Acyl Donor Stringency and Dehydroaminoacyl Intermediates in β-Lactam Formation by a Non-ribosomal Peptide Synthetase

Overview

Journal ACS Chem Biol

Publisher American Chemical Society

Specialties Biochemistry
Biology

Date 2021 Apr 13

PMID 33847484

Citations 3

Authors

Darcie H Long

Craig A Townsend

Affiliations

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Abstract

Condensation (C) domains in non-ribosomal peptide synthetases catalyze peptide elongation steps whereby activated amino acid or peptidyl acyl donors are coupled with specific amino acid acceptors. In the biosynthesis of the β-lactam antibiotic nocardicin A, an unusual C domain converts a seryl tetrapeptide into its pentapeptide product containing an integrated β-lactam ring. While indirect evidence for the intermediacy of a dehydroalanyl species has been reported, here we describe observation of the elusive enzyme-bound dehydroamino acyl intermediate generated from the corresponding -threonyl tetrapeptide and partitioned into pentapeptide products containing either a dehydrobutyrine residue or an embedded β-lactam. Contrary to trends in the literature where condensation domains have been deemed flexible as to acyl donor structure, this β-lactam synthesizing domain is highly discriminating. The observation of dehydrobutyrine formation links this C domain to related clades associated with natural products containing dehydroamino acid and d-configured residues, suggesting a common mechanistic link.

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References

Davidsen J, Bartley D, Townsend C . Non-ribosomal propeptide precursor in nocardicin A biosynthesis predicted from adenylation domain specificity dependent on the MbtH family protein NocI. J Am Chem Soc. 2013; 135(5):1749-59. PMC: 3571714. DOI: 10.1021/ja307710d. View

Townsend C . Convergent biosynthetic pathways to β-lactam antibiotics. Curr Opin Chem Biol. 2016; 35:97-108. PMC: 5161666. DOI: 10.1016/j.cbpa.2016.09.013. View

Ziemert N, Podell S, Penn K, Badger J, Allen E, Jensen P . The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS One. 2012; 7(3):e34064. PMC: 3315503. DOI: 10.1371/journal.pone.0034064. View

Fischbach M, Walsh C . Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms. Chem Rev. 2006; 106(8):3468-96. DOI: 10.1021/cr0503097. View

Hart K, Clarke A, Wigley D, Waldman A, Chia W, Barstow D . A strong carboxylate-arginine interaction is important in substrate orientation and recognition in lactate dehydrogenase. Biochim Biophys Acta. 1987; 914(3):294-8. DOI: 10.1016/0167-4838(87)90289-5. View

Bloudoff K, Schmeing T . Structural and functional aspects of the nonribosomal peptide synthetase condensation domain superfamily: discovery, dissection and diversity. Biochim Biophys Acta Proteins Proteom. 2017; 1865(11 Pt B):1587-1604. DOI: 10.1016/j.bbapap.2017.05.010. View

de Crecy-Lagard V, Marliere P, Saurin W . Multienzymatic non ribosomal peptide biosynthesis: identification of the functional domains catalysing peptide elongation and epimerisation. C R Acad Sci III. 1995; 318(9):927-36. View

Bachovchin D, Cravatt B . The pharmacological landscape and therapeutic potential of serine hydrolases. Nat Rev Drug Discov. 2012; 11(1):52-68. PMC: 3665514. DOI: 10.1038/nrd3620. View

Reeve A, Breazeale S, Townsend C . Purification, characterization, and cloning of an S-adenosylmethionine-dependent 3-amino-3-carboxypropyltransferase in nocardicin biosynthesis. J Biol Chem. 1998; 273(46):30695-703. DOI: 10.1074/jbc.273.46.30695. View

10.

Gaudelli N, Townsend C . Stereocontrolled syntheses of peptide thioesters containing modified seryl residues as probes of antibiotic biosynthesis. J Org Chem. 2013; 78(13):6412-26. PMC: 3898789. DOI: 10.1021/jo4007893. View

11.

Sieber S, Marahiel M . Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem Rev. 2005; 105(2):715-38. DOI: 10.1021/cr0301191. View

12.

Lohans C, Huang Z, van Belkum M, Giroud M, Sit C, Steels E . Structural characterization of the highly cyclized lantibiotic paenicidin A via a partial desulfurization/reduction strategy. J Am Chem Soc. 2012; 134(48):19540-3. DOI: 10.1021/ja3089229. View

13.

Kelly W, Townsend C . Mutational analysis of nocK and nocL in the nocardicin a producer Nocardia uniformis. J Bacteriol. 2005; 187(2):739-46. PMC: 543527. DOI: 10.1128/JB.187.2.739-746.2005. View

14.

Buller A, Townsend C . Intrinsic evolutionary constraints on protease structure, enzyme acylation, and the identity of the catalytic triad. Proc Natl Acad Sci U S A. 2013; 110(8):E653-61. PMC: 3581919. DOI: 10.1073/pnas.1221050110. View

15.

Rausch C, Hoof I, Weber T, Wohlleben W, Huson D . Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution. BMC Evol Biol. 2007; 7:78. PMC: 1894796. DOI: 10.1186/1471-2148-7-78. View

16.

Mitscher L, Showalter H, Shirahata K, Foltz R . Chemical-ionization mass spectrometry of beta-lactam antibiotics. J Antibiot (Tokyo). 1975; 28(9):668-75. DOI: 10.7164/antibiotics.28.668. View

17.

Oliver R, Li R, Townsend C . Monobactam formation in sulfazecin by a nonribosomal peptide synthetase thioesterase. Nat Chem Biol. 2017; 14(1):5-7. PMC: 5726899. DOI: 10.1038/nchembio.2526. View

18.

Lambalot R, Gehring A, Flugel R, Zuber P, Lacelle M, Marahiel M . A new enzyme superfamily - the phosphopantetheinyl transferases. Chem Biol. 1996; 3(11):923-36. DOI: 10.1016/s1074-5521(96)90181-7. View

19.

Ehmann D, Trauger J, Stachelhaus T, WALSH C . Aminoacyl-SNACs as small-molecule substrates for the condensation domains of nonribosomal peptide synthetases. Chem Biol. 2000; 7(10):765-72. DOI: 10.1016/s1074-5521(00)00022-3. View

20.

Belshaw P, WALSH C, Stachelhaus T . Aminoacyl-CoAs as probes of condensation domain selectivity in nonribosomal peptide synthesis. Science. 1999; 284(5413):486-9. DOI: 10.1126/science.284.5413.486. View