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Updated information on history, nomenclature, reaction classification, clinical considerations and applications in drug discovery and development for radical SAM
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Some radical SAMs release [[methyl radical]]s.<ref>{{cite journal | vauthors = Ribbe MW, Hu Y, Hodgson KO, Hedman B | title = Biosynthesis of nitrogenase metalloclusters | journal = Chemical Reviews | volume = 114 | issue = 8 | pages = 4063–80 | date = April 2014 | pmid = 24328215 | pmc = 3999185 | doi = 10.1021/cr400463x }}</ref>
Some radical SAMs release [[methyl radical]]s.<ref>{{cite journal | vauthors = Ribbe MW, Hu Y, Hodgson KO, Hedman B | title = Biosynthesis of nitrogenase metalloclusters | journal = Chemical Reviews | volume = 114 | issue = 8 | pages = 4063–80 | date = April 2014 | pmid = 24328215 | pmc = 3999185 | doi = 10.1021/cr400463x }}</ref>


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== History ==
In 2001, by utilizing iterative profile searches, powerful bioinformatics and information visualization methods, a diverse group of 645 unique radical SAM enzymes from 126 species of all three domains of life was first discovered and documented. <ref>{{Cite journal|last=Sofia|first=Heidi J.|last2=Chen|first2=Guang|last3=Hetzler|first3=Beth G.|last4=Reyes-Spindola|first4=Jorge F.|last5=Miller|first5=Nancy E.|date=2001-03-01|title=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|url=https://academic.oup.com/nar/article/29/5/1097/2381179|journal=Nucleic Acids Research|language=en|volume=29|issue=5|pages=1097–1106|doi=10.1093/nar/29.5.1097|issn=0305-1048}}</ref> Currently, according to the EFI ([https://enzymefunction.org/]) and SFLD ([http://sfld.rbvi.ucsf.edu/]) databases, there are more than '''220,000''' radical SAM enzymes predicted to be involved in '''85''' types of biochemical transformations. <ref>{{Cite journal|last=Benjdia|first=Alhosna|last2=Balty|first2=Clémence|last3=Berteau|first3=Olivier|date=2017|title=Radical SAM Enzymes in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs)|url=https://www.frontiersin.org/articles/10.3389/fchem.2017.00087/full|journal=Frontiers in Chemistry|language=English|volume=5|doi=10.3389/fchem.2017.00087|issn=2296-2646}}</ref>
<br />

== Nomenclature ==
All enzymes including radical SAM superfamily follow an easy guideline for systematic naming. Systematic naming of enzymes allows a uniform naming process that is recognized by all scientists to understand corresponding function. The first word of the enzyme name often shows the [[Substrate (chemistry)|substrate]] of the enzyme. The position of the reaction on the substrate will also be in the beginning portion of the name. Lastly, the class of the enzyme will be described in the other half of the name which will end in suffix -ase. The class of an enzyme will describe what the enzyme is doing or changing on the substrate. For example, a ligase combines two molecules to form a new bond. <ref>{{Cite web|url=https://www.qmul.ac.uk/sbcs/iubmb/enzyme/rules.html|title=Enzyme Classification|website=www.qmul.ac.uk|access-date=2020-03-27}}</ref>
<br />

== Reaction classification and corresponding function(s) ==
Representative/Prototype enzymes will only be mentioned for each reaction scheme. The audience is highly encouraged to research more into current studies on radical SAM enzymes. Many of which are responsible for fascinating yet important reactions.

Radical SAM enzymes and their mechanisms known before 2008 are well-summarized by Frey ''et al'', 2008 ([https://www.ncbi.nlm.nih.gov/pubmed/18307109]). Since 2015, more review articles on radical SAM enzymes are open to the public. The following are only a few out of many informative resources on radical SAM enzymes.

# Recent Advances in Radical SAM Enzymology: New Structures and Mechanisms: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168785/]
# Radical S-Adenosylmethionine Enzymes: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4002137/]
# Radical S-Adenosylmethionine (SAM) Enzymes in Cofactor Biosynthesis: A Treasure Trove of Complex Organic Radical Rearrangement Reactions: [https://www.jbc.org/content/290/7/3980.full]
# Molecular architectures and functions of radical enzymes and their (re)activating proteins: [https://academic.oup.com/jb/article/158/4/271/1906404]

=== Carbon methylation in nucleic acid modifications and secondary metabolites/cofactor/antibiotics biosynthesis ===
Radical SAM [[Methyltransferase|methylases/methyltransferases]] are one of the largest yet diverse subgroups and are capable of methylating a broad range of unreactive carbon and phosphorus centers. These enzymes are divided into four classes (Class A, B, C and D) with representative methylation mechanisms. The shared characteristic of the three major classes A, B and C is the usage of SAM, split into two distinct roles: one as a source of a methyl group donor, and the second as a source of 5'-dAdo radical. <ref name=":0">{{Cite journal|last=Fujimori|first=Danica Galonić|date=2013-8|title=Radical SAM-Mediated Methylation Reactions|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799849/|journal=Current opinion in chemical biology|volume=17|issue=4|pages=597–604|doi=10.1016/j.cbpa.2013.05.032|issn=1367-5931|pmc=3799849|pmid=23835516}}</ref><ref>{{Cite journal|last=Allen|first=K. D.|last2=Xu|first2=H.|last3=White|first3=R. H.|date=2014-07-07|title=Identification of a Unique Radical S-Adenosylmethionine Methylase Likely Involved in Methanopterin Biosynthesis in Methanocaldococcus jannaschii|url=http://dx.doi.org/10.1128/jb.01903-14|journal=Journal of Bacteriology|volume=196|issue=18|pages=3315–3323|doi=10.1128/jb.01903-14|issn=0021-9193}}</ref> The recently documented class D utilizes a different methylation mechanism.

==== ''Class A sub-family enzymes:'' ====

* Class A enzymes methylates specific [[adenosine]] residues on [[Ribosomal RNA|rRNA]] and/or tRNA. <ref name=":1">{{Cite journal|last=Benítez-Páez|first=Alfonso|last2=Villarroya|first2=Magda|last3=Armengod|first3=M.-Eugenia|date=2012-10|title=The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446703/|journal=RNA|volume=18|issue=10|pages=1783–1795|doi=10.1261/rna.033266.112|issn=1355-8382|pmc=3446703|pmid=22891362}}</ref><ref name=":2">{{Cite journal|last=Bauerle|first=Matthew R.|last2=Schwalm|first2=Erica L.|last3=Booker|first3=Squire J.|date=2014-12-04|title=Mechanistic Diversity of RadicalS-Adenosylmethionine (SAM)-dependent Methylation|url=http://dx.doi.org/10.1074/jbc.r114.607044|journal=Journal of Biological Chemistry|volume=290|issue=7|pages=3995–4002|doi=10.1074/jbc.r114.607044|issn=0021-9258}}</ref> In other words, they are RNA base-modifying radical SAM enzymes.
* The most mechanistically well-characterized are enzymes '''RlmN''' and '''Cfr'''. Both enzymes methylates substrate by adding a methylene fragment originating from SAM molecule. <ref name=":0" /><ref>{{Cite journal|last=Yan|first=Feng|last2=Fujimori|first2=Danica Galonić|date=2011-03-08|title=RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3054002/|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=108|issue=10|pages=3930–3934|doi=10.1073/pnas.1017781108|issn=0027-8424|pmc=3054002|pmid=21368151}}</ref> Therefore, RlmN and Cfr are considered methyl synthases instead of methyltransferases.

