquisite regioselectively of Fl-Hal enzymes can provide halogenated building blocks which are inaccessible using standard halogenation chemistries. Consequently, Fl-Hal are potentially useful biocatalysts for the chemoenzymatic synthesis of pharmaceuticals and other valuable products, which are derived from haloaromatic precursors. However, the application of Fl-Hal enzymes, in vitro, has been hampered by their poor catalytic activity and lack of stability. To overcome these issues, we identified a thermophilic tryptophan halogenase (Th-Hal), which has significantly improved catalytic activity and stability, compared with other Fl-Hal characterised to date. When used in combination with a thermostable flavin reductase, Th-Hal can efficiently halogenate a number of aromatic substrates. X-ray crystal structures of Th-Hal, and the reductase partner (Th-Fre), provide insights into the factors that contribute to enzyme stability, which could guide the discovery and engineering of more robust and productive halogenase biocatalysts.


  • Organizational Affiliation
    • School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. jason.micklefield@manchester.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 40.28 kDa 
  • Atom Count: 2,967 
  • Modeled Residue Count: 346 
  • Deposited Residue Count: 348 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD(P)H-FMN oxidoreductase
A, B
174Bacillus subtilisMutation(s): 0 
Gene Names: frb
UniProt
Find proteins for Q75V96 (Bacillus subtilis)
Explore Q75V96 
Go to UniProtKB:  Q75V96
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75V96
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free:  0.238 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.84α = 90
b = 66.84β = 90
c = 335γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references