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

• Published in: Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2020-07, Vol.76 (7), p.687-697
• Main Authors: Widmann, Christiane, Ismail, Mohamed, Sewald, Norbert, Niemann, Hartmut H.
• Format: Article
• Language: English
• Subjects: Adenine; Bacterial Proteins - chemistry; Binding Sites; Bromides - chemistry; Bromination; Catalytic Domain; cofactor binding; Conformation; crystal soaking; Crystal structure; Crystals; Electron density; enzymatic halogenation; Enzymes; FAD‐dependent halogenase; Flavin; Flavin-adenine dinucleotide; Flavin-Adenine Dinucleotide - chemistry; Halogenation; Models, Molecular; Peptides; Protein Binding; Research Papers; Soaking; Substrates; Tryptophan; Xanthomonas campestris - enzymology
• ISSN: 2059-7983; 0907-4449; 2059-7983; 1399-0047
• DOI: 10.1107/S2059798320007731

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. Xcc4156 is a flavin‐dependent halogenase from Xanthomonas campestris. Here, an apo structure is presented which, in combination with soaking experiments, provides functional insight into the binding of FAD and bromide to the halogenase.