==== ''Class B sub-family enzymes:'' ====

* Class B enzymes are the largest and most versatile which can methylate a wide range of carbon and phosphorus centers. <ref name=":2" />
* These enzymes require a cobalamin ([[vitamin B12]]) cofactor as an intermediate methyl group carrier to transfer a methyl group from SAM to substrate. <ref name=":1" />
* One well-investigated representative enzyme is '''TsrM''' which involves in [[tryptophan]] methylation in [[thiostrepton]] biosynthesis. <ref name=":0" />

==== ''Class C sub-family enzymes:'' ====

* Class C enzymes are reported to play roles in biosynthesis of complex natural products and secondary metabolites. These enzymes methylate heteroaromatic substrates <ref name=":1" /><ref name=":2" /> and are cobalamin-independent. <ref>{{Cite journal|last=Mahanta|first=Nilkamal|last2=Hudson|first2=Graham A.|last3=Mitchell|first3=Douglas A.|date=2017-10-10|title=Radical SAM enzymes involved in RiPP biosynthesis|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5634935/|journal=Biochemistry|volume=56|issue=40|pages=5229–5244|doi=10.1021/acs.biochem.7b00771|issn=0006-2960|pmc=5634935|pmid=28895719}}</ref>
* These enzymes contain both the radical SAM motif and exhibit striking sequence similarity to [[Coproporphyrinogen III oxidase|coproporhyrinogen III oxidase]] (HemN), a radical SAM enzyme involved in heme biosynthesis <ref name=":0" /><ref name=":2" />
* Recently, detailed mechanistic investigation on two important class C radical SAM methylases have been reported:
*# '''TbtI''' is involved in the biosynthesis of potent [[Thiopeptide|thiopeptide antibiotic]] thiomuracin. <ref>{{Cite journal|last=Zhang|first=Zhengan|last2=Mahanta|first2=Nilkamal|last3=Hudson|first3=Graham A.|last4=Mitchell|first4=Douglas A.|last5=van der Donk|first5=Wilfred A.|date=2017-12-27|title=Mechanism of a Class C Radical S-Adenosyl-l-methionine Thiazole Methyl Transferase|url=https://doi.org/10.1021/jacs.7b10203|journal=Journal of the American Chemical Society|volume=139|issue=51|pages=18623–18631|doi=10.1021/jacs.7b10203|issn=0002-7863|pmc=PMC5748327|pmid=29190095}}</ref>
*# '''Jaw5''' is suggested to be responsible for [[cyclopropane]] modifications. <ref>{{Cite journal|last=Jin|first=Wen-Bing|last2=Wu|first2=Sheng|last3=Jian|first3=Xiao-Hong|last4=Yuan|first4=Hua|last5=Tang|first5=Gong-Li|date=2018-07-17|title=A radical S -adenosyl-L-methionine enzyme and a methyltransferase catalyze cyclopropane formation in natural product biosynthesis|url=https://www.nature.com/articles/s41467-018-05217-1|journal=Nature Communications|language=en|volume=9|issue=1|pages=1–10|doi=10.1038/s41467-018-05217-1|issn=2041-1723}}</ref>

==== ''Class D sub-family enzymes:'' ====

* Class D is the most recently discovered and has been shown to not use SAM for methylation which is different from the three classes described above. <ref name=":3">{{Cite journal|last=Allen|first=K. D.|last2=Xu|first2=H.|last3=White|first3=R. H.|date=2014-07-07|title=Identification of a Unique Radical S-Adenosylmethionine Methylase Likely Involved in Methanopterin Biosynthesis in Methanocaldococcus jannaschii|url=http://dx.doi.org/10.1128/jb.01903-14|journal=Journal of Bacteriology|volume=196|issue=18|pages=3315–3323|doi=10.1128/jb.01903-14|issn=0021-9193}}</ref> Instead, these enzymes use [[methylenetetrahydrofolate]] as the methyl donor.
* The prototype '''MJ0619''' is proposed to play a role in the biosynthesis of cofactor methanopterin which is required in methanogesis, an essential methane-producing pathway dominantly found in the Archaean domain. <ref name=":2" /><ref name=":3" />

=== Methylthiolation of tRNAs ===
Methythiotransferases belong to a subset of radical SAM enzymes that contain two [4Fe-4S]<sup>+</sup> clusters and one radical SAM domain. Methylthiotransferases play a major role in catalyzing methylthiolation on tRNA nucleotides or [[anticodons]] through a redox mechanism. [[Thiolation]] modification is believed to maintain translational efficiency and fidelity. <ref>{{Cite journal|last=Wang|first=Jiarui|last2=Woldring|first2=Rory P.|last3=Román-Meléndez|first3=Gabriel D.|last4=McClain|first4=Alan M.|last5=Alzua|first5=Brian
R.|last6=Marsh|first6=E. Neil G.|date=2014-09-19|title=Recent Advances in Radical SAM Enzymology: New Structures
and Mechanisms|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168785/|journal=ACS Chemical Biology|volume=9|issue=9|pages=1929–1938|doi=10.1021/cb5004674|issn=1554-8929|pmc=4168785|pmid=25009947}}</ref><ref>{{Citation|last=Agris|first=Paul F.|title=The Importance of Being Modified: Roles of Modified Nucleosides and Mg2+ in RNA Structure and Function|date=1996|url=http://dx.doi.org/10.1016/s0079-6603(08)60143-9|work=Progress in Nucleic Acid Research and Molecular Biology|pages=79–129|publisher=Elsevier|isbn=978-0-12-540053-4|access-date=2020-03-24}}</ref><ref>{{Cite journal|last=Urbonavicius|first=J.|date=2001-09-03|title=Improvement of reading frame maintenance is a common function for several tRNA modifications|url=http://dx.doi.org/10.1093/emboj/20.17.4863|journal=The EMBO Journal|volume=20|issue=17|pages=4863–4873|doi=10.1093/emboj/20.17.4863|issn=1460-2075}}</ref><ref>{{Cite journal|last=Leipuviene|first=R.|last2=Qian|first2=Q.|last3=Bjork|first3=G. R.|date=2004-01-16|title=Formation of Thiolated Nucleosides Present in tRNA from Salmonella enterica serovar Typhimurium Occurs in Two Principally Distinct Pathways|url=http://dx.doi.org/10.1128/jb.186.3.758-766.2004|journal=Journal of Bacteriology|volume=186|issue=3|pages=758–766|doi=10.1128/jb.186.3.758-766.2004|issn=0021-9193}}</ref>.

MiaB and RimO are both well-characterized and bacterial prototypes for tRNA-modifying methylthiotransferases

