Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens

Abstract

Phenazines produced by Pseudomonas and Streptomyces spp. are heterocyclic nitrogen-containing metabolites with antibiotic, antitumor, and antiparasitic activity. The antibiotic properties of pyocyanin, produced by Pseudomonas aeruginosa, were recognized in the 1890s, although this blue phenazine is now known to be a virulence factor in human disease. Despite their biological significance, the biosynthesis of phenazines is not fully understood. Here we present structural and functional studies of PhzF, an enzyme essential for phenazine synthesis in Pseudomonas spp. PhzF shares topology with diaminopimelate epimerase DapF but lacks the same catalytic residues. The structure of PhzF in complex with its substrate, trans-2,3-dihydro-3-hydroxyanthranilic acid, suggests that it is an isomerase using the conserved glutamate E45 to abstract a proton from C3 of the substrate. The proton is returned to C1 of the substrate after rearrangement of the double-bond system, yielding an enol that converts to the corresponding ketone. PhzF is a dimer that may be bifunctional, providing a shielded cavity for ketone dimerization via double Schiff-base formation to produce the phenazine scaffold. Our proposed mechanism is supported by mass and NMR spectroscopy. The results are discussed in the context of related structures and protein sequences of unknown biochemical function.

Fig. 1.

Biosynthesis of PCA from chorismic acid via DHHA. Also shown is the proposed mechanism of action of PhzF.

Fig. 2.

Ribbon diagrams of PhzF in the open and closed forms, substrate binding to the active site, and comparison to the active sites of related proteins. Overall structure of PhzF in the open (A) and closed (B) forms. Binding partners are sulfate (A) and 3OHAA (B). Key building blocks of the C-terminal domain in one monomer are color-coded: green, central α-helix; blue, eight-stranded β-barrel; and red, decorating α-helices. Secondary structure is labeled in the other monomer. The surface in B demonstrates the size of the intermonomer cavity in the closed form. (C) Stereoview of DHHA binding to the active site of PhzF. The proposed position of E45 in reprotonation is shown in red. Conserved residues are shown in magenta, and the positions of the catalytic cysteines in DapF are shown in cyan. (D) Active sites of DapF (Left), YddE (Center), and phenazine-biosynthesis protein from Enterococcus faecalis V583 (Right). All structures were prepared with bobscript (32).

Fig. 3.

¹H-NMR spectra of DHHA and PhzF in H₂O(A) or ²H₂O(B) 5 min after addition of the enzyme. Resonances of DHHA have been crossed. The assignment of the first product of PhzF is indicated. Strong peaks not belonging to this product are highlighted in gray, and methylene resonances are shown in a black box. Note that the proton at C1 is present in both solvents.