8FOX | pdb_00008fox

AbeH (Tryptophan-5-halogenase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8FOX

This is version 1.2 of the entry. See complete history

Literature

Crystallographic and Thermodynamic Evidence of Negative Coupling in the Flavin-Dependent Tryptophan Halogenases AbeH and BorH.

Ashaduzzaman, M.Lingkon, K.De Silva, A.J.Bellizzi 3rd, J.J.

(2025) ACS Omega 10: 5849-5865

  • DOI: https://doi.org/10.1021/acsomega.4c09590
  • Primary Citation Related Structures: 
    8FOV, 8FOX, 8TTI, 8TTJ, 8TTK

  • PubMed Abstract: 

    Flavin-dependent halogenases (FDHs) regioselectively halogenate aromatic substrates using halide ions, O 2 , and reduced flavin (FADH 2 ) at physiological temperatures in aqueous solution, making them a green alternative to conventional synthetic methods for aryl halide preparation. To better understand mechanistic details that limit FDH catalytic efficiency and potentially hinder their application as in vitro biocatalysts, we investigated the halogenation activity, substrate scope, crystal structures, and ligand binding of the Trp-5-halogenase AbeH and the Trp-6-halogenase BorH. Partitioning of FAD and Trp into different subunits of BorH crystals and an inability to incorporate Trp into AbeH/FAD crystals suggested that binding of flavin and Trp are negatively coupled in both proteins. Isothermal titration calorimetry and fluorescence quenching experiments confirmed that both AbeH and BorH formed binary complexes with FAD or Trp, but Trp could not form ternary complexes with preincubated AbeH/FAD or BorH/FAD complexes. FAD could not bind to BorH/Trp complexes, but FAD appears to displace Trp from AbeH/Trp complexes in an endothermic entropically driven process. Observation of negative coupling in halogenases from two different clades with topological differences in their substrate binding sites suggests that this property and the limitations it places on catalytic efficiency may be a general characteristic of the FDH family.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, The University of Toledo, Toledo, Ohio 43606, United States.

Macromolecule Content 

  • Total Structure Weight: 234.55 kDa 
  • Atom Count: 17,806 
  • Modeled Residue Count: 1,963 
  • Deposited Residue Count: 2,064 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tryptophan 5-halogenase
A, B, C, D
516uncultured bacteriumMutation(s): 0 
Gene Names: abeH
UniProt
Find proteins for F6LWA5 (uncultured bacterium AB1650)
Explore F6LWA5 
Go to UniProtKB:  F6LWA5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6LWA5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.45α = 90
b = 251.13β = 108.71
c = 68.01γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R15GM144877

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Database references
  • Version 1.2: 2025-07-23
    Changes: Database references, Structure summary