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Mechanism of Diol Dehydration by a Promiscuous Radical-SAM Enzyme Homologue of the Antiviral Enzyme Viperin (RSAD2).
- Source :
-
Chembiochem : a European journal of chemical biology [Chembiochem] 2020 Jun 02; Vol. 21 (11), pp. 1605-1612. Date of Electronic Publication: 2020 Feb 27. - Publication Year :
- 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.<br /> (© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Subjects :
- Binding Sites
Biocatalysis
Crystallography, X-Ray
Cytidine Triphosphate metabolism
Fungal Proteins genetics
Fungal Proteins metabolism
Humans
Kinetics
Molecular Docking Simulation
Molecular Dynamics Simulation
Oxidoreductases Acting on CH-CH Group Donors
Phylogeny
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
Proteins genetics
Proteins metabolism
Recombinant Proteins chemistry
Recombinant Proteins genetics
Recombinant Proteins metabolism
S-Adenosylmethionine metabolism
Sordariales classification
Sordariales enzymology
Structural Homology, Protein
Substrate Specificity
Thermodynamics
Uridine Triphosphate analogs & derivatives
Uridine Triphosphate chemistry
Uridine Triphosphate metabolism
Cytidine Triphosphate chemistry
Fungal Proteins chemistry
Proteins chemistry
S-Adenosylmethionine chemistry
Sordariales chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 1439-7633
- Volume :
- 21
- Issue :
- 11
- Database :
- MEDLINE
- Journal :
- Chembiochem : a European journal of chemical biology
- Publication Type :
- Academic Journal
- Accession number :
- 31951306
- Full Text :
- https://doi.org/10.1002/cbic.201900776