Mechanism of Radical Initiation in the Radical SAM Enzyme Superfamily - PubMed (original) (raw)

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Mechanism of Radical Initiation in the Radical SAM Enzyme Superfamily

Brian M Hoffman et al. Annu Rev Biochem. 2023.

Abstract

Radical _S_-adenosylmethionine (SAM) enzymes use a site-differentiated [4Fe-4S] cluster and SAM to initiate radical reactions through liberation of the 5'-deoxyadenosyl (5'-dAdo•) radical. They form the largest enzyme superfamily, with more than 700,000 unique sequences currently, and their numbers continue to grow as a result of ongoing bioinformatics efforts. The range of extremely diverse, highly regio- and stereo-specific reactions known to be catalyzed by radical SAM superfamily members is remarkable. The common mechanism of radical initiation in the radical SAM superfamily is the focus of this review. Most surprising is the presence of an organometallic intermediate, Ω, exhibiting an Fe-C5'-adenosyl bond. Regioselective reductive cleavage of the SAM S-C5' bond produces 5'-dAdo• to form Ω, with the regioselectivity originating in the Jahn-Teller effect. Ω liberates the free 5'-dAdo• as the catalytically active intermediate through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12, which was once viewed as biology's choice of radical generator.

Keywords: 5′-deoxyadenosyl radical; S-adenosylmethionine; organometallic; radical SAM.

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Figures

Figure 1.

Figure 1.

Radical SAM reactions are initiated by the reductive cleavage of SAM to generate methionine and a 5′-dAdo• radical that abstracts H• from a substrate (RH) to produce a substrate radical R• (top). The substrates and their radical transformations vary widely, with six representative reactions shown (bottom). RS enzyme names are in blue and substrates are labeled in purple. GRE-AE, glycyl radical enzyme activating enzyme; LipA, lipoyl synthase; SPL, spore photoprodut lyase; HemN, coproporphyrinogen III synthase; HydG, hydrogenase maturase; TYW1, tRNA modifying enzyme.

Figure 2.

Figure 2.

SAM coordinates to the unique iron of the [4Fe-4S] cluster via the amino and carboxylate groups. SAM is shown in blue and the protein cysteinate ligands in green.

Figure 3.

Figure 3.

PFL-AE has a specific cation binding site near the catalytic [4Fe-4S] cluster, bridged to the cluster by the SAM carboxylate. SAM is shown in teal and the cation K+ in purple.

Figure 4.

Figure 4.

EPR spectra of the [4Fe-4S]+/SAM, Ω, and Gly• species.

Figure 5.

Figure 5.

The Ω intermediate trapped by RFQ.

Figure 6.

Figure 6.

Ω is formed in a wide array of radical SAM enzymes. Reprinted with permission from ref. 21. Copyright 2018 American Chemical Society.

Figure 7.

Figure 7.

Coenzyme B12 (left) and the structurally analogous Ω (right). Both harbor organometallic M-C bonds to an adenosyl moiety, and both liberate a reactive 5′-dAdo• species by homolytic cleavage of the M-C bond.

Figure 8.

Figure 8.

Photoinduced electron transfer in the PFL-AE [4Fe-4S]+/SAM complex results in reductive S-C5′ bond cleavage to generate the 5’-dAdo• radical, as revealed by EPR. Adapted with permission from ref. 40. Copyright 2019 American Chemical Society.

Figure 9.

Figure 9.

Photoinduced electron transfer in the HydG [4Fe-4S]+/SAM complex results in reductive S-CH3 bond cleavage to generate a •CH3 radical, as revealed by EPR. Adapted with permission from ref. 42. Copyright 2019 American Chemical Society.

Figure 10.

Figure 10.

Organometallic species methyl-omega (ΩM) and ethyl-omega (ΩE) observed upon photolysis of radical SAM enzymes with SAM and SAE.

Figure 11.

Figure 11.

SAM ribose conformations in radical SAM enzyme active sites, either 2’-endo or 3’-endo, correlate with photoinduced reductive cleavage regioselectivity (left). Regioselectivity is introduced by active-site forces that favor one Jahn-Teller distortion, with a single elongated S-C bond that is favored for cleavage (right). Adapted with permission from ref. 44. Copyright 2021 American Chemical Society.

Figure 12.

Figure 12.

Reaction of PFL-AE with SAM and Dha-pep gives Ω (left) followed by 5′-dAdo• (center), and then the product Ado-Dha-pep• radical (right). Adapted with permission from ref. 46. Copyright 2022 American Chemical Society.

Figure 13.

Figure 13.

Mechanistic model for radical initiation in RS enzymes, with the three sequential intermediates observed in recent work boxed in purple

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References

    1. 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 Res. 29: 1097–106 - PMC - PubMed
    1. Cheek J, Broderick JB. 2001. Adenosylmethionine-dependent iron-sulfur enzymes: versatile clusters in a radical new role. J. Biol. Inorg. Chem. 6: 209–26 - PubMed
    1. Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, et al. 2018. Atlas of the radical SAM superfamily: Divergent evolution of function using a “Plug and Play” domain. Methods Enzymol. 606: 1–71 - PMC - PubMed
    1. Oberg N, Precord TW, Mitchell DA, Gerlt JA. 2022. RadicalSAM.org: A resource to interpret sequence-function space and discover new radical SAM chemistry. ACS Bio Med Chem Au 2: 22–35 - PMC - PubMed
    1. Nicolet Y 2020. Structure-function relationships of radical of radical SAM enzymes. Nat. Catal. 3: 337–2020

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