radical SAM family protein may generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity; contains a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; transfers a single electron from the iron-sulfur cluster to SAM leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
21-356
1.87e-119
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
The actual alignment was detected with superfamily member PRK14464:
Pssm-ID: 450244 Cd Length: 344 Bit Score: 348.64 E-value: 1.87e-119
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and ...
20-343
5.33e-110
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and biogenesis]; Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 is part of the Pathway/BioSystem: 23S rRNA modification
Pssm-ID: 440582 Cd Length: 338 Bit Score: 324.29 E-value: 5.33e-110
23S rRNA (adenine(2503)-C(2))-methyltransferase; Members of this family are RlmN, a 23S rRNA ...
20-354
2.09e-63
23S rRNA (adenine(2503)-C(2))-methyltransferase; Members of this family are RlmN, a 23S rRNA m2A2503 methyltransferase in the radical SAM enzyme family. Closely related is Cfr, a Staphylococcus sciuri plasmid-borne homolog to this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol. Cfr methylates 23S RNA at a different site. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 272874 Cd Length: 355 Bit Score: 205.82 E-value: 2.09e-63
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
114-270
3.76e-11
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Pssm-ID: 427681 [Multi-domain] Cd Length: 159 Bit Score: 61.00 E-value: 3.76e-11
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
117-319
2.34e-04
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
Pssm-ID: 100105 [Multi-domain] Cd Length: 204 Bit Score: 41.94 E-value: 2.34e-04
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and ...
20-343
5.33e-110
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and biogenesis]; Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 is part of the Pathway/BioSystem: 23S rRNA modification
Pssm-ID: 440582 Cd Length: 338 Bit Score: 324.29 E-value: 5.33e-110
23S rRNA (adenine(2503)-C(2))-methyltransferase; Members of this family are RlmN, a 23S rRNA ...
20-354
2.09e-63
23S rRNA (adenine(2503)-C(2))-methyltransferase; Members of this family are RlmN, a 23S rRNA m2A2503 methyltransferase in the radical SAM enzyme family. Closely related is Cfr, a Staphylococcus sciuri plasmid-borne homolog to this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol. Cfr methylates 23S RNA at a different site. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 272874 Cd Length: 355 Bit Score: 205.82 E-value: 2.09e-63
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
114-270
3.76e-11
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Pssm-ID: 427681 [Multi-domain] Cd Length: 159 Bit Score: 61.00 E-value: 3.76e-11
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
140-313
7.06e-05
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal structure and biogenesis]; Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440495 [Multi-domain] Cd Length: 248 Bit Score: 43.64 E-value: 7.06e-05
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
117-319
2.34e-04
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
Pssm-ID: 100105 [Multi-domain] Cd Length: 204 Bit Score: 41.94 E-value: 2.34e-04
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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