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Tryptophan-7-halogenase (RebH) is a halogenating enzyme with the systematic name L-tryptophan: FADH₂ oxidoreductase (7-halogenating). It catalyzes the formation of carbon-halogen bonds at the nucleophilic carbon 7 position found on the indole ring of the amino acid tryptophan. Other tryptophan-7-halogenases include PrnA.

Background

The first tryptophan-7-halogenase was identified in 1998, during studies of the pyrrolnitrin biosynthetic gene cluster of Pseudomonas fluorescens. The gene, PrnA, was found to halogenate tryptophan at the C7 position. Until this point, halogenation mechanisms were known to proceed via haloperoxidases and perhydrolases; and most halogenation reactions employed haloperoxidases. Further studies of tryptophan-7-halogenase indicated a reliance on the presence of flavin reductase, implicating the cofactor FADH₂ in the mechanism. Specificity of the flavin reductase is not required, as different flavin reductases all supported halogenase activity. In nature, these halogenation enzymes are found in the biosynthetic pathways of chlorinated natural products such as vancomycin and cryptophycin A, and (in the case of RebH) Rebeccamycin.

These enzymes catalyze the formation of carbon-halogen bonds at nucleophilic carbon positions, their transformation facilitated by the cofactor FADH₂ (FAD is reduced by the enzyme flavin reductase), molecular oxygen, and a chloride ion. The tryptophan 7-halogenase (RebH) found in Lechevalieria aerocolonigenes is employed in the initial steps of the biosynthesis of chemotherapeutic Rebeccamycin.

Overall reaction catalyzed by tryptophan 7-halogenase.

Mechanism

Flavin-reductase partner and mechanism

FADH₂ production by flavin reductase for HOCl generation and halogenase activity.

Tryptophan 7-halogenases are FADH₂-dependent, meaning they require an FADH₂ cofactor in order to carry out their reaction. Flavin reductases are responsible for the conversion of FAD to FADH₂. In the case of the halogenase RebH, it found co-expressed with a flavin reductase, RebF.  For sustained activity in an in vitro setting, halogenases thus require either excess FADH₂ or the presence of a flavin reductase. Since flavin reductase is itself NAD(P)H-dependent, a recent work employed a cofactor regeneration system wherein glucose dehydrogenase reduces NAD(P)+ to NAD(P)H which RebF then uses to reduce FAD to FADH₂ for subsequent generation of HOCl in RebH’s active site.

Halogenation mechanism

Proposed mechanism for halogenation by Tryptophan 7 halogenase.

Halogenation of tryptophan’s indole ring at carbon 7 is a result of electrophilic attack on Cl⁺ species. The Cl⁺ species arises as a result from the following sequence of reactions: FADH₂ reacts with O₂ to produce FAD-OOH, capturing a chloride ion to produce the potent oxidant HOCl. Next, an ~10Å tunnel within the active site directs HOCl toward a lysine residue (Lys79, conserved in the active site of all flavin-dependent halogenases) to form a chloramine intermediate, a relatively long lived species (half-life > 28 hours).

This Lys-𝜖NH-Cl species, the formation of which is believed to be the rate limiting step of the catalytic cycle, is near the 7 position of the indole ring. Once both the substrate and intermediate are in sufficient proximity, the indole ring undergoes electrophilic aromatic substitution, resulting in chlorination at the 7 position (bromination is also possible) and then product release.

It is worth noting that conformational changes in the protein accompany many of the above steps, greatly increasing affinity of the active site for the substrate. It is also worth noting that HOCl is an extremely reactive species that could potentially react unselectively with many residues within the enzyme’s active site. To get around this, the enzyme promotes fast reaction with lysine 79, and only once the chlorinating intermediate is formed does the substrate, tryptophan, bind to the enzyme.

Flecks et al have proposed a slightly differing mechanism wherein a conserved glutamic acid residue in the active site, Glu346, along with Lys79, enhance the electrophilicity of Cl⁺ within the chlorinating intermediate HOCl, properly positioning it for C7 insertion. Their proposed mechanism does not involve the chloramine species.

Active site of tryptophan 7-halogenase PrnA (PDB: 2AQJ). From left: tryptophan substrate, conserved lysine 79 residue involved in halogenation mechanism, chloride ion, FADH₂ co-factor.

Regiochemistry

Like other enzymes, tryptophan 7-halogenases catalyze their reaction with high specificity. Particularly interesting with respect to this sub-class of halogenases is their ability to react at the 7 position of tryptophan’s indole ring, a relatively unreactive position for electrophilic aromatic substitution compared to the more activated 2 position. By studying x-ray crystal structures, researchers believe the position of the substrate appears to direct the site of halogenation. In tryptophan 7-halogenases, carbon 7 of the indole ring is located at the end of the tunnel through which the active chlorine species is transferred. Tryptophan 5-halogenases, which have a similar shape, position the substrate such that carbon 5 is in that location.

Biotechnology

Halogenation reactions are a cornerstone of synthetic organic chemistry. A diverse array of halides are employed both for their synthetic versatility as well as their own desirable properties. Tryptophan itself is a desirable starting material, given many biologically active molecules are derived from it. The halogenase Rebeccamycin tryptophan 7 halogenase, RebH, is routinely employed in the initial step in the biosynthesis of rebeccamysin, a weak topoisomerase I inhibitor. Similarly, PrnA has been employed in the biosynthesis of the antibiotic pacidamycin. Due to these early successes, halogenases have become valuable targets for protein engineering efforts, where they are tailored for expanded substrate scope and enhanced catalytic activity.