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
anaerobic sulfatase-maturating enzyme; Members of this protein family are radical SAM family ...
19-353
6.46e-20
anaerobic sulfatase-maturating enzyme; Members of this protein family are radical SAM family enzymes, maturases that prepare the oxygen-sensitive radical required in the active site of anaerobic sulfatases. This maturase role has led to many misleading legacy annotations suggesting that this enzyme maturase is instead a sulfatase regulatory protein. All members of the seed alignment are radical SAM enzymes encoded next to or near an anaerobic sulfatase. Note that a single genome may encode more than one sulfatase/maturase pair. [Protein fate, Protein modification and repair]
Pssm-ID: 188457 [Multi-domain] Cd Length: 363 Bit Score: 89.98 E-value: 6.46e-20
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
19-215
9.83e-15
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: 72.37 E-value: 9.83e-15
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
16-164
3.34e-06
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: 46.75 E-value: 3.34e-06
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide ...
11-333
1.75e-05
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide maturase most closely related to the darobactin maturase DarE.
Pssm-ID: 469197 [Multi-domain] Cd Length: 415 Bit Score: 46.42 E-value: 1.75e-05
anaerobic sulfatase-maturating enzyme; Members of this protein family are radical SAM family ...
19-353
6.46e-20
anaerobic sulfatase-maturating enzyme; Members of this protein family are radical SAM family enzymes, maturases that prepare the oxygen-sensitive radical required in the active site of anaerobic sulfatases. This maturase role has led to many misleading legacy annotations suggesting that this enzyme maturase is instead a sulfatase regulatory protein. All members of the seed alignment are radical SAM enzymes encoded next to or near an anaerobic sulfatase. Note that a single genome may encode more than one sulfatase/maturase pair. [Protein fate, Protein modification and repair]
Pssm-ID: 188457 [Multi-domain] Cd Length: 363 Bit Score: 89.98 E-value: 6.46e-20
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
19-215
9.83e-15
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: 72.37 E-value: 9.83e-15
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
12-160
1.32e-11
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: 62.23 E-value: 1.32e-11
radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055) ...
20-123
1.05e-10
radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055)/SPASM domain (TIGR04085) fusion subfamily distinct from PqqE, MftC, anaerobic sulfatase maturases, and other peptide maturases. The combined region described in this model can itself be fused to another domain, such as TIGR04267, or stand alone. Members occurring in the same cassette as a member of family TIGR04268 should be designated FxsB.
Pssm-ID: 275093 [Multi-domain] Cd Length: 363 Bit Score: 62.44 E-value: 1.05e-10
putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are ...
20-123
1.25e-08
putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are radical SAM enzymes, homologous to a variety of other peptide-modifying radical SAM, and found primarily in methanogenic archaea.
Pssm-ID: 274966 [Multi-domain] Cd Length: 376 Bit Score: 56.27 E-value: 1.25e-08
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
16-164
3.34e-06
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: 46.75 E-value: 3.34e-06
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide ...
11-333
1.75e-05
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide maturase most closely related to the darobactin maturase DarE.
Pssm-ID: 469197 [Multi-domain] Cd Length: 415 Bit Score: 46.42 E-value: 1.75e-05
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
10-69
1.05e-03
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the more distant in sequence.
Pssm-ID: 211974 [Multi-domain] Cd Length: 353 Bit Score: 40.59 E-value: 1.05e-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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Functional characterization of the conserved domain architecture found on the query.
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The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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