Xcc4156, a flavin-dependent halogenase from Xanthomonas campestris

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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This is version 1.2 of the entry. See complete history


Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties.

Widmann, C.Ismail, M.Sewald, N.Niemann, H.H.

(2020) Acta Crystallogr D Struct Biol 76: 687-697

  • DOI: https://doi.org/10.1107/S2059798320007731
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Flavin-dependent halogenases regioselectively introduce halide substituents into electron-rich substrates under mild reaction conditions. For the enzyme Xcc4156 from Xanthomonas campestris, the structure of a complex with the cofactor flavin adenine dinucleotide (FAD) and a bromide ion would be of particular interest as this enzyme exclusively brominates model substrates in vitro. Apo Xcc4156 crystals diffracted to 1.6 Å resolution. The structure revealed an open substrate-binding site lacking the loop regions that close off the active site and contribute to substrate binding in tryptophan halogenases. Therefore, Xcc4156 might accept larger substrates, possibly even peptides. Soaking of apo Xcc4156 crystals with FAD led to crumbling of the intergrown crystals. Around half of the crystals soaked with FAD did not diffract, while in the others there was no electron density for FAD. The FAD-binding loop, which changes its conformation between the apo and the FAD-bound form in related enzymes, is involved in a crystal contact in the apo Xcc4156 crystals. The conformational change that is predicted to occur upon FAD binding would disrupt this crystal contact, providing a likely explanation for the destruction of the apo crystals in the presence of FAD. Soaking with only bromide did not result in bromide bound to the catalytic halide-binding site. Simultaneous soaking with FAD and bromide damaged the crystals more severely than soaking with only FAD. Together, these latter two observations suggest that FAD and bromide bind to Xcc4156 with positive cooperativity. Thus, apo Xcc4156 crystals provide functional insight into FAD and bromide binding, even though neither the cofactor nor the halide is visible in the structure.

  • Organizational Affiliation

    Structural Biochemistry (BCIV), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tryptophan halogenase
A, B
523Xanthomonas campestris pv. campestris str. B100Mutation(s): 0 
Gene Names: XCCB100_4156
Find proteins for B0RXY9 (Xanthomonas campestris pv. campestris (strain B100))
Explore B0RXY9 
Go to UniProtKB:  B0RXY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0RXY9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MES

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
R [auth B],
S [auth B]
C6 H13 N O4 S
Query on TLA

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D [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
C4 H6 O6
Query on PO4

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O4 P
Query on BU9

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M [auth A]Meso-2,3-Butanediol
C4 H10 O2
Query on BUD

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
T [auth B],
U [auth B],
V [auth B]
C4 H10 O2
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.96α = 90
b = 119.96β = 90
c = 70.4γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description