Structural Evidence for DUF512 as a Radical -Adenosylmethionine Cobalamin-Binding Domain.

Cobalamin (Cbl)-dependent radical -adenosylmethionine (SAM) enzymes constitute a large subclass of radical SAM (RS) enzymes that use Cbl to catalyze various types of reactions, the most common of which are methylations. Most Cbl-dependent RS enzymes contain an N-terminal Rossmann fold that aids Cbl binding. Recently, it has been demonstrated that the methanogenesis marker protein 10 (Mmp10) requires Cbl to methylate an arginine residue in the α-subunit of methyl coenzyme M reductase.

First Step in Catalysis of the Radical -Adenosylmethionine Methylthiotransferase MiaB Yields an Intermediate with a [3Fe-4S]-Like Auxiliary Cluster.

The enzyme MiaB catalyzes the attachment of a methylthio (-SCH) group at the C2 position of -(isopentenyl)adenosine (iA) in the final step of the biosynthesis of the hypermodified tRNA nucleotide 2-methythio--(isopentenyl)adenosine (msiA). MiaB belongs to the expanding subgroup of enzymes of the radical -adenosylmethionine (SAM) superfamily that harbor one or more auxiliary [4Fe-4S] clusters in addition to the [4Fe-4S] cluster that all family members require for the reductive cleavage of SAM to afford the common 5'-deoxyadenosyl 5'-radical (5'-dA) intermediate. While the role of the radical SAM cluster in generating the 5'-dA is well understood, the detailed role of the auxiliary cluster, which is essential for MiaB catalysis, remains unclear.

Methanogenesis marker protein 10 (Mmp10) from is a radical -adenosylmethionine methylase that unexpectedly requires cobalamin.

Methyl coenzyme M reductase (MCR) catalyzes the last step in the biological production of methane by methanogenic archaea, as well as the first step in the anaerobic oxidation of methane to methanol by methanotrophic archaea. MCR contains a number of unique post-translational modifications in its α subunit, including thioglycine, 1--methylhistidine, -methylcysteine, 5-C-()-methylarginine, and 2-C-()-methylglutamine. Recently, genes responsible for the thioglycine and methylarginine modifications have been identified in bioinformatics studies and complementation of select mutants; however, none of these reactions has been verified Herein, we purified and biochemically characterized the radical -adenosylmethionine (SAM) protein Mmp10, the product of the methanogenesis marker protein 10 gene in the methane-producing archaea Using an array of approaches, including kinetic assays, LC-MS-based quantification, and MALDI TOF-TOF MS analyses, we found that Mmp10 catalyzes the methylation of the equivalent of Arg in a peptide substrate surrogate, but only in the presence of cobalamin.

Engineered biosynthesis of bacteriochlorophyll g in Rhodobacter sphaeroides.

Engineering photosynthetic bacteria to utilize a heterologous reaction center that contains a different (bacterio) chlorophyll could improve solar energy conversion efficiency by allowing cells to absorb a broader range of the solar spectrum. One promising candidate is the homodimeric type I reaction center from Heliobacterium modesticaldum. It is the simplest known reaction center and uses bacteriochlorophyll (BChl) g, which absorbs in the near-infrared region of the spectrum.

Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN.

RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein-nucleic acid cross-linked species.

Further characterization of Cys-type and Ser-type anaerobic sulfatase maturating enzymes suggests a commonality in the mechanism of catalysis.

The anaerobic sulfatase-maturating enzyme from Clostridium perfringens (anSMEcpe) catalyzes the two-electron oxidation of a cysteinyl residue on a cognate protein to a formylglycyl residue (FGly) using a mechanism that involves organic radicals. The FGly residue plays a unique role as a cofactor in a class of enzymes termed arylsulfatases, which catalyze the hydrolysis of various organosulfate monoesters. anSMEcpe has been shown to be a member of the radical S-adenosylmethionine (SAM) family of enzymes, [4Fe-4S] cluster-requiring proteins that use a 5'-deoxyadenosyl 5'-radical (5'-dA(•)) generated from a reductive cleavage of SAM to initiate radical-based catalysis.

Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation.

The radical SAM (RS) proteins RlmN and Cfr catalyze methylation of carbons 2 and 8, respectively, of adenosine 2503 in 23S rRNA. Both reactions are similar in scope, entailing the synthesis of a methyl group partially derived from S-adenosylmethionine (SAM) onto electrophilic sp(2)-hybridized carbon atoms via the intermediacy of a protein S-methylcysteinyl (mCys) residue. Both proteins contain five conserved Cys residues, each required for turnover.

A radically different mechanism for S-adenosylmethionine-dependent methyltransferases.

Methylation of small molecules and macromolecules is crucial in metabolism, cell signaling, and epigenetic programming and is most often achieved by S-adenosylmethionine (SAM)-dependent methyltransferases. Most employ an S(N)2 mechanism to methylate nucleophilic sites on their substrates, but recently, radical SAM enzymes have been identified that methylate carbon atoms that are not inherently nucleophilic via the intermediacy of a 5'-deoxyadenosyl 5'-radical. We have determined the mechanisms of two such reactions targeting the sp(2)-hybridized carbons at positions 2 and 8 of adenosine 2503 in 23S ribosomal RNA, catalyzed by RlmN and Cfr, respectively.