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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

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The first tryptophan-7-halogenase was identified in 1998, during studies of the pyrrolnitrin biosynthetic gene cluster of Pseudomonas fluorescens.[1] 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.[2] 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.[3] In nature, these halogenation enzymes are found in the biosynthetic pathways of chlorinated natural products such as vancomycin and cryptophycin A,[4] and (in the case of RebH) Rebeccamycin.[5]

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.[5]

Overall reaction catalyzed by tryptophan 7-halogenase.

Mechanism

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Flavin-reductase partner and mechanism

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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.[6] 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.[7]

Halogenation mechanism

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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)[6].

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.[8]

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.[8]

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.[5][9]

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

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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.[10] 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.[11]

Biotechnology

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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.[12][13]

  1. ^ Kirner, S.; Hammer, P. E.; Hill, D. S.; Altmann, A.; Fischer, I.; Weislo, L. J.; Lanahan, M.; van Pée, K. H.; Ligon, J. M. (1998-04-01). "Functions encoded by pyrrolnitrin biosynthetic genes from Pseudomonas fluorescens". Journal of Bacteriology. 180 (7): 1939–1943. ISSN 0021-9193. PMC 107110. PMID 9537395.
  2. ^ van Pée, Karl Heinz; Unversucht, Susanne (2003-07-01). "Biological dehalogenation and halogenation reactions". Chemosphere. 52 (2): 299–312. doi:10.1016/S0045-6535(03)00204-2. ISSN 0045-6535. PMID 12738254.
  3. ^ Keller, null; Wage, null; Hohaus, null; Hölzer, null; Eichhorn, null; van Pée KH, null (2000-07-03). "Purification and Partial Characterization of Tryptophan 7-Halogenase (PrnA) from Pseudomonas fluorescens". Angewandte Chemie (International Ed. in English). 39 (13): 2300–2302. ISSN 1521-3773. PMID 10941070.
  4. ^ Dong, Changjiang; Flecks, Silvana; Unversucht, Susanne; Haupt, Caroline; van Pée, Karl-Heinz; Naismith, James H (2005-09-30). "The structure of tryptophan 7-halogenase (PrnA) suggests a mechanism for regioselective chlorination". Science (New York, N.Y.). 309 (5744): 2216–2219. doi:10.1126/science.1116510. ISSN 0036-8075. PMC 3315827. PMID 16195462.
  5. ^ a b c Dong, Changjiang; Flecks, Silvana; Unversucht, Susanne; Haupt, Caroline; van Pée, Karl-Heinz; Naismith, James H (2005-09-30). "The structure of tryptophan 7-halogenase (PrnA) suggests a mechanism for regioselective chlorination". Science (New York, N.Y.). 309 (5744): 2216–2219. doi:10.1126/science.1116510. ISSN 0036-8075. PMC 3315827. PMID 16195462.
  6. ^ a b Yeh, Ellen; Garneau, Sylvie; Walsh, Christopher T. (2005-03-15). "Robust in vitro activity of RebF and RebH, a two-component reductase/halogenase, generating 7-chlorotryptophan during rebeccamycin biosynthesis". Proceedings of the National Academy of Sciences of the United States of America. 102 (11): 3960–3965. doi:10.1073/pnas.0500755102. ISSN 0027-8424. PMC 554827. PMID 15743914.
  7. ^ Payne, James T.; Andorfer, Mary C.; Lewis, Jared C. (2013-05-10). "Regioselective arene halogenation using the FAD-dependent halogenase RebH". Angewandte Chemie (International Ed. in English). 52 (20): 5271–5274. doi:10.1002/anie.201300762. ISSN 1521-3773. PMC 3824154. PMID 23592388.
  8. ^ a b Yeh, Ellen; Blasiak, Leah C.; Koglin, Alexander; Drennan, Catherine L.; Walsh, Christopher T. (2007-02-06). "Chlorination by a long-lived intermediate in the mechanism of flavin-dependent halogenases". Biochemistry. 46 (5): 1284–1292. doi:10.1021/bi0621213. ISSN 0006-2960. PMID 17260957.
  9. ^ Yeh, Ellen; Garneau, Sylvie; Walsh, Christopher T. (2005-03-15). "Robust in vitro activity of RebF and RebH, a two-component reductase/halogenase, generating 7-chlorotryptophan during rebeccamycin biosynthesis". Proceedings of the National Academy of Sciences of the United States of America. 102 (11): 3960–3965. doi:10.1073/pnas.0500755102. ISSN 0027-8424. PMC 554827. PMID 15743914.
  10. ^ Lewis, Jared C.; Coelho, Pedro S.; Arnold, Frances H. (2011-03-21). "Enzymatic functionalization of carbon–hydrogen bonds". Chemical Society Reviews. 40 (4). doi:10.1039/C0CS00067A. ISSN 1460-4744.
  11. ^ Shepherd, Sarah A.; Menon, Binuraj R. K.; Fisk, Heidi; Struck, Anna‐Winona; Levy, Colin; Leys, David; Micklefield, Jason (2016-05-03). "A Structure‐Guided Switch in the Regioselectivity of a Tryptophan Halogenase". Chembiochem. 17 (9): 821–824. doi:10.1002/cbic.201600051. ISSN 1439-4227. PMC 5071727. PMID 26840773.
  12. ^ Smith, Duncan R. M.; Grüschow, Sabine; Goss, Rebecca J. M. (2013-04-01). "Scope and potential of halogenases in biosynthetic applications". Current Opinion in Chemical Biology. 17 (2): 276–283. doi:10.1016/j.cbpa.2013.01.018. ISSN 1879-0402. PMID 23433955.
  13. ^ Andorfer, Mary C.; Park, Hyun June; Vergara-Coll, Jaylie; Lewis, Jared C. (2016-05-23). "Directed evolution of RebH for catalyst-controlled halogenation of indole C–H bonds". Chemical Science. 7 (6). doi:10.1039/C5SC04680G. ISSN 2041-6539. PMC 4917012. PMID 27347367.