Mechanism of Diol Dehydration by a Promiscuous Radical-SAM Enzyme Homologue of the Antiviral Enzyme Viperin (RSAD2) - PubMed (original) (raw)

. 2020 Jun 2;21(11):1605-1612.

doi: 10.1002/cbic.201900776. Epub 2020 Feb 27.

Affiliations

• PMID: 31951306
• DOI: 10.1002/cbic.201900776

Mechanism of Diol Dehydration by a Promiscuous Radical-SAM Enzyme Homologue of the Antiviral Enzyme Viperin (RSAD2)

Kourosh Honarmand Ebrahimi et al. Chembiochem. 2020.

Abstract

3'-Deoxynucleotides are an important class of drugs because they interfere with the metabolism of nucleotides, and their incorporation into DNA or RNA terminates cell division and viral replication. These compounds are generally produced by multi-step chemical synthesis, and an enzyme with the ability to catalyse the removal of the 3'-deoxy group from different nucleotides has yet to be described. Here, using a combination of HPLC, HRMS and NMR spectroscopy, we demonstrate that a thermostable fungal radical S-adenosylmethionine (SAM) enzyme, with similarity to the vertebrate antiviral enzyme viperin (RSAD2), can catalyse the transformation of CTP, UTP and 5-bromo-UTP to their 3'-deoxy-3',4'-didehydro (ddh) analogues. We show that, unlike the fungal enzyme, human viperin only catalyses the transformation of CTP to ddhCTP. Using electron paramagnetic resonance spectroscopy and molecular docking and dynamics simulations in combination with mutagenesis studies, we provide insight into the origin of the unprecedented substrate promiscuity of the enzyme and the mechanism of dehydration of a nucleotide. Our findings highlight the evolution of substrate specificity in a member of the radical-SAM enzymes. We predict that our work will help in using a new class of the radical-SAM enzymes for the biocatalytic synthesis of 3'-deoxy nucleotide/nucleoside analogues.

Keywords: antiviral agents; nucleotide analogues; radical-SAM enzyme; tyrosyl radicals; viperin.

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References

1. 1. L. P. Jordheim, D. Durantel, F. Zoulim, C. Dumontet, Nat. Rev. Drug Discovery 2013, 12, 447-464.
2. 1. E. De Clercq, G. Li, Clin. Microbiol. Rev. 2016, 29, 695-747.
3. 1. S. I. Maffioli, Y. Zhang, D. Degen, T. Garzaniga, G. Del Gatto, S. Serina, P. Monciardini, C. Mazzetti, P. Guglierame, G. Candiani, A. I. Chiriac, G. Facchetti, P. Kaltofen, H.-G. Sahl, G. Dehò, S. Donadio, R. H. Ebright, Cell 2017, 169, 1240-1248.
4. 1. C. L. Lai, N. Leung, E. K. Teo, M. Tong, F. Wong, H. W. Hann, S. Han, T. Poynard, M. Myers, G. Chao, D. Lloyd, N. A. Brown, Gastroenterology 2005, 129, 528-536.
5. 1. C. J. Torrance, V. Agrawal, B. Vogelstein, K. W. Kinzler, Nat. Biotechnol. 2001, 19, 940-945.

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