* '''MiaB''' introduces a methylthio group to the isopentenylated A37 derivatives in the tRNA of [[Salmonella enterica subsp. enterica|''S.'' Typhimurium]] and ''[[Escherichia coli|E. coli]]'' by utilizing one SAM molecule to generate 5'-dAdo radical to activate the substrate and a second SAM to donate a sulfur atom to the substrate. <ref>{{Cite journal|last=Pierrel|first=Fabien|last2=Douki|first2=Thierry|last3=Fontecave|first3=Marc|last4=Atta|first4=Mohamed|date=2004-08-30|title=MiaB Protein Is a Bifunctional Radical-S-Adenosylmethionine Enzyme Involved in Thiolation and Methylation of tRNA|url=http://dx.doi.org/10.1074/jbc.m408562200|journal=Journal of Biological Chemistry|volume=279|issue=46|pages=47555–47563|doi=10.1074/jbc.m408562200|issn=0021-9258}}</ref><ref>{{Cite journal|last=Esberg|first=Birgitta|last2=Leung|first2=Hon-Chiu Eastwood|last3=Tsui|first3=Ho-Ching Tiffany|last4=Björk|first4=Glenn R.|last5=Winkler|first5=Malcolm E.|date=1999|title=Identification of the miaB Gene, Involved in Methylthiolation of Isopentenylated A37 Derivatives in the tRNA of Salmonella typhimurium andEscherichia coli|url=http://dx.doi.org/10.1128/jb.181.23.7256-7265.1999|journal=Journal of Bacteriology|volume=181|issue=23|pages=7256–7265|doi=10.1128/jb.181.23.7256-7265.1999|issn=1098-5530}}</ref>
* '''RimO''' is responsible for post-translational modification of Asp88 of the ribosomal protein S12 in ''E. coli''. <ref>{{Cite journal|last=Kowalak|first=Jeffrey A.|last2=Walsh|first2=Kenneth A.|date=1996-08|title=β-Methylthio-aspartic acid: Identification of a novel posttranslational modification in ribosomal protein S12 from escherichia coli|url=http://dx.doi.org/10.1002/pro.5560050816|journal=Protein Science|volume=5|issue=8|pages=1625–1632|doi=10.1002/pro.5560050816|issn=0961-8368}}</ref><ref>{{Cite journal|last=Anton|first=B. P.|last2=Saleh|first2=L.|last3=Benner|first3=J. S.|last4=Raleigh|first4=E. A.|last5=Kasif|first5=S.|last6=Roberts|first6=R. J.|date=2008-02-05|title=RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli|url=http://dx.doi.org/10.1073/pnas.0708608105|journal=Proceedings of the National Academy of Sciences|volume=105|issue=6|pages=1826–1831|doi=10.1073/pnas.0708608105|issn=0027-8424}}</ref> A recently determined crystal structure sheds light on the mechanistic action of RimO. The enzyme catalyzes pentasulfide bridge formation linking two Fe-S clusters to allow for sulfur insertion to the substrate. <ref>{{Cite journal|last=Forouhar|first=Farhad|last2=Arragain|first2=Simon|last3=Atta|first3=Mohamed|last4=Gambarelli|first4=Serge|last5=Mouesca|first5=Jean-Marie|last6=Hussain|first6=Munif|last7=Xiao|first7=Rong|last8=Kieffer-Jaquinod|first8=Sylvie|last9=Seetharaman|first9=Jayaraman|last10=Acton|first10=Thomas B|last11=Montelione|first11=Gaetano T|date=2013-03-31|title=Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases|url=http://dx.doi.org/10.1038/nchembio.1229|journal=Nature Chemical Biology|volume=9|issue=5|pages=333–338|doi=10.1038/nchembio.1229|issn=1552-4450}}</ref>

'''eMtaB''' is the designated methylthiotransferase in eukaryotic and archaeal cells. eMtaB catalyzes the methylthiolation of tRNA at position 37 on N6-threonylcarbamoyladenosine. <ref>{{Cite journal|last=Arragain|first=Simon|last2=Handelman|first2=Samuel K.|last3=Forouhar|first3=Farhad|last4=Wei|first4=Fan-Yan|last5=Tomizawa|first5=Kazuhito|last6=Hunt|first6=John F.|last7=Douki|first7=Thierry|last8=Fontecave|first8=Marc|last9=Mulliez|first9=Etienne|last10=Atta|first10=Mohamed|date=2010-06-28|title=Identification of Eukaryotic and Prokaryotic Methylthiotransferase for Biosynthesis of 2-Methylthio-N6-threonylcarbamoyladenosine in tRNA|url=http://dx.doi.org/10.1074/jbc.m110.106831|journal=Journal of Biological Chemistry|volume=285|issue=37|pages=28425–28433|doi=10.1074/jbc.m110.106831|issn=0021-9258}}</ref> A bacterial homologue of eMtaB, '''YqeV''' has been reported and suggested to function similarly to MiaB and RimO. <ref>{{Cite journal|last=Arragain|first=Simon|last2=Handelman|first2=Samuel K.|last3=Forouhar|first3=Farhad|last4=Wei|first4=Fan-Yan|last5=Tomizawa|first5=Kazuhito|last6=Hunt|first6=John F.|last7=Douki|first7=Thierry|last8=Fontecave|first8=Marc|last9=Mulliez|first9=Etienne|last10=Atta|first10=Mohamed|date=2010-06-28|title=Identification of Eukaryotic and Prokaryotic Methylthiotransferase for Biosynthesis of 2-Methylthio-N6-threonylcarbamoyladenosine in tRNA|url=http://dx.doi.org/10.1074/jbc.m110.106831|journal=Journal of Biological Chemistry|volume=285|issue=37|pages=28425–28433|doi=10.1074/jbc.m110.106831|issn=0021-9258}}</ref>

=== Sulfur insertion into unreactive C-H bonds in biotin and lipoate biosyntheses ===
Sulfurtransferases are a small subset of radical SAM enzymes. Two well-known examples are BioB and LipA which are independently responsible for biotin synthesis and lipoic acid metabolism, respectively. <ref name=":4">{{Cite journal|last=Broderick|first=Joan B.|last2=Duffus|first2=Benjamin R.|last3=Duschene|first3=Kaitlin S.|last4=Shepard|first4=Eric M.|date=2014-01-29|title=RadicalS-Adenosylmethionine Enzymes|url=http://dx.doi.org/10.1021/cr4004709|journal=Chemical Reviews|volume=114|issue=8|pages=4229–4317|doi=10.1021/cr4004709|issn=0009-2665}}</ref>

* '''BioB''' or [[biotin synthase]] is a radical SAM enzyme that employs one [4Fe-4S] center to thiolate dethiobitin, thus converting it to [[biotin]] or also known as vitamin B7. [[Vitamin B7]] is a cofactor used in [[carboxylation]], [[decarboxylation]], and transcarboxylation reactions in many organisms. <ref name=":4" />
* '''LipA''' or [[lipoyl synthase]] is radical SAM sulfurtransferase utilizing two [4Fe-4S] clusters to catalyze the final step in lipoic acid biosynthesis. <ref name=":4" />

=== Anaerobic oxidative decarboxylation ===

* One well-studied example is HemN. '''HemN''' or anaerobic [[coproporphyrinogen III oxidase]] is a radical SAM enzyme that catalyzes the oxidative decarboxylation of coproporphyrinogen III to protoporhyrinogen IX, an important intermediate in heme biosynthesis. A recently published study shows evidence supporting HemN utilizes two SAM molecules to mediate radical-mediated hydrogen transfer for the sequential decarboxylation of the two propionate groups of coproporphyrinogen III. <ref>{{Cite journal|last=Ji|first=Xinjian|last2=Mo|first2=Tianlu|last3=Liu|first3=Wan-Qiu|last4=Ding|first4=Wei|last5=Deng|first5=Zixin|last6=Zhang|first6=Qi|date=2019|title=Revisiting the Mechanism of the Anaerobic Coproporphyrinogen III Oxidase HemN|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201814708|journal=Angewandte Chemie International Edition|language=en|volume=58|issue=19|pages=6235–6238|doi=10.1002/anie.201814708|issn=1521-3773}}</ref>
* [[Hyperthermophile|Hyperthermophilic]] sulfate-reducing archaen ''[[Archaeoglobus fulgidus]]'' has been recently reported to enable anaerobic oxidation of long chain ''n''-alkanes. <ref>{{Cite journal|last=Khelifi|first=Nadia|last2=Amin Ali|first2=Oulfat|last3=Roche|first3=Philippe|last4=Grossi|first4=Vincent|last5=Brochier-Armanet|first5=Céline|last6=Valette|first6=Odile|last7=Ollivier|first7=Bernard|last8=Dolla|first8=Alain|last9=Hirschler-Réa|first9=Agnès|date=2014-04-24|title=Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus|url=http://dx.doi.org/10.1038/ismej.2014.58|journal=The ISME Journal|volume=8|issue=11|pages=2153–2166|doi=10.1038/ismej.2014.58|issn=1751-7362}}</ref> '''PflD''' is reported to be responsible for the capacity of ''A. fulgidus'' to grow on a wide range of unsaturated carbons and fatty acids. A detailed biochemical and mechanistic characterization of PflD is still undergoing but preliminary data suggest PflD may be a radical SAM enzyme.

