Pyridoxal-5′-phosphate-dependent alkyl transfer in nucleoside antibiotic biosynthesis

Zheng Cui; Jonathan Overbay; Xiachang Wang; Xiaodong Liu; Yinan Zhang; Minakshi Bhardwaj; Anke Lemke; Daniel Wiegmann; Giuliana Niro; Jon S. Thorson; Christian Ducho; Steven G. Van Lanen

doi:10.1038/s41589-020-0548-3

Pyridoxal-5′-phosphate-dependent alkyl transfer in nucleoside antibiotic biosynthesis

Zheng Cui, Jonathan Overbay, Xiachang Wang, Xiaodong Liu, Yinan Zhang, Minakshi Bhardwaj, Anke Lemke, Daniel Wiegmann, Giuliana Niro, Jon S. Thorson, Christian Ducho, Steven G. Van Lanen

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17 Citations (SciVal)

Abstract

Several nucleoside antibiotics are structurally characterized by a 5″-amino-5″-deoxyribose (ADR) appended via a glycosidic bond to a high-carbon sugar nucleoside (5′S,6′S)-5′-C-glycyluridine (GlyU). GlyU is further modified with an N-alkylamine linker, the biosynthetic origin of which has yet to be established. By using a combination of feeding experiments with isotopically labeled precursors and characterization of recombinant proteins from multiple pathways, the biosynthetic mechanism for N-alkylamine installation for ADR–GlyU-containing nucleoside antibiotics has been uncovered. The data reveal S-adenosyl-l-methionine (AdoMet) as the direct precursor of the N-alkylamine, but, unlike conventional AdoMet- or decarboxylated AdoMet-dependent alkyltransferases, the reaction is catalyzed by a pyridoxal-5′-phosphate-dependent aminobutyryltransferase (ABTase) using a stepwise γ-replacement mechanism that couples γ-elimination of AdoMet with aza-γ-addition onto the disaccharide alkyl acceptor. In addition to using a conceptually different strategy for AdoMet-dependent alkylation, the newly discovered ABTases require a phosphorylated disaccharide alkyl acceptor, revealing a cryptic intermediate in the biosynthetic pathway. [Figure not available: see fulltext.]

Original language	English
Pages (from-to)	904-911
Number of pages	8
Journal	Nature Chemical Biology
Volume	16
Issue number	8
DOIs	https://doi.org/10.1038/s41589-020-0548-3
State	Published - Aug 1 2020

Bibliographical note

Funding Information:
This work was supported in part by the National Institutes of Health (NIH, grant nos. AI087849 and GM115261), the National Center for Advancing Translational Sciences (grant nos. UL1TR000117 and UL1TR001998), the Deutsche Forschungsgemeinschaft (grant no. DU1095/5-1), the state of Lower Saxony (Lichtenberg doctoral fellowship (CaSuS program) for A.L.), the Konrad-Adenauer-Stiftung (doctoral fellowship for D.W.) and the Fonds der Chemischen Industrie (doctoral fellowship for G.N.). NMR (600MHz) data were collected at the NMR facility of the Center for Environmental Systems Biochemistry supported in part by the NIH (grant no. DK097215). We thank the Department of Pharmaceutical Sciences and the College of Pharmacy for financial support for MS and NMR instrumentation.

Publisher Copyright:
© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.

ASJC Scopus subject areas

Molecular Biology
Cell Biology

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10.1038/s41589-020-0548-3

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title = "Pyridoxal-5′-phosphate-dependent alkyl transfer in nucleoside antibiotic biosynthesis",

abstract = "Several nucleoside antibiotics are structurally characterized by a 5″-amino-5″-deoxyribose (ADR) appended via a glycosidic bond to a high-carbon sugar nucleoside (5′S,6′S)-5′-C-glycyluridine (GlyU). GlyU is further modified with an N-alkylamine linker, the biosynthetic origin of which has yet to be established. By using a combination of feeding experiments with isotopically labeled precursors and characterization of recombinant proteins from multiple pathways, the biosynthetic mechanism for N-alkylamine installation for ADR–GlyU-containing nucleoside antibiotics has been uncovered. The data reveal S-adenosyl-l-methionine (AdoMet) as the direct precursor of the N-alkylamine, but, unlike conventional AdoMet- or decarboxylated AdoMet-dependent alkyltransferases, the reaction is catalyzed by a pyridoxal-5′-phosphate-dependent aminobutyryltransferase (ABTase) using a stepwise γ-replacement mechanism that couples γ-elimination of AdoMet with aza-γ-addition onto the disaccharide alkyl acceptor. In addition to using a conceptually different strategy for AdoMet-dependent alkylation, the newly discovered ABTases require a phosphorylated disaccharide alkyl acceptor, revealing a cryptic intermediate in the biosynthetic pathway. [Figure not available: see fulltext.]",

author = "Zheng Cui and Jonathan Overbay and Xiachang Wang and Xiaodong Liu and Yinan Zhang and Minakshi Bhardwaj and Anke Lemke and Daniel Wiegmann and Giuliana Niro and Thorson, {Jon S.} and Christian Ducho and {Van Lanen}, {Steven G.}",

