radical SAM protein generates 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; transfer of a single electron from the iron-sulfur cluster to SAM leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical; similar to Priestia megaterium cobalamin-dependent SAM enzyme OxsB (may be cobalamin dependent)
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
210-399
1.01e-28
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Pssm-ID: 214792 [Multi-domain] Cd Length: 216 Bit Score: 114.42 E-value: 1.01e-28
B12 binding domain_like associated with radical SAM domain. This domain shows similarity with ...
20-151
2.18e-24
B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
Pssm-ID: 239019 [Multi-domain] Cd Length: 127 Bit Score: 98.93 E-value: 2.18e-24
ribosomal peptide maturation radical SAM protein 1; Models TIGR03793 and TIGR03798 describe ...
24-371
1.35e-23
ribosomal peptide maturation radical SAM protein 1; Models TIGR03793 and TIGR03798 describe bacteriocin precursor families to occur often in large paralogous families and are subject to various modifications, including by LanM family lantibiotic synthases and by cyclodehydratases. This model represents a radical SAM protein family that regularly occurs in the context of these bacteriocins, and may occur where other familiar peptide modification enzymes are absent. [Cellular processes, Toxin production and resistance]
Pssm-ID: 274893 [Multi-domain] Cd Length: 606 Bit Score: 105.87 E-value: 1.35e-23
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several ...
17-131
2.48e-19
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.
Pssm-ID: 426713 [Multi-domain] Cd Length: 121 Bit Score: 84.30 E-value: 2.48e-19
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
210-399
1.01e-28
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Pssm-ID: 214792 [Multi-domain] Cd Length: 216 Bit Score: 114.42 E-value: 1.01e-28
B12 binding domain_like associated with radical SAM domain. This domain shows similarity with ...
20-151
2.18e-24
B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
Pssm-ID: 239019 [Multi-domain] Cd Length: 127 Bit Score: 98.93 E-value: 2.18e-24
ribosomal peptide maturation radical SAM protein 1; Models TIGR03793 and TIGR03798 describe ...
24-371
1.35e-23
ribosomal peptide maturation radical SAM protein 1; Models TIGR03793 and TIGR03798 describe bacteriocin precursor families to occur often in large paralogous families and are subject to various modifications, including by LanM family lantibiotic synthases and by cyclodehydratases. This model represents a radical SAM protein family that regularly occurs in the context of these bacteriocins, and may occur where other familiar peptide modification enzymes are absent. [Cellular processes, Toxin production and resistance]
Pssm-ID: 274893 [Multi-domain] Cd Length: 606 Bit Score: 105.87 E-value: 1.35e-23
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several ...
17-131
2.48e-19
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.
Pssm-ID: 426713 [Multi-domain] Cd Length: 121 Bit Score: 84.30 E-value: 2.48e-19
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
217-372
2.04e-18
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: 82.96 E-value: 2.04e-18
B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 ...
23-135
6.11e-09
B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif.
Pssm-ID: 239016 [Multi-domain] Cd Length: 125 Bit Score: 54.70 E-value: 6.11e-09
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
217-395
1.35e-08
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: 55.42 E-value: 1.35e-08
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase ...
299-384
3.33e-04
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase [Coenzyme transport and metabolism]; Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase is part of the Pathway/BioSystem: Heme biosynthesis
Pssm-ID: 440400 [Multi-domain] Cd Length: 400 Bit Score: 43.63 E-value: 3.33e-04
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
220-351
2.66e-03
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];
Pssm-ID: 440301 [Multi-domain] Cd Length: 159 Bit Score: 39.12 E-value: 2.66e-03
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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