=== Protein radical formation ===
Glycyl radical enzyme activating enzymes (GRE-AEs) are radical SAM subset that can house a stable and catalytically essential glycyl radical in their active state. The underlying chemistry is considered to be the simplest in the radical SAM superfamily with H-atom abstration by the 5'-dAdo radical being the product of the reaction. <ref name=":5">{{Cite journal|last=Broderick|first=Joan B.|last2=Duffus|first2=Benjamin
R.|last3=Duschene|first3=Kaitlin S.|last4=Shepard|first4=Eric M.|date=2014-04-23|title=Radical S-Adenosylmethionine
Enzymes|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4002137/|journal=Chemical Reviews|volume=114|issue=8|pages=4229–4317|doi=10.1021/cr4004709|issn=0009-2665|pmc=4002137|pmid=24476342}}</ref> A few examples include:

* '''Pyruvate formate-lyase activating enzyme''' (PFL-AE) catalyzes the activation of PFL, a central enzyme in anaerobic glucose metabolism in microbes. <ref name=":5" />
* '''Benzylsuccinate synthase (BSS)''' is a central enzyme in anaerobic [[toluene]] [[catabolism]]. <ref name=":5" />

=== Peptide modifications ===
Radical SAM enzymes that can catalyze sulfur-to-alpha carbon or sulfur-to-beta thioether cross-linked peptides (sactipeptides and lanthipeptides, respectively) are important to generate an essential class of peptide with significant antibacterial, spermicidal and hemolytic properties. <ref>{{Cite journal|last=Flühe|first=Leif|last2=Marahiel|first2=Mohamed A|date=2013-08|title=Radical S-adenosylmethionine enzyme catalyzed thioether bond formation in sactipeptide biosynthesis|url=http://dx.doi.org/10.1016/j.cbpa.2013.06.031|journal=Current Opinion in Chemical Biology|volume=17|issue=4|pages=605–612|doi=10.1016/j.cbpa.2013.06.031|issn=1367-5931}}</ref> Another common name for this peptide class is [[ribosomally synthesized and post-translationally modified peptides]] (RiPPs). <ref>{{Cite journal|last=Benjdia|first=Alhosna|last2=Balty|first2=Clémence|last3=Berteau|first3=Olivier|date=2017|title=Radical SAM Enzymes in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs)|url=https://www.frontiersin.org/articles/10.3389/fchem.2017.00087/full|journal=Frontiers in Chemistry|language=English|volume=5|doi=10.3389/fchem.2017.00087|issn=2296-2646}}</ref><ref>{{Cite journal|last=Davis|first=Katherine M.|last2=Schramma|first2=Kelsey R.|last3=Hansen|first3=William A.|last4=Bacik|first4=John P.|last5=Khare|first5=Sagar D.|last6=Seyedsayamdost|first6=Mohammad R.|last7=Ando|first7=Nozomi|date=2017-09-26|title=Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition|url=https://www.pnas.org/content/114/39/10420|journal=Proceedings of the National Academy of Sciences|language=en|volume=114|issue=39|pages=10420–10425|doi=10.1073/pnas.1703663114|issn=0027-8424|pmid=28893989}}</ref>

Another important subset of peptide-modifying radical SAM enzymes is SPASM/Twitch domain-carrying enzymes. SPASM/Twitch enzymes carry a functionalized C-terminal extension for the binding of two [4Fe-4S] clusters, especially important in post-translational modifications of peptides. <ref>{{Cite journal|last=Haft|first=Daniel H|date=2011-01-11|title=Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners|url=http://dx.doi.org/10.1186/1471-2164-12-21|journal=BMC Genomics|volume=12|issue=1|doi=10.1186/1471-2164-12-21|issn=1471-2164}}</ref><ref>{{Cite journal|last=Haft|first=D. H.|last2=Basu|first2=M. K.|date=2011-04-08|title=Biological Systems Discovery In Silico: Radical S-Adenosylmethionine Protein Families and Their Target Peptides for Posttranslational Modification|url=http://dx.doi.org/10.1128/jb.00040-11|journal=Journal of Bacteriology|volume=193|issue=11|pages=2745–2755|doi=10.1128/jb.00040-11|issn=0021-9193}}</ref><ref>{{Cite journal|last=Grell|first=Tsehai A. J.|last2=Goldman|first2=Peter J.|last3=Drennan|first3=Catherine L.|date=2015-02-13|title=SPASM and Twitch Domains in S-Adenosylmethionine (SAM) Radical Enzymes|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326806/|journal=The Journal of Biological Chemistry|volume=290|issue=7|pages=3964–3971|doi=10.1074/jbc.R114.581249|issn=0021-9258|pmc=4326806|pmid=25477505}}</ref>

The following examples are representative enzymes that can catalyze peptide modifications to generate specific natural products or cofactors.

# '''TsrM''' in [[thiostrepton]] biosynthesis <ref name=":6">{{Cite journal|last=Mahanta|first=Nilkamal|last2=Hudson|first2=Graham A.|last3=Mitchell|first3=Douglas A.|date=2017-10-10|title=Radical SAM enzymes involved in RiPP biosynthesis|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5634935/|journal=Biochemistry|volume=56|issue=40|pages=5229–5244|doi=10.1021/acs.biochem.7b00771|issn=0006-2960|pmc=5634935|pmid=28895719}}</ref>
# '''PoyD''' and '''PoyC''' in polytheonamide biosynthesis <ref name=":6" />
# '''TbtI''' in thiomuracin biosynthesis <ref name=":6" />
# '''NosN''' in [[nosiheptide]] biosynthesis <ref name=":7">{{Cite journal|last=Yokoyama|first=Kenichi|last2=Lilla|first2=Edward A.|date=2018-07-18|title=C–C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6051890/|journal=Natural product reports|volume=35|issue=7|pages=660–694|doi=10.1039/c8np00006a|issn=0265-0568|pmc=6051890|pmid=29633774}}</ref>
# '''MoaA''' in [[molybdenum cofactor]] biosynthesis <ref name=":7" /><ref name=":8">{{Cite journal|last=Mehta|first=Angad P.|last2=Abdelwahed|first2=Sameh H.|last3=Mahanta|first3=Nilkamal|last4=Fedoseyenko|first4=Dmytro|last5=Philmus|first5=Benjamin|last6=Cooper|first6=Lisa E.|last7=Liu|first7=Yiquan|last8=Jhulki|first8=Isita|last9=Ealick|first9=Steven E.|last10=Begley|first10=Tadhg P.|date=2015-02-13|title=Radical S-Adenosylmethionine (SAM) Enzymes in Cofactor Biosynthesis: A Treasure Trove of Complex Organic Radical Rearrangement Reactions|url=http://www.jbc.org/content/290/7/3980|journal=Journal of Biological Chemistry|language=en|volume=290|issue=7|pages=3980–3986|doi=10.1074/jbc.R114.623793|issn=0021-9258|pmid=25477515}}</ref>
# '''PqqE''' in [[Pyrroloquinoline quinone|pyrroloquinonline quinone]] biosynthesis <ref name=":7" />
# '''TunB''' in [[tunicamycin]] biosynthesis <ref name=":7" />
# '''OxsB''' in oxetanocin biosynthesis <ref name=":7" />
# '''BchE''' in anaerobic [[bacteriochlorophyll]] biosynthesis <ref name=":7" />
# '''F0 synthases''' in F420 cofactor biosynthesis <ref name=":7" />
# '''MqnE''' and '''MqnC''' in [[Vitamin K2|menaquinone]] biosynthesis <ref name=":7" /><ref name=":8" />
# '''QhpD''' in post-translational processing of quinohemoprotein amine dehydrogenase <ref>{{Cite journal|last=Nakai|first=Tadashi|last2=Ito|first2=Hiroto|last3=Kobayashi|first3=Kazuo|last4=Takahashi|first4=Yasuhiro|last5=Hori|first5=Hiroshi|last6=Tsubaki|first6=Motonari|last7=Tanizawa|first7=Katsuyuki|last8=Okajima|first8=Toshihide|date=2015-04-24|title=The Radical S-Adenosyl-l-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds|url=http://www.jbc.org/content/290/17/11144|journal=Journal of Biological Chemistry|language=en|volume=290|issue=17|pages=11144–11166|doi=10.1074/jbc.M115.638320|issn=0021-9258|pmid=25778402}}</ref>