note = "Funding Information: This work was supported in part by the National Institutes of Health (NIH, grant nos. AI087849 and GM115261), the National Center for Advancing Translational Sciences (grant nos. UL1TR000117 and UL1TR001998), the Deutsche Forschungsgemeinschaft (grant no. DU1095/5-1), the state of Lower Saxony (Lichtenberg doctoral fellowship (CaSuS program) for A.L.), the Konrad-Adenauer-Stiftung (doctoral fellowship for D.W.) and the Fonds der Chemischen Industrie (doctoral fellowship for G.N.). NMR (600MHz) data were collected at the NMR facility of the Center for Environmental Systems Biochemistry supported in part by the NIH (grant no. DK097215). We thank the Department of Pharmaceutical Sciences and the College of Pharmacy for financial support for MS and NMR instrumentation. Publisher Copyright: {\textcopyright} 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.",

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AU - Cui, Zheng

AU - Overbay, Jonathan

AU - Wang, Xiachang

AU - Liu, Xiaodong

AU - Zhang, Yinan

AU - Bhardwaj, Minakshi

AU - Lemke, Anke

AU - Wiegmann, Daniel

AU - Niro, Giuliana

AU - Thorson, Jon S.

AU - Ducho, Christian

AU - Van Lanen, Steven G.

N1 - Funding Information: This work was supported in part by the National Institutes of Health (NIH, grant nos. AI087849 and GM115261), the National Center for Advancing Translational Sciences (grant nos. UL1TR000117 and UL1TR001998), the Deutsche Forschungsgemeinschaft (grant no. DU1095/5-1), the state of Lower Saxony (Lichtenberg doctoral fellowship (CaSuS program) for A.L.), the Konrad-Adenauer-Stiftung (doctoral fellowship for D.W.) and the Fonds der Chemischen Industrie (doctoral fellowship for G.N.). NMR (600MHz) data were collected at the NMR facility of the Center for Environmental Systems Biochemistry supported in part by the NIH (grant no. DK097215). We thank the Department of Pharmaceutical Sciences and the College of Pharmacy for financial support for MS and NMR instrumentation. Publisher Copyright: © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.

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N2 - Several nucleoside antibiotics are structurally characterized by a 5″-amino-5″-deoxyribose (ADR) appended via a glycosidic bond to a high-carbon sugar nucleoside (5′S,6′S)-5′-C-glycyluridine (GlyU). GlyU is further modified with an N-alkylamine linker, the biosynthetic origin of which has yet to be established. By using a combination of feeding experiments with isotopically labeled precursors and characterization of recombinant proteins from multiple pathways, the biosynthetic mechanism for N-alkylamine installation for ADR–GlyU-containing nucleoside antibiotics has been uncovered. The data reveal S-adenosyl-l-methionine (AdoMet) as the direct precursor of the N-alkylamine, but, unlike conventional AdoMet- or decarboxylated AdoMet-dependent alkyltransferases, the reaction is catalyzed by a pyridoxal-5′-phosphate-dependent aminobutyryltransferase (ABTase) using a stepwise γ-replacement mechanism that couples γ-elimination of AdoMet with aza-γ-addition onto the disaccharide alkyl acceptor. In addition to using a conceptually different strategy for AdoMet-dependent alkylation, the newly discovered ABTases require a phosphorylated disaccharide alkyl acceptor, revealing a cryptic intermediate in the biosynthetic pathway. [Figure not available: see fulltext.]

AB - Several nucleoside antibiotics are structurally characterized by a 5″-amino-5″-deoxyribose (ADR) appended via a glycosidic bond to a high-carbon sugar nucleoside (5′S,6′S)-5′-C-glycyluridine (GlyU). GlyU is further modified with an N-alkylamine linker, the biosynthetic origin of which has yet to be established. By using a combination of feeding experiments with isotopically labeled precursors and characterization of recombinant proteins from multiple pathways, the biosynthetic mechanism for N-alkylamine installation for ADR–GlyU-containing nucleoside antibiotics has been uncovered. The data reveal S-adenosyl-l-methionine (AdoMet) as the direct precursor of the N-alkylamine, but, unlike conventional AdoMet- or decarboxylated AdoMet-dependent alkyltransferases, the reaction is catalyzed by a pyridoxal-5′-phosphate-dependent aminobutyryltransferase (ABTase) using a stepwise γ-replacement mechanism that couples γ-elimination of AdoMet with aza-γ-addition onto the disaccharide alkyl acceptor. In addition to using a conceptually different strategy for AdoMet-dependent alkylation, the newly discovered ABTases require a phosphorylated disaccharide alkyl acceptor, revealing a cryptic intermediate in the biosynthetic pathway. [Figure not available: see fulltext.]

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Pyridoxal-5′-phosphate-dependent alkyl transfer in nucleoside antibiotic biosynthesis

Abstract

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