An Unprecedented Ring-Contraction Mechanism in Cobalamin-Dependent Radical S-Adenosylmethionine Enzymes. 2020

Shuo-Qi Sun, and Shi-Lu Chen
Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China.

A unique member of the family of cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) enzymes, OxsB, catalyzes the ring constriction of deoxyadenosine triphosphate (dATP) to the base oxetane aldehyde phosphate, a crucial precursor for oxetanocin A (OXT-A), which is an antitumor, antiviral, and antibacterial compound. This enzyme reveals a new catalytic function for this big family that is different from the common methylation. On the basis of density functional theory calculations, a mechanism has been proposed to mainly include that the generation of 5'-deoxyadenosine radical, a hydrogen transfer forming 2'-dATP radical, and a Cbl-catalyzed ring contraction of the deoxyribose in 2'-dATP radical. The ring contraction is a concerted rearrangement step accompanied by an electron transfer from the deoxyribose hydroxyl oxygen to CoIII without any ring-opening intermediate. CoIICbl has been ruled out as an active state. Other mechanistic characteristics are also revealed. This unprecedented non-methylation mechanism provides a new catalytic repertoire for the family of radical SAM enzymes, representing a new class of ring-contraction enzymes.

UI MeSH Term Description Entries
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D003838 Deoxyadenine Nucleotides Adenine nucleotides which contain deoxyribose as the sugar moiety. Deoxyadenosine Phosphates,Nucleotides, Deoxyadenine,Phosphates, Deoxyadenosine
D005609 Free Radicals Highly reactive molecules with an unsatisfied electron valence pair. Free radicals are produced in both normal and pathological processes. Free radicals include reactive oxygen and nitrogen species (RONS). They are proven or suspected agents of tissue damage in a wide variety of circumstances including radiation, damage from environment chemicals, and aging. Natural and pharmacological prevention of free radical damage is being actively investigated. Free Radical
D000077318 Density Functional Theory A theory that is used to describe the electronic ground state properties of matter. It forms the basis of methods in obtaining a solution to the Schrodinger equation for a many-body system, and to investigate the structural, magnetic, and electronic properties of molecules and materials. Density Functional Calculations,Density Functional Computations,Density Functional Theory Calculations,Density Functional Theory Computations,Td-DFT,Td-DFT Calculations,Td-DFT Computations,Time-Dependent Density Functional Theory,Time-Dependent Density Functional Theory Calculations,Time-Dependent Density Functional Theory Computations,DFT Calculations,KS-DFT,Kohn-Sham Density Functional Theory,Calculation, Density Functional,Calculation, Td-DFT,Computation, Density Functional,Computation, Td-DFT,DFT Calculation,Density Functional Calculation,Density Functional Computation,Density Functional Theories,Functional Calculation, Density,Functional Calculations, Density,Functional Computation, Density,Kohn Sham Density Functional Theory,Td DFT Calculations,Td DFT Computations,Td-DFT Calculation,Td-DFT Computation,Time Dependent Density Functional Theory,Time Dependent Density Functional Theory Calculations,Time Dependent Density Functional Theory Computations
D000429 Alcohol Oxidoreductases A subclass of enzymes which includes all dehydrogenases acting on primary and secondary alcohols as well as hemiacetals. They are further classified according to the acceptor which can be NAD+ or NADP+ (subclass 1.1.1), cytochrome (1.1.2), oxygen (1.1.3), quinone (1.1.5), or another acceptor (1.1.99). Carbonyl Reductase,Ketone Reductase,Carbonyl Reductases,Ketone Reductases,Oxidoreductases, Alcohol,Reductase, Carbonyl,Reductase, Ketone,Reductases, Carbonyl,Reductases, Ketone
D001410 Bacillus megaterium A species of bacteria whose spores vary from round to elongate. It is a common soil saprophyte. Bacillus megatherium
D001426 Bacterial Proteins Proteins found in any species of bacterium. Bacterial Gene Products,Bacterial Gene Proteins,Gene Products, Bacterial,Bacterial Gene Product,Bacterial Gene Protein,Bacterial Protein,Gene Product, Bacterial,Gene Protein, Bacterial,Gene Proteins, Bacterial,Protein, Bacterial,Proteins, Bacterial
D012436 S-Adenosylmethionine Physiologic methyl radical donor involved in enzymatic transmethylation reactions and present in all living organisms. It possesses anti-inflammatory activity and has been used in treatment of chronic liver disease. (From Merck, 11th ed) AdoMet,Ademetionine,FO-1561,Gumbaral,S Amet,S-Adenosyl-L-Methionine,S-Adenosylmethionine Sulfate Tosylate,SAM-e,Samyr,FO 1561,FO1561,S Adenosyl L Methionine,S Adenosylmethionine,S Adenosylmethionine Sulfate Tosylate
D055162 Biocatalysis The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.
D056004 Molecular Dynamics Simulation A computer simulation developed to study the motion of molecules over a period of time. Molecular Dynamics Simulations,Molecular Dynamics,Dynamic, Molecular,Dynamics Simulation, Molecular,Dynamics Simulations, Molecular,Dynamics, Molecular,Molecular Dynamic,Simulation, Molecular Dynamics,Simulations, Molecular Dynamics

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