=== Epimerization in polytheonamide and epipeptide biosyntheses ===
Radical SAM [[Epimerase and racemase|epimerases]] are responsible for the [[Regioselectivity|regioselective]] introduction of [[D-Amino acid|D-amino acids]] into RiPPs. Two well-known enzymes have been thoroughly described in RiPP biosynthetic pathways.

* '''PoyD''' installs numerous D-stereocenters in enzyme PoyA to ultimately help facilitate polytheonamide biosynthesis. <ref name=":6" /> Polytheoamide is a natural potent cytoxic agent by forming pores in membranes. <ref>{{Cite journal|last=Itoh|first=Hiroaki|last2=Inoue|first2=Masayuki|date=2012-11-01|title=Structural Permutation
of Potent Cytotoxin, Polytheonamide
B: Discovery of Cytotoxic Peptide with Altered Activity|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027433/|journal=ACS Medicinal Chemistry Letters|volume=4|issue=1|pages=52–56|doi=10.1021/ml300264c|issn=1948-5875|pmc=4027433|pmid=24900563}}</ref> This peptide cytotoxin is naturally produced by uncultivated bacteria that exist as symbionts in a marine sponge. <ref>{{Cite journal|last=Freeman|first=Michael F.|last2=Helf|first2=Maximilian J.|last3=Bhushan|first3=Agneya|last4=Morinaka|first4=Brandon I.|last5=Piel|first5=Jörn|date=2017-04|title=Seven enzymes create extraordinary molecular complexity in an uncultivated bacterium|url=https://www.nature.com/articles/nchem.2666|journal=Nature Chemistry|language=en|volume=9|issue=4|pages=387–395|doi=10.1038/nchem.2666|issn=1755-4349}}</ref>
* '''YydG''' epimerase modifies two amino acid positions on YydF in Gram-positive ''[[Bacillus subtilis]]''. <ref name=":6" /> A recent study has reported the extrinsically added YydF mediates subsequent dissipation of membrane potential via membrane permeabilization, resulting in death of the organism. <ref>{{Cite journal|last=Popp|first=Philipp F.|last2=Benjdia|first2=Alhosna|last3=Strahl|first3=Henrik|last4=Berteau|first4=Olivier|last5=Mascher|first5=Thorsten|date=2020|title=The Epipeptide YydF Intrinsically Triggers the Cell Envelope Stress Response of Bacillus subtilis and Causes Severe Membrane Perturbations|url=https://www.frontiersin.org/articles/10.3389/fmicb.2020.00151/full|journal=Frontiers in Microbiology|language=English|volume=11|doi=10.3389/fmicb.2020.00151|issn=1664-302X}}</ref>

=== Complex carbon skeleton rearrangements in DNA repair and cofactors/natural products biosyntheses ===
Another subset of radical SAM superfamily has been shown to catalyze carbon skeleton rearrangements especially in the areas of DNA repair and cofactor biosynthesis.

* '''DNA [[Spore photoproduct lyase|spore photoproduct lysase]]''' (SPL) is a radical SAM that can repair DNA [[thymine dimers]] (spore product, SP) caused by UV radiation. Despite of remaining unknowns and controversies involving SPL-catalyzed reaction, it is certain that SPL utilizes SAM as a cofactor to generate 5'-dAdo radical to revert SP to two thymine residues. <ref name=":9">{{Cite journal|last=Wang|first=Jiarui|last2=Woldring|first2=Rory P.|last3=Román-Meléndez|first3=Gabriel D.|last4=McClain|first4=Alan M.|last5=Alzua|first5=Brian
R.|last6=Marsh|first6=E. Neil G.|date=2014-09-19|title=Recent Advances in Radical SAM Enzymology: New Structures
and Mechanisms|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168785/|journal=ACS Chemical Biology|volume=9|issue=9|pages=1929–1938|doi=10.1021/cb5004674|issn=1554-8929|pmc=4168785|pmid=25009947}}</ref><ref>{{Cite journal|last=Yang|first=Linlin|last2=Li|first2=Lei|date=2015-02-13|title=Spore Photoproduct Lyase: The Known, the Controversial, and the Unknown|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326811/|journal=The Journal of Biological Chemistry|volume=290|issue=7|pages=4003–4009|doi=10.1074/jbc.R114.573675|issn=0021-9258|pmc=4326811|pmid=25477522}}</ref>
* '''HydG''' is a radical SAM responsible for generating [[Carbon monoxide|CO]] and [[Cyanide|CN<sup>-</sup>]] ligands in the [Fe-Fe]-hydrogenase (HydA) in various anaerobic bacteria. <ref name=":9" />
* Radical SAM '''MoaA''' and '''MoaC''' are involved in converting GTP into cyclic pyranopterin monophosphate (cPMP). Overall, both play important roles in [[molybdopterin]] biosynthesis. <ref name=":9" />

=== Other reactions with unique biological functions ===

* A recent study has reported a novel radical SAM enzyme with intrinsic lyase activity that is able to catalyze lysine trasnfer reaction, generating archaea-specific archaosine-containing tRNAs. <ref>{{Cite journal|last=Yokogawa|first=Takashi|last2=Nomura|first2=Yuichiro|last3=Yasuda|first3=Akihiro|last4=Ogino|first4=Hiromi|last5=Hiura|first5=Keita|last6=Nakada|first6=Saori|last7=Oka|first7=Natsuhisa|last8=Ando|first8=Kaori|last9=Kawamura|first9=Takuya|last10=Hirata|first10=Akira|last11=Hori|first11=Hiroyuki|date=2019-11-18|title=Identification of a radical SAM enzyme involved in the synthesis of archaeosine|url=http://dx.doi.org/10.1038/s41589-019-0390-7|journal=Nature Chemical Biology|volume=15|issue=12|pages=1148–1155|doi=10.1038/s41589-019-0390-7|issn=1552-4450}}</ref>
* Viperin is a radical SAM enzyme with multifaceted role especially in the cellular antiviral response. A recently published study has reported the likely mechanism of this antiviral radical SAM enzyme. <ref>{{Cite journal|last=Dumbrepatil|first=Arti B.|last2=Ghosh|first2=Soumi|last3=Patel|first3=Ayesha M.|last4=Malec|first4=Paige A.|last5=Zegalia|first5=Kelcie|last6=Hoff|first6=J. Damon|last7=Kennedy|first7=Robert T.|last8=Marsh|first8=E. Neil G.|date=2018-05-21|title=Regulation of IRAK1 Ubiquitination by the Antiviral Radical SAM Enzyme Viperin|url=https://www.biorxiv.org/content/10.1101/318840v1|journal=bioRxiv|language=en|pages=318840|doi=10.1101/318840}}</ref>

