Assembly of Dimanganese and Heterometallic Manganese Proteins

Abstract

Manganese is an essential trace element in all domains of life, and manganese‐dependent enzymes catalyze a wide range of reactions including hydrolysis, phosphorylation, water oxidation, nucleotide reduction, and protection against oxidative stress. Dinuclear manganese‐containing cofactors are both homonuclear and heteronuclear centers. Due to its rich redox chemistry, manganese is found in a number of redox‐active enzymes, where the oxidation state of the metal ion ranges from Mn II to Mn IV . Non‐redox‐active metal sites are found in, for example, sweet potato purple acid phosphatase (Mn II Fe III ), concanavalin A (Mn II Ca II ), arginase (Mn II 2 ), and prolidase (Mn II 2 ). Proteins with redox‐active Mn‐containing dinuclear centers generally belong to the ferritin‐like superfamily. Whereas most members of the superfamily have an Fe 2 center, Mn‐containing metal sites are found in Mn catalase (Mn 2 ), some RNR β subunits (subclasses Ib and Id have Mn 2 , and subclass Ic has MnFe), and R2lox (MnFe). In addition, a member of DNA‐binding protein from starved cells ( Dps ) can form an MnFe center. No manganese chaperones are known and Mn‐dependent enzymes plausibly acquire their metals directly from the intracellular pool of Mn 2+ , which is balanced via different import and efflux transporter systems: Mn catalase catalyzes the disproportionation of the reactive species hydrogen peroxide by alternating between Mn III 2 and Mn II 2 in two consecutive reactions, detoxifying two hydrogen peroxide molecules to oxygen and water. RNR subclass Ib β subunit has an oxidized metal center and a tyrosyl radical. It initially binds Mn 2+ and forms a complex with a specific flavodoxin‐like protein that oxidizes the metal center to a transient Mn IV/III species, which converts to the active Mn III 2 ‐Tyr • cofactor. RNR subclass Ic β subunit has an Mn IV Fe III cofactor. It is formed by O 2 oxidation of a Mn II Fe II center, and the initial transient Mn IV Fe IV center is reduced to the active cofactor via an external electron transfer pathway. RNR subclass Id β subunit is suggested to contain an oxidized Mn 2 center formed in the absence of a flavodoxin‐like maturase and lacks the tyrosyl radical. R2‐like ligand‐binding oxidase (R2lox) has an Mn III Fe III cofactor that is generated from Mn II Fe II by O 2 oxidation. It is assumed that an Mn IV Fe IV intermediate generates a valine–tyrosine cross‐link adjacent to the metal site. Despite the apparent simplicity of manganese cofactor assembly, nature has developed a number of different methods to control the metalation of manganese proteins and activate the relatively redox‐inert Mn II ion.

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

“…Classes Ia and Ib generate a stable tyrosyl radical while class Ic forms a radical-equivalent Mn IV /Fe III high-valent oxidation state of the metal site13,14. A class Id, containing a Mn IV /Mn III cofactor, was also recently proposed15–17. The metal sites in classes Ia and Ic perform direct oxygen activation while class Ib requires a flavoprotein, NrdI, to generate superoxide that oxidizes the di-manganese site18–20.…”

Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton

“…Known Class I subclasses are either monophyletic or contain members that are closely related (Berggren et al, 2017; Rozman Grinberg et al, 2018a). Thus, phylogenetic trees were constructed to confirm proper subclass assignment of the P-SSP7 RNR using Class I β subunit sequences from the RNRdb clustered at 70%, 75%, and 80% and β subunits from the Cyano SP clade members.…”

“…Sequences were then divided into smaller groups of similar sequences identified by the RNRdb. RNRdb group assignment is based on phylogenetic clade membership (Berggren et al, 2017; Rozman Grinberg et al, 2018a), so division increased sequence alignment quality. Group names and subclass membership are presented in Table 2.…”

“…The subclasses are divided based on the identity of the metallocofactor (or absence thereof), the identity of the oxidant, and whether the β subunit contains (and utilizes) the tyrosine radical site (Figure 1B). Class I RNRs are generally presumed to be subclass Ia enzymes unless they can be assigned to another subclass based on sequence homology to a close relative that has been biochemically characterized (Berggren et al, 2017).…”