TIGR01212 family radical SAM protein such as Bacillus subtilis protein YtqA that 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
radical SAM protein, TIGR01212 family; Members of this family are apparent radical-SAM enzymes, ...
6-302
4.79e-161
radical SAM protein, TIGR01212 family; Members of this family are apparent radical-SAM enzymes, related to the N-terminal region of the bifunctional ELP3, whose C-terminal region is part of the elongator complex and appears to acetylate histones and other proteins. ELP3 binds S-adenosylmethionine (SAM) and was recently shown to be involved in a DNA demethylation process in eukaryotes. Close sequence similarity of this family (with lacks the GNAT family acetyltransferase domain) to the ELP3 N-terminal region and a strong match to the pfam04055 support identification of this family as radical SAM despite the atypical spacing between first and second Cys residues in the 4Fe4S-binding motif. [Unknown function, Enzymes of unknown specificity]
Pssm-ID: 130279 [Multi-domain] Cd Length: 302 Bit Score: 450.75 E-value: 4.79e-161
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
23-243
5.88e-37
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: 131.37 E-value: 5.88e-37
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of ...
208-290
1.29e-25
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of Radical_SAM domains. It is found in archaeal, bacterial, fungal, plant and human proteins.
Pssm-ID: 465061 [Multi-domain] Cd Length: 83 Bit Score: 97.47 E-value: 1.29e-25
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
33-228
1.07e-07
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: 51.57 E-value: 1.07e-07
radical SAM protein, TIGR01212 family; Members of this family are apparent radical-SAM enzymes, ...
6-302
4.79e-161
radical SAM protein, TIGR01212 family; Members of this family are apparent radical-SAM enzymes, related to the N-terminal region of the bifunctional ELP3, whose C-terminal region is part of the elongator complex and appears to acetylate histones and other proteins. ELP3 binds S-adenosylmethionine (SAM) and was recently shown to be involved in a DNA demethylation process in eukaryotes. Close sequence similarity of this family (with lacks the GNAT family acetyltransferase domain) to the ELP3 N-terminal region and a strong match to the pfam04055 support identification of this family as radical SAM despite the atypical spacing between first and second Cys residues in the 4Fe4S-binding motif. [Unknown function, Enzymes of unknown specificity]
Pssm-ID: 130279 [Multi-domain] Cd Length: 302 Bit Score: 450.75 E-value: 4.79e-161
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
23-243
5.88e-37
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: 131.37 E-value: 5.88e-37
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of ...
208-290
1.29e-25
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of Radical_SAM domains. It is found in archaeal, bacterial, fungal, plant and human proteins.
Pssm-ID: 465061 [Multi-domain] Cd Length: 83 Bit Score: 97.47 E-value: 1.29e-25
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
44-191
7.79e-17
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: 76.41 E-value: 7.79e-17
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase ...
144-248
1.75e-11
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: 64.43 E-value: 1.75e-11
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
33-228
1.07e-07
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: 51.57 E-value: 1.07e-07
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA A37 methylthiotransferase MiaB is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440386 [Multi-domain] Cd Length: 435 Bit Score: 40.07 E-value: 1.44e-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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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