== Clinical considerations ==

* Deficiency in human tRNA methylthiotransferase '''eMtaB''' has been shown to be responsible for abnormal insulin synthesis and predisposition to [[type 2 diabetes]]. <ref>{{Cite book|last=Wei, Fan-Yan Suzuki, Takeo Watanabe, Sayaka Kimura, Satoshi Kaitsuka, Taku Fujimura, Atsushi Matsui, Hideki Atta, Mohamed Michiue, Hiroyuki Fontecave, Marc Yamagata, Kazuya Suzuki, Tsutomu Tomizawa, Kazuhito|url=http://worldcat.org/oclc/759579098|title=Deficit of tRNALys modification by Cdkal1 causes the development of type 2 diabetes in mice|date=2011-08-15|publisher=American Society for Clinical Investigation|oclc=759579098}}</ref>
* Mutations in human GTP cyclase '''MoaA''' has been reported to lead to molybdenum cofactor deficiency, a usually fatal disease accompanied by severe neurological symptoms. <ref>{{Cite journal|last=Hänzelmann|first=Petra|last2=Schindelin|first2=Hermann|date=2004-08-31|title=Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans|url=https://www.pnas.org/content/101/35/12870|journal=Proceedings of the National Academy of Sciences|language=en|volume=101|issue=35|pages=12870–12875|doi=10.1073/pnas.0404624101|issn=0027-8424|pmid=15317939}}</ref>
* Mutations in human [[wybutosine]]-tRNA modifying enzyme '''Tyw1''' promotes [[retrovirus]] infection. <ref name=":10">{{Cite journal|last=Landgraf|first=Bradley J.|last2=McCarthy|first2=Erin L.|last3=Booker|first3=Squire J.|date=2016-06-02|title=RadicalS-Adenosylmethionine Enzymes in Human Health and Disease|url=http://dx.doi.org/10.1146/annurev-biochem-060713-035504|journal=Annual Review of Biochemistry|volume=85|issue=1|pages=485–514|doi=10.1146/annurev-biochem-060713-035504|issn=0066-4154}}</ref>
* Alterations in human tRNA-modifying enzyme '''Elp3''' results in progression into [[amyotrophic lateral sclerosis]] (ALS). <ref name=":10" />
* Mutations in human antiviral '''RSAD1''' has been shown to be associated with congenital heart disease. <ref name=":10" />
* Mutations in human sulfurtransferase '''LipA''' has been implicated in [[glycine encephalopathy]], [[pyruvate dehydrogenase]] and lipoic acid synthetase deficiency. <ref name=":10" />
* Mutations in human methylthiotransferase '''MiaB''' are related to impaired cardiac and respiratory functions. <ref name=":10" />

<br />

== Application in drug discovery and development ==
Microbes have been extensively used for the discovery of new antibiotics. However, a growing public concern of multi-drug resistant pathogens has been emerging in the last few decades. Thus, newly developed or novel antibiotics are in utmost demand. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are getting more attention as a newer and major group of antibiotics thanks to having a very narrow of activity spectrum, which can benefit patients, as their side effects will be lesser than the broad-spectrum antibiotics. <ref>{{Cite journal|last=Letzel|first=Anne-Catrin|last2=Pidot|first2=Sacha J|last3=Hertweck|first3=Christian|date=2014|title=Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria|url=http://dx.doi.org/10.1186/1471-2164-15-983|journal=BMC Genomics|volume=15|issue=1|pages=983|doi=10.1186/1471-2164-15-983|issn=1471-2164}}</ref><ref>{{Cite journal|last=Papagianni|first=Maria|date=2003-09|title=Ribosomally synthesized peptides with antimicrobial properties: biosynthesis, structure, function, and applications|url=http://dx.doi.org/10.1016/s0734-9750(03)00077-6|journal=Biotechnology Advances|volume=21|issue=6|pages=465–499|doi=10.1016/s0734-9750(03)00077-6|issn=0734-9750}}</ref> Below are a few examples of radical SAM enzymes have been shown to be promising targets for antibiotic and antiviral development.

* Inhibition of radical SAM enzyme '''MnqE''' in menaoquinone biosynthesis is reported to be an effective antibacterial strategy against [[Helicobacter pylori|''H.'' pylori]]. <ref>{{Cite journal|last=Joshi|first=Sumedh|last2=Fedoseyenko|first2=Dmytro|last3=Mahanta|first3=Nilkamal|last4=Ducati|first4=Rodrigo G.|last5=Feng|first5=Mu|last6=Schramm|first6=Vern L.|last7=Begley|first7=Tadhg P.|date=2019-03-14|title=Antibacterial Strategy against H. pylori: Inhibition of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis|url=https://einstein.pure.elsevier.com/en/publications/antibacterial-strategy-against-h-pylori-inhibition-of-the-radical|journal=ACS Medicinal Chemistry Letters|volume=10|issue=3|pages=363–366|doi=10.1021/acsmedchemlett.8b00649|issn=1948-5875}}</ref>
* Radical SAM enzyme '''BlsE''' has recently been discovered to be a central enzyme in [[blasticidin S]] biosynthetic pathway. Blasticidin S produced by ''[[Streptomyces griseochromogenes]]'' exhibits strong inhibitory activity against rice blast caused by ''[[Pyricularia oryzae]]'' Cavara. This compound specificially inhibits protein synthesis in both prokaryotes and eukaryotes through inhibition of peptide bond formation in the ribosome machinery. <ref>{{Cite journal|last=Feng|first=Jun|last2=Wu|first2=Jun|last3=Dai|first3=Nan|last4=Lin|first4=Shuangjun|last5=Xu|first5=H. Howard|last6=Deng|first6=Zixin|last7=He|first7=Xinyi|date=2013-07-18|title=Discovery and Characterization of BlsE, a Radical S-Adenosyl-L-methionine Decarboxylase Involved in the Blasticidin S Biosynthetic Pathway|url=https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068545|journal=PLOS ONE|language=en|volume=8|issue=7|pages=e68545|doi=10.1371/journal.pone.0068545|issn=1932-6203|pmc=PMC3715490|pmid=23874663}}</ref>
* A new fungal radical SAM enzyme has also been recently reported to facilitate the biocatalytic routes for synthesis of 3'-deoxy nucleotides/nucleosides. 3'deoxynucleotides are an important class of drugs since they interfere with the metabolism of nucleotides, and their incorporation into DNA or RNA terminates cell division and replication. This activity explains why this compound is an essential group of antiviral, antibacterial or anticancer drug. <ref>{{Cite journal|last=Ebrahimi|first=Kourosh Honarmand|last2=Rowbotham|first2=Jack S.|last3=McCullagh|first3=James|last4=James|first4=William S.|title=Mechanism of Diol Dehydration by a Promiscuous Radical-SAM Enzyme Homologue of the Antiviral Enzyme Viperin (RSAD2)|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.201900776|journal=ChemBioChem|language=en|volume=n/a|issue=n/a|doi=10.1002/cbic.201900776|issn=1439-7633}}</ref>

<br />
== Examples ==
== Examples ==
An estimated 100,000 enzymes are classified as radical SAMs as of 2018.<ref name=Atlas/>
An estimated 100,000 enzymes are classified as radical SAMs as of 2018.<ref name=Atlas/>

Revision as of 21:36, 29 March 2020

Radical_SAM
Identifiers
SymbolRadical_SAM
PfamPF04055
InterProIPR007197
SCOP2102114 / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

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][2] These enzymes utilize this potent radical intermediate to perform an array of unusual (from the perspective of organic chemistry) transformations, often to functionalize unactivated C-H bonds. More than 110,000 enzymes use adomet.[3] Radical SAM enzymes are 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,[4][5] and have a cysteine-rich motif that matches or resembles CxxxCxxC.

