Radical SAM is a designation for a superfamily of enzymes that use a [4Fe-4S]+ cluster to reductively cleave S-adenosyl-L-methionine (SAM) to generate a radical, usually a 5′-deoxyadenosyl radical, as a critical intermediate. These enzymes utilize this potent radical intermediate to perform an array of unusual and chemically difficult transformations, often to functionalize unactivated C-H bonds. Examples of radical SAM enzymes include various enzymes involved in cofactor biosynthesis, enzyme activation, peptide modification, post-transcriptional and post-translational modifications, metalloprotein cluster formation, tRNA modification, lipid metabolism, biosynthesis of antibiotics and natural products etc. The vast majority of known radical SAM enzymes belong to the radical SAM superfamily, and have a cysteine-rich motif that matches or resembles CxxxCxxC.
Examples of radical SAM enzymes found within the radical SAM superfamily include:
AblA - lysine 2,3-aminomutase (osmolyte biosynthesis - N-epsilon-acetyl-beta-lysine)
AlbA - subtilosin maturase (peptide modification)
AtsB - anaerobic sulfatase activase (enzyme activation)
BchE - anaerobic magnesium protoporphyrin-IX oxidative cyclase (cofactor biosynthesis - chlorophyll)
BioB - biotin synthase (cofactor biosynthesis - biotin)
BlsE - cytosylglucuronic acid decarboxylase - blasticidin S biosynthesis
BtrN - butirosin biosynthesis pathway oxidoreductase (aminoglycoside antibiotic biosynthesis)
Cfr - 23S rRNA (adenine(2503)-C(8))-methyltransferase - rRNA modification for antibiotic resistance
CofG - FO synthase, CofG subunit (cofactor biosynthesis - F420)
CofH - FO synthase, CofH subunit (cofactor biosynthesis - F420)
CutD - trimethylamine lyase-activating enzyme
DesII - D-desosamine biosynthesis deaminase (sugar modification for macrolide antibiotic biosynthesis)
EpmB - elongation factor P beta-lysylation protein (protein modification)
HemN - oxygen-independent coproporphyrinogen III oxidase (cofactor biosynthesis - heme)
HmdB - 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdB (note unusual CX5CX2C motif)
HpnR - hopanoid C-3 methylase (lipid biosynthesis - 3-methylhopanoid production)
HydE - [FeFe] hydrogenase H-cluster radical SAM maturase (metallocluster assembly)
HydG - [FeFe] hydrogenase H-cluster radical SAM maturase (metallocluster assembly)
LipA - lipoyl synthase (cofactor biosynthesis - lipoyl)
MftC - mycofactocin system maturase (peptide modification/cofactor biosynthesis - predicted)
MiaB - tRNA methylthiotransferase (tRNA modification)
MoaA - GTP 3',8-cyclase (cofactor biosynthesis - molybdenum cofactor)
MqnC - dehypoxanthine futalosine cyclase (cofactor biosynthesis - menaquinone via futalosine)
MqnE - aminofutalosine synthase (cofactor biosynthesis - menaquinone via futalosine)
NifB - cofactor biosynthesis protein NifB (cofactor biosynthesis - FeMo cofactor)
NirJ - heme d1 biosynthesis radical SAM protein NirJ (cofactor biosynthesis - heme d1)
NosL - complex rearrangement of tryptophan to 3-methyl-2-indolic acid - nosiheptide biosynthesis
NrdG - anaerobic ribonucleoside-triphosphate reductase activase (enzyme activation)
PflA - pyruvate formate-lyase activating enzyme (enzyme activation)
PhpK - radical SAM P-methyltransferase - antibiotic biosynthesis
PqqE - PQQ biosynthesis enzyme (peptide modification / cofactor biosynthesis - PQQ)
PylB - pyrrolysine biosynthesis protein PylB (amino acid biosynthesis - pyrrolysine)
QhpD (PeaB) - quinohemoprotein amine dehydrogenase maturation protein (enzyme activation)
QueE - 7-carboxy-7-deazaguanine (CDG) synthase
RimO - ribosomal protein S12 methylthiotransferase
RlmN - 23S rRNA (adenine(2503)-C(2))-methyltransferase (rRNA modification)
ScfB - SCIFF maturase (peptide modification by thioether cross-link formation)
SkfB - sporulation killing factor maturase
SplB - spore photoproduct lyase (DNA repair)
ThiH - thiazole biosynthesis protein ThiH (cofactor biosynthesis - thiamine)
TrnC - thuricin biosynthesis
TrnD - thuricin biosynthesis
TsrT - tryptophan 2-C-methyltransferase (amino acid modification - antibiotic biosynthesis)
TYW1 - 4-demethylwyosine synthase (tRNA modification)
YqeV - tRNA methylthiotransferase (tRNA modification)
In addition, several non-canonical radical SAM enzymes have been described. These cannot be recognized by the Pfam hidden Markov model PF04055, but still use three Cys residues as ligands to a 4Fe4S cluster and produce a radical from S-adenosylmethionine. These include
ThiC (PF01964) - thiamine biosynthesis protein ThiC (cofactor biosynthesis - thiamine) (Cys residues near extreme C-terminus)
Dph2 (PF01866) - diphthamide biosynthesis enzyme Dph2 (protein modification - diphthamide in translation elongation factor 2) (note different radical production, a 3-amino-3-carboxypropyl radical)
PhnJ (PF06007) - phosphonate metabolism protein PhnJ (C-P phosphonate bond cleavage)
