Structural perspective on enzymatic halogenation

Abstract

Simple halogen substituents frequently afford key structural features that account for the potency and selectivity of natural products, including antibiotics and hormones. For example, when a single chlorine atom on the antibiotic vancomycin is replaced by hydrogen, the resulting antibacterial activity decreases by up to 70% ( Harris , C. M. ; Kannan , R. ; Kopecka , H. ; Harris , T. M. J. Am. Chem. Soc. 1985 , 107 , 6652 - 6658 ). This Account analyzes how structure underlies mechanism in halogenases, the molecular machines designed by nature to incorporate halogens into diverse substrates. Traditional synthetic methods of integrating halogens into complex molecules are often complicated by a lack of specificity and regioselectivity. Nature, however, has developed a variety of elegant mechanisms for halogenating specific substrates with both regio- and stereoselectivity. An improved understanding of the biological routes toward halogenation could lead to the development of novel synthetic methods for the creation of new compounds with enhanced functions. Already, researchers have co-opted a fluorinase from the microorganism Streptomyces cattleya to produce (18)F-labeled molecules for use in positron emission tomography (PET) ( Deng , H. ; Cobb , S. L. ; Gee , A. D. ; Lockhart , A. ; Martarello , L. ; McGlinchey , R. P. ; O'Hagan , D. ; Onega , M. Chem. Commun. 2006 , 652 - 654 ). Therefore, the discovery and characterization of naturally occurring enzymatic halogenation mechanisms has become an active area of research. The catalogue of known halogenating enzymes has expanded from the familiar haloperoxidases to include oxygen-dependent enzymes and fluorinases. Recently, the discovery of a nucleophilic halogenase that catalyzes chlorinations has expanded the repertoire of biological halogenation chemistry ( Dong , C. ; Huang , F. ; Deng , H. ; Schaffrath , C. ; Spencer , J. B. ; O'Hagan , D. ; Naismith , J. H. Nature 2004 , 427 , 561 - 565 ). Structural characterization has provided a basis toward a mechanistic understanding of the specificity and chemistry of these enzymes. In particular, the latest crystallographic snapshots of active site architecture and halide binding sites have provided key insights into enzyme catalysis. Herein is a summary of the five classes of halogenases, focusing on the three most recently discovered: flavin-dependent halogenases, non-heme iron-dependent halogenases, and nucleophilic halogenases. Further, the potential roles of halide-binding sites in determining halide selectivity are discussed, as well as whether or not binding-site composition is always a seminal factor for selectivity. Expanding our understanding of the basic chemical principles that dictate the activity of the halogenases will advance both biology and chemistry. A thorough mechanistic analysis will elucidate the biological principles that dictate specificity, and the application of those principles to new synthetic techniques will expand the utility of halogenations in small-molecule development.

Scheme 1. Examples of Enzymatic Halogenation Reactions

Figure 1

The five classes of halogenating enzymes. (A) Human MPO (PDBID 1D2V) dimer with heavy chains in gray and blue and light chains in cyan and green. The heme (orange sticks) is coordinated by the proximal ligand His336 (magenta sticks). Disulfides are shown as yellow sticks. (B) Vanadium-dependent chloroperoxidase from Curvularia inaequalis (PDBID 1IDQ). The vanadate cofactor (spheres) is coordinated by His496 (magenta sticks). (C) Flavin-dependent halogenase PrnA from Pseudomonas fluorescens (PDBID 2AQJ) dimer showing flavin and l-tryptophan substrate (orange sticks). Lys79 is shown as pink sticks, and chloride is shown as a green sphere. (D) Non-heme iron halogenase SyrB2 from Pseudomonas syringae (PDBID 2FCT). αKG is shown as orange sticks and the iron-coordinating ligands (His116 and His235) as magenta sticks. Iron (brown) and chloride (green) are shown as spheres. (E) Trimer of the nucleophilic fluorinase 5′-FDAS from Streptomyces cattleya (PDBID 1RQR) with monomers in gray, green, and blue and the 5′-FDA product shown as orange sticks.

Figure 2

Comparison of halide binding sites. Halides shown as translucent spheres representing the halide ionic radius with Br in purple, Cl in green, and F in orange. Water is shown as small red spheres, and iron as a brown sphere. (A) MPO with bound Br⁻ (Br1, PDBID 1D2V). The heme is shown as cyan sticks. (B) MPO with bound Br⁻ and CN⁻ (Br2, PDBID 1D7W) in the same orientation as panel A. The heme is shown as cyan sticks. (C) PrnA (PDBID 2AQJ) with bound FAD (cyan sticks) and Cl⁻. (D) SyrB2 with bound Cl⁻ (PDBID 2FCT). The cosubstrate αKG is shown as cyan sticks. (E) 5′-FDAS (PDBID 1RQP) with bound 5′-FDA shown as cyan sticks. (F) SalL (PDBID 2Q6I) with 5′-ClDA and l-Met shown as cyan sticks.