Some radical SAMs release methyl radicals.[6]


History

In 2001, by utilizing iterative profile searches, powerful bioinformatics and information visualization methods, a diverse group of 645 unique radical SAM enzymes from 126 species of all three domains of life was first discovered and documented. [7] Currently, according to the EFI ([1]) and SFLD ([2]) databases, there are more than 220,000 radical SAM enzymes predicted to be involved in 85 types of biochemical transformations. [8]

Nomenclature

All enzymes including radical SAM superfamily follow an easy guideline for systematic naming. Systematic naming of enzymes allows a uniform naming process that is recognized by all scientists to understand corresponding function. The first word of the enzyme name often shows the substrate of the enzyme. The position of the reaction on the substrate will also be in the beginning portion of the name. Lastly, the class of the enzyme will be described in the other half of the name which will end in suffix -ase. The class of an enzyme will describe what the enzyme is doing or changing on the substrate. For example, a ligase combines two molecules to form a new bond. [9]

Reaction classification and corresponding function(s)

Representative/Prototype enzymes will only be mentioned for each reaction scheme. The audience is highly encouraged to research more into current studies on radical SAM enzymes. Many of which are responsible for fascinating yet important reactions.

Radical SAM enzymes and their mechanisms known before 2008 are well-summarized by Frey et al, 2008 ([3]). Since 2015, more review articles on radical SAM enzymes are open to the public. The following are only a few out of many informative resources on radical SAM enzymes.

  1. Recent Advances in Radical SAM Enzymology: New Structures and Mechanisms: [4]
  2. Radical S-Adenosylmethionine Enzymes: [5]
  3. Radical S-Adenosylmethionine (SAM) Enzymes in Cofactor Biosynthesis: A Treasure Trove of Complex Organic Radical Rearrangement Reactions: [6]
  4. Molecular architectures and functions of radical enzymes and their (re)activating proteins: [7]

Carbon methylation in nucleic acid modifications and secondary metabolites/cofactor/antibiotics biosynthesis

Radical SAM methylases/methyltransferases are one of the largest yet diverse subgroups and are capable of methylating a broad range of unreactive carbon and phosphorus centers. These enzymes are divided into four classes (Class A, B, C and D) with representative methylation mechanisms. The shared characteristic of the three major classes A, B and C is the usage of SAM, split into two distinct roles: one as a source of a methyl group donor, and the second as a source of 5'-dAdo radical. [10][11] The recently documented class D utilizes a different methylation mechanism.

Class A sub-family enzymes:

  • Class A enzymes methylates specific adenosine residues on rRNA and/or tRNA. [12][13] In other words, they are RNA base-modifying radical SAM enzymes.
  • The most mechanistically well-characterized are enzymes RlmN and Cfr. Both enzymes methylates substrate by adding a methylene fragment originating from SAM molecule. [10][14] Therefore, RlmN and Cfr are considered methyl synthases instead of methyltransferases.

Class B sub-family enzymes:

  • Class B enzymes are the largest and most versatile which can methylate a wide range of carbon and phosphorus centers. [13]
  • These enzymes require a cobalamin (vitamin B12) cofactor as an intermediate methyl group carrier to transfer a methyl group from SAM to substrate. [12]
  • One well-investigated representative enzyme is TsrM which involves in tryptophan methylation in thiostrepton biosynthesis. [10]

Class C sub-family enzymes:

  • Class C enzymes are reported to play roles in biosynthesis of complex natural products and secondary metabolites. These enzymes methylate heteroaromatic substrates [12][13] and are cobalamin-independent. [15]
  • These enzymes contain both the radical SAM motif and exhibit striking sequence similarity to coproporhyrinogen III oxidase (HemN), a radical SAM enzyme involved in heme biosynthesis [10][13]
  • Recently, detailed mechanistic investigation on two important class C radical SAM methylases have been reported:
    1. TbtI is involved in the biosynthesis of potent thiopeptide antibiotic thiomuracin. [16]
    2. Jaw5 is suggested to be responsible for cyclopropane modifications. [17]

Class D sub-family enzymes:

  • Class D is the most recently discovered and has been shown to not use SAM for methylation which is different from the three classes described above. [18] Instead, these enzymes use methylenetetrahydrofolate as the methyl donor.
  • The prototype MJ0619 is proposed to play a role in the biosynthesis of cofactor methanopterin which is required in methanogesis, an essential methane-producing pathway dominantly found in the Archaean domain. [13][18]

Methylthiolation of tRNAs

Methythiotransferases belong to a subset of radical SAM enzymes that contain two [4Fe-4S]+ clusters and one radical SAM domain. Methylthiotransferases play a major role in catalyzing methylthiolation on tRNA nucleotides or anticodons through a redox mechanism. Thiolation modification is believed to maintain translational efficiency and fidelity. [19][20][21][22].

MiaB and RimO are both well-characterized and bacterial prototypes for tRNA-modifying methylthiotransferases

  • MiaB introduces a methylthio group to the isopentenylated A37 derivatives in the tRNA of S. Typhimurium and E. coli by utilizing one SAM molecule to generate 5'-dAdo radical to activate the substrate and a second SAM to donate a sulfur atom to the substrate. [23][24]
  • RimO is responsible for post-translational modification of Asp88 of the ribosomal protein S12 in E. coli. [25][26] A recently determined crystal structure sheds light on the mechanistic action of RimO. The enzyme catalyzes pentasulfide bridge formation linking two Fe-S clusters to allow for sulfur insertion to the substrate. [27]

eMtaB is the designated methylthiotransferase in eukaryotic and archaeal cells. eMtaB catalyzes the methylthiolation of tRNA at position 37 on N6-threonylcarbamoyladenosine. [28] A bacterial homologue of eMtaB, YqeV has been reported and suggested to function similarly to MiaB and RimO. [29]

Sulfur insertion into unreactive C-H bonds in biotin and lipoate biosyntheses

Sulfurtransferases are a small subset of radical SAM enzymes. Two well-known examples are BioB and LipA which are independently responsible for biotin synthesis and lipoic acid metabolism, respectively. [30]

  • BioB or biotin synthase is a radical SAM enzyme that employs one [4Fe-4S] center to thiolate dethiobitin, thus converting it to biotin or also known as vitamin B7. Vitamin B7 is a cofactor used in carboxylation, decarboxylation, and transcarboxylation reactions in many organisms. [30]
  • LipA or lipoyl synthase is radical SAM sulfurtransferase utilizing two [4Fe-4S] clusters to catalyze the final step in lipoic acid biosynthesis. [30]

Anaerobic oxidative decarboxylation

  • One well-studied example is HemN. HemN or anaerobic coproporphyrinogen III oxidase is a radical SAM enzyme that catalyzes the oxidative decarboxylation of coproporphyrinogen III to protoporhyrinogen IX, an important intermediate in heme biosynthesis. A recently published study shows evidence supporting HemN utilizes two SAM molecules to mediate radical-mediated hydrogen transfer for the sequential decarboxylation of the two propionate groups of coproporphyrinogen III. [31]
  • Hyperthermophilic sulfate-reducing archaen Archaeoglobus fulgidus has been recently reported to enable anaerobic oxidation of long chain n-alkanes. [32] PflD is reported to be responsible for the capacity of A. fulgidus to grow on a wide range of unsaturated carbons and fatty acids. A detailed biochemical and mechanistic characterization of PflD is still undergoing but preliminary data suggest PflD may be a radical SAM enzyme.

