Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD

Roose, Benjamin W.; Christianson, David W.

doi:10.1021/acs.biochem.9b00399

Title: Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD

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Abstract

Indole prenyltransferases catalyze the prenylation of l-tryptophan (l-Trp) and other indoles to produce a diverse set of natural products in bacteria, fungi, and plants, many of which possess useful biological properties. Among this family of enzymes, CymD from Salinispora arenicola catalyzes the reverse N1 prenylation of l-Trp, an unusual reaction given the poor nucleophilicity of the indole nitrogen. CymD utilizes dimethylallyl diphosphate (DMAPP) as the prenyl donor, catalyzing the dissociation of the diphosphate leaving group followed by nucleophilic attack of the indole nitrogen at the tertiary carbon of the dimethylallyl cation. To better understand the structural basis of selective indole N-alkylation reactions in biology, we have determined the X-ray crystal structures of CymD, the CymD–l-Trp complex, and the CymD–l-Trp–DMSPP complex (DMSPP is dimethylallyl S-thiolodiphosphate, an unreactive analogue of DMAPP). The orientation of l-Trp with respect to DMSPP reveals how the active site contour of CymD serves as a template to direct the reverse prenylation of the indole nitrogen. Furthermore, comparison to PriB, a C6 bacterial indole prenyltransferase, offers further insight regarding the structural basis of regioselective indole prenylation. Isothermal titration calorimetry measurements indicate a synergistic relationship between l-Trp and DMSPP binding. Finally, activity assays demonstrate the selectivity of CymD formore »« less

Authors:

Roose, Benjamin W. ^[1];

^[1]

Univ. of Pennsylvania, Philadelphia, PA (United States). Roy and Diana Vagelos Labs.

Publication Date:: Fri Jun 28 00:00:00 EDT 2019

Research Org.:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)

OSTI Identifier:: 1559335

Grant/Contract Number:: AC02-06CH11357; AC02-76SF00515; P41 GM103403; S10 RR029205; P41GM103393; SC0012704; KP1605010

Resource Type:: Accepted Manuscript

Journal Name:: Biochemistry

Additional Journal Information:: Journal Volume: 58; Journal Issue: 30; Journal ID: ISSN 0006-2960

Publisher:: American Chemical Society (ACS)

Country of Publication:: United States

Language:: ENGLISH

Subject:: 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Anions; peptides and proteins; indoles; nitrogen; aromatic compounds

Citation Formats


                    Roose, Benjamin W., and Christianson, David W. Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD.  United States: N. p., 2019. 
Web.  doi:10.1021/acs.biochem.9b00399.

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                    Roose, Benjamin W., & Christianson, David W. Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD.  United States.  https://doi.org/10.1021/acs.biochem.9b00399

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                    Roose, Benjamin W., and Christianson, David W. Fri .  
"Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD".  United States.  https://doi.org/10.1021/acs.biochem.9b00399.  https://www.osti.gov/servlets/purl/1559335.

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@article{osti_1559335,

  title        = {Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD},

  author       = {Roose, Benjamin W. and Christianson, David W.},

  abstractNote = {Indole prenyltransferases catalyze the prenylation of l-tryptophan (l-Trp) and other indoles to produce a diverse set of natural products in bacteria, fungi, and plants, many of which possess useful biological properties. Among this family of enzymes, CymD from Salinispora arenicola catalyzes the reverse N1 prenylation of l-Trp, an unusual reaction given the poor nucleophilicity of the indole nitrogen. CymD utilizes dimethylallyl diphosphate (DMAPP) as the prenyl donor, catalyzing the dissociation of the diphosphate leaving group followed by nucleophilic attack of the indole nitrogen at the tertiary carbon of the dimethylallyl cation. To better understand the structural basis of selective indole N-alkylation reactions in biology, we have determined the X-ray crystal structures of CymD, the CymD–l-Trp complex, and the CymD–l-Trp–DMSPP complex (DMSPP is dimethylallyl S-thiolodiphosphate, an unreactive analogue of DMAPP). The orientation of l-Trp with respect to DMSPP reveals how the active site contour of CymD serves as a template to direct the reverse prenylation of the indole nitrogen. Furthermore, comparison to PriB, a C6 bacterial indole prenyltransferase, offers further insight regarding the structural basis of regioselective indole prenylation. Isothermal titration calorimetry measurements indicate a synergistic relationship between l-Trp and DMSPP binding. Finally, activity assays demonstrate the selectivity of CymD for l-Trp and indole as prenyl acceptors. Collectively, these data establish a foundation for understanding and engineering the regioselectivity of indole prenylation by members of the prenyltransferase protein family.},

  doi          = {10.1021/acs.biochem.9b00399},

  journal      = {Biochemistry},

  number       = 30,

  volume       = 58,

  place        = {United States},

  year         = {Fri Jun 28 00:00:00 EDT 2019},

  month        = {Fri Jun 28 00:00:00 EDT 2019}

}

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