Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens

Abstract

Ribonucleotide reductase (RNR) catalyzes the only known de-novo pathway for production of all four deoxyribonucleotides required for DNA synthesis1,2. It is essential for all organisms with DNA as genetic material and a current drug target3,4. Since the discovery that iron is required for function in the aerobic, class I RNR found in all eukaryotes and many bacteria, a di-nuclear metal site has been viewed as a requirement for generating and stabilizing a catalytic radical, essential for RNR activity5,6,7. Here, we describe a new group of RNR proteins in Mollicutes, including Mycoplasma pathogens, which possesses a metal-independent stable radical residing on a modified tyrosyl residue. Structural, biochemical and spectroscopic characterization reveal an unprecedented stable DOPA radical species that directly supports ribonucleotide reduction in vitro and in vivo. This observation overturns the presumed requirement of a dinuclear metal site in aerobic RNR. The metal-independent radical compels completely novel mechanisms for radical generation and stabilization, processes that are targeted by RNR inhibitors. Conceivably, this RNR variant provides an advantage under metal starvation induced by the immune system. Organisms encoding this type of RNR are involved in diseases of the respiratory, urinary and genital tracts, some with developing resistance to antibiotics. Further characterization of this novel RNR family and its mechanism for cofactor generation will provide insight into new enzymatic chemistry and be of value to devise strategies to combat the pathogens that utilize it. We propose that the new RNR subclass is denoted class Ie.

Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins

“…In subclass Ic (R2c), which contains a mixed manganese/iron complex (15)(16)(17), and probably also in the recently proposed dimanganese subclass Id (18,19), the metal complex itself acts as the catalytic radical, with the Mn ion shuttling between the III and IV oxidation states. A metal-free subclass Ie was also recently discovered (20)(21)(22).…”

Iroki: automatic customization and visualization of phylogenetic trees

“…There are several different types of RNR, each with specific biochemical mechanisms and nutrient requirements (Nordlund and Reichard, 2006). Accordingly, the type of RNR carried by a cell or virus often reflects the environmental conditions in which DNA replication occurs (Reichard, 1993; Cotruvo and Stubbe, 2011; Sakowski et al, 2014; Srinivas et al, 2018; Harrison et al, 2019). A survey based on RNR, then, may provide more sensitivity in detecting environmental effects on viral community structure.…”

Multielectron Redox Catalysis with Efficient Tyrosinase Activity Based on a Visible‐Light Controlled Artificial Photoenzyme

“…Two oxidative metabolites of L ‐tyrosine, 1 and L ‐DOPA, 2 are known to show a conspicuous peak at 383 nm, which has been chosen to follow the concentration of this reaction intermediate over time. One of the potential candidates is the recently characterized stable dihydroxyphenylalanine radical (DOPA · ), which displays a phenoxyl radical type spectral feature at 383 nm (620 m –1 cm –1 ) . An accumulation of millimolar concentrations of such a radical species under steady‐state conditions, however, can be clearly excluded under the given experimental conditions.…”