Protein radical formation

Glycyl radical enzyme activating enzymes (GRE-AEs) are radical SAM subset that can house a stable and catalytically essential glycyl radical in their active state. The underlying chemistry is considered to be the simplest in the radical SAM superfamily with H-atom abstration by the 5'-dAdo radical being the product of the reaction. [33] A few examples include:

  • Pyruvate formate-lyase activating enzyme (PFL-AE) catalyzes the activation of PFL, a central enzyme in anaerobic glucose metabolism in microbes. [33]
  • Benzylsuccinate synthase (BSS) is a central enzyme in anaerobic toluene catabolism. [33]

Peptide modifications

Radical SAM enzymes that can catalyze sulfur-to-alpha carbon or sulfur-to-beta thioether cross-linked peptides (sactipeptides and lanthipeptides, respectively) are important to generate an essential class of peptide with significant antibacterial, spermicidal and hemolytic properties. [34] Another common name for this peptide class is ribosomally synthesized and post-translationally modified peptides (RiPPs). [35][36]

Another important subset of peptide-modifying radical SAM enzymes is SPASM/Twitch domain-carrying enzymes. SPASM/Twitch enzymes carry a functionalized C-terminal extension for the binding of two [4Fe-4S] clusters, especially important in post-translational modifications of peptides. [37][38][39]

The following examples are representative enzymes that can catalyze peptide modifications to generate specific natural products or cofactors.

  1. TsrM in thiostrepton biosynthesis [40]
  2. PoyD and PoyC in polytheonamide biosynthesis [40]
  3. TbtI in thiomuracin biosynthesis [40]
  4. NosN in nosiheptide biosynthesis [41]
  5. MoaA in molybdenum cofactor biosynthesis [41][42]
  6. PqqE in pyrroloquinonline quinone biosynthesis [41]
  7. TunB in tunicamycin biosynthesis [41]
  8. OxsB in oxetanocin biosynthesis [41]
  9. BchE in anaerobic bacteriochlorophyll biosynthesis [41]
  10. F0 synthases in F420 cofactor biosynthesis [41]
  11. MqnE and MqnC in menaquinone biosynthesis [41][42]
  12. QhpD in post-translational processing of quinohemoprotein amine dehydrogenase [43]

Epimerization in polytheonamide and epipeptide biosyntheses

Radical SAM epimerases are responsible for the regioselective introduction of D-amino acids into RiPPs. Two well-known enzymes have been thoroughly described in RiPP biosynthetic pathways.

  • PoyD installs numerous D-stereocenters in enzyme PoyA to ultimately help facilitate polytheonamide biosynthesis. [40] Polytheoamide is a natural potent cytoxic agent by forming pores in membranes. [44] This peptide cytotoxin is naturally produced by uncultivated bacteria that exist as symbionts in a marine sponge. [45]
  • YydG epimerase modifies two amino acid positions on YydF in Gram-positive Bacillus subtilis. [40] A recent study has reported the extrinsically added YydF mediates subsequent dissipation of membrane potential via membrane permeabilization, resulting in death of the organism. [46]

Complex carbon skeleton rearrangements in DNA repair and cofactors/natural products biosyntheses

Another subset of radical SAM superfamily has been shown to catalyze carbon skeleton rearrangements especially in the areas of DNA repair and cofactor biosynthesis.

  • DNA spore photoproduct lysase (SPL) is a radical SAM that can repair DNA thymine dimers (spore product, SP) caused by UV radiation. Despite of remaining unknowns and controversies involving SPL-catalyzed reaction, it is certain that SPL utilizes SAM as a cofactor to generate 5'-dAdo radical to revert SP to two thymine residues. [47][48]
  • HydG is a radical SAM responsible for generating CO and CN- ligands in the [Fe-Fe]-hydrogenase (HydA) in various anaerobic bacteria. [47]
  • Radical SAM MoaA and MoaC are involved in converting GTP into cyclic pyranopterin monophosphate (cPMP). Overall, both play important roles in molybdopterin biosynthesis. [47]

Other reactions with unique biological functions

  • A recent study has reported a novel radical SAM enzyme with intrinsic lyase activity that is able to catalyze lysine trasnfer reaction, generating archaea-specific archaosine-containing tRNAs. [49]
  • Viperin is a radical SAM enzyme with multifaceted role especially in the cellular antiviral response. A recently published study has reported the likely mechanism of this antiviral radical SAM enzyme. [50]

Clinical considerations

  • Deficiency in human tRNA methylthiotransferase eMtaB has been shown to be responsible for abnormal insulin synthesis and predisposition to type 2 diabetes. [51]
  • Mutations in human GTP cyclase MoaA has been reported to lead to molybdenum cofactor deficiency, a usually fatal disease accompanied by severe neurological symptoms. [52]
  • Mutations in human wybutosine-tRNA modifying enzyme Tyw1 promotes retrovirus infection. [53]
  • Alterations in human tRNA-modifying enzyme Elp3 results in progression into amyotrophic lateral sclerosis (ALS). [53]
  • Mutations in human antiviral RSAD1 has been shown to be associated with congenital heart disease. [53]
  • Mutations in human sulfurtransferase LipA has been implicated in glycine encephalopathy, pyruvate dehydrogenase and lipoic acid synthetase deficiency. [53]
  • Mutations in human methylthiotransferase MiaB are related to impaired cardiac and respiratory functions. [53]


Application in drug discovery and development

Microbes have been extensively used for the discovery of new antibiotics. However, a growing public concern of multi-drug resistant pathogens has been emerging in the last few decades. Thus, newly developed or novel antibiotics are in utmost demand. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are getting more attention as a newer and major group of antibiotics thanks to having a very narrow of activity spectrum, which can benefit patients, as their side effects will be lesser than the broad-spectrum antibiotics. [54][55] Below are a few examples of radical SAM enzymes have been shown to be promising targets for antibiotic and antiviral development.

  • Inhibition of radical SAM enzyme MnqE in menaoquinone biosynthesis is reported to be an effective antibacterial strategy against H. pylori. [56]
  • Radical SAM enzyme BlsE has recently been discovered to be a central enzyme in blasticidin S biosynthetic pathway. Blasticidin S produced by Streptomyces griseochromogenes exhibits strong inhibitory activity against rice blast caused by Pyricularia oryzae Cavara. This compound specificially inhibits protein synthesis in both prokaryotes and eukaryotes through inhibition of peptide bond formation in the ribosome machinery. [57]
  • A new fungal radical SAM enzyme has also been recently reported to facilitate the biocatalytic routes for synthesis of 3'-deoxy nucleotides/nucleosides. 3'deoxynucleotides are an important class of drugs since they interfere with the metabolism of nucleotides, and their incorporation into DNA or RNA terminates cell division and replication. This activity explains why this compound is an essential group of antiviral, antibacterial or anticancer drug. [58]


Examples

An estimated 100,000 enzymes are classified as radical SAMs as of 2018.[2]

Radical

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
  • DarE - darobactin maturase
  • 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 [59]
  • 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 - methylornithine synthase, 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) [60]
  • 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)

Non-canonical

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) [61]
  • Dph2 (PF01866) - diphthamide biosynthesis enzyme Dph2 (protein modification - diphthamide in translation elongation factor 2) (note different radical production, a 3-amino-3-carboxypropyl radical) [62]
  • PhnJ (PF06007) - phosphonate metabolism protein PhnJ (C-P phosphonate bond cleavage) [63]

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