Radical SAM

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Radical_SAM
Identifiers
Symbol Radical_SAM
Pfam PF04055
InterPro IPR007197
SCOP 102114
SUPERFAMILY 102114

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.[1] 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,[2][3] 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 - Mo cofactor biosynthesis protein A (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 [4]
  • 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) [5]
  • 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) [6]
  • Dph2 (PF01866) - diphthamide biosynthesis enzyme Dph2 (protein modification - diphthamide in translation elongation factor 2) (note different radical production, a 3-amino-3-carboxypropyl radical) [7]
  • PhnJ (PF06007) - phosphonate metabolism protein PhnJ (C-P phosphonate bond cleavage) [8]
  1. ^ Booker, SJ; Grove, TL (2010). "Mechanistic and functional versatility of radical SAM enzymes". F1000 biology reports. 2: 52. doi:10.3410/B2-52. PMC 2996862free to read. PMID 21152342. 
  2. ^ Sofia, HJ; Chen, G; Hetzler, BG; Reyes-Spindola, JF; Miller, NE (2001). "Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: Functional characterization using new analysis and information visualization methods". Nucleic Acids Research. 29 (5): 1097–106. doi:10.1093/nar/29.5.1097. PMC 29726free to read. PMID 11222759. 
  3. ^ Frey, PA; Hegeman, AD; Ruzicka, FJ (2008). "The Radical SAM Superfamily". Critical reviews in biochemistry and molecular biology. 43 (1): 63–88. doi:10.1080/10409230701829169. PMID 18307109. 
  4. ^ Zhang, Q; Li, Y; Chen, D; Yu, Y; Duan, L; Shen, B; Liu, W (2011). "Radical-mediated enzymatic carbon chain fragmentation-recombination". Nature Chemical Biology. 7 (3): 154–60. doi:10.1038/nchembio.512. PMC 3079562free to read. PMID 21240261. 
  5. ^ Bruender, NA; Wilcoxen, J; Britt, RD; Bandarian, V (2016). "Biochemical and Spectroscopic Characterization of a Radical S‐Adenosyl‐L‐methionine Enzyme Involved in the Formation of a Peptide Thioether Cross-Link". Biochemistry. 55: 2122–34. doi:10.1021/acs.biochem.6b00145. PMID 27007615. 
  6. ^ Chatterjee, A; Li, Y; Zhang, Y; Grove, TL; Lee, M; Krebs, C; Booker, SJ; Begley, TP; Ealick, SE (2008). "Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily". Nature Chemical Biology. 4 (12): 758–65. doi:10.1038/nchembio.121. PMC 2587053free to read. PMID 18953358. 
  7. ^ Zhang, Y; Zhu, X; Torelli, AT; Lee, M; Dzikovski, B; Koralewski, RM; Wang, E; Freed, J; et al. (2010). "Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme". Nature. 465 (7300): 891–6. doi:10.1038/nature09138. PMC 3006227free to read. PMID 20559380. 
  8. ^ Kamat, SS; Williams, HJ; Raushel, FM (2011). "Intermediates in the transformation of phosphonates to phosphate by bacteria". Nature. 480 (7378): 570–3. doi:10.1038/nature10622. PMC 3245791free to read. PMID 22089136. 

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