viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
6-291
2.01e-137
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery.
The actual alignment was detected with superfamily member NF038283:
Pssm-ID: 468450 [Multi-domain] Cd Length: 280 Bit Score: 389.99 E-value: 2.01e-137
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
6-291
2.01e-137
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery.
Pssm-ID: 468450 [Multi-domain] Cd Length: 280 Bit Score: 389.99 E-value: 2.01e-137
antiviral radical SAM protein viperin; Viperin (Virus Inhibitory Protein, ER-associated, ...
9-290
1.63e-25
antiviral radical SAM protein viperin; Viperin (Virus Inhibitory Protein, ER-associated, Iterferon-inducible) is a radical SAM enzyme found in human and other vertebrates. It is both induced by interferon and demonstrably active in blocking replication by several types of virus, apparently by modifying lipid chemistries in lipid droplets and membrane rafts.
Pssm-ID: 212001 Cd Length: 347 Bit Score: 104.04 E-value: 1.63e-25
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
8-132
7.40e-14
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: 68.01 E-value: 7.40e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
14-225
1.24e-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: 54.26 E-value: 1.24e-08
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
13-142
4.11e-08
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: 51.76 E-value: 4.11e-08
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
13-149
2.58e-05
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: 44.31 E-value: 2.58e-05
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
6-291
2.01e-137
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery.
Pssm-ID: 468450 [Multi-domain] Cd Length: 280 Bit Score: 389.99 E-value: 2.01e-137
antiviral radical SAM protein viperin; Viperin (Virus Inhibitory Protein, ER-associated, ...
9-290
1.63e-25
antiviral radical SAM protein viperin; Viperin (Virus Inhibitory Protein, ER-associated, Iterferon-inducible) is a radical SAM enzyme found in human and other vertebrates. It is both induced by interferon and demonstrably active in blocking replication by several types of virus, apparently by modifying lipid chemistries in lipid droplets and membrane rafts.
Pssm-ID: 212001 Cd Length: 347 Bit Score: 104.04 E-value: 1.63e-25
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
8-132
7.40e-14
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: 68.01 E-value: 7.40e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
14-225
1.24e-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: 54.26 E-value: 1.24e-08
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
13-142
4.11e-08
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: 51.76 E-value: 4.11e-08
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
13-149
2.58e-05
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: 44.31 E-value: 2.58e-05
radical SAM peptide maturase, CXXX-repeat target family; Members of this radical SAM domain ...
9-81
6.14e-04
radical SAM peptide maturase, CXXX-repeat target family; Members of this radical SAM domain protein are predicted peptide maturases, similar to PqqE, AlbA, the mycofactocin radical SAM maturase, and many others that share the peptide modification radical SAM protein C-terminal additional 4Fe4S-binding domain (TIGR04085). Members co-occur with a protein of unknown function that may be a chaperone or immunity protein and with a peptide that may have twelve or more cysteines occurring regularly spaced every fourth residue. These Cys residues tend to be flanked by residues with small side chains that provide minimal steric hindrance to crosslink formation by the radical SAM enzyme as in the subtilosin A system.
Pssm-ID: 200366 [Multi-domain] Cd Length: 359 Bit Score: 41.03 E-value: 6.14e-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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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