anaerobic sulfatase-maturating enzyme; Members of this protein family are radical SAM family ...
12-392
3.63e-172
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]
The actual alignment was detected with superfamily member TIGR03942:
Pssm-ID: 188457 [Multi-domain] Cd Length: 363 Bit Score: 485.96 E-value: 3.63e-172
anaerobic sulfatase-maturating enzyme; Members of this protein family are radical SAM family ...
12-392
3.63e-172
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: 485.96 E-value: 3.63e-172
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide ...
1-384
5.53e-53
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: 182.39 E-value: 5.53e-53
Iron-sulfur cluster-binding SPASM domain of anaerobic sulfatase maturating enzyme; Anaerobic sulfatase maturating enzyme (anSME) is a radical S-adenosylmethionine (SAM) enzyme that catalyzes, under anaerobic conditions, the co- or post-translational modification of arylsulfatases to form a catalytically essential formylglycine (FGly) residue to perform their hydrolysis function, removing sulfate groups from a wide array of substrates. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster; anSME contains two auxillary 4Fe-4S clusters in its SPASM domain.
Pssm-ID: 410611 [Multi-domain] Cd Length: 107 Bit Score: 155.90 E-value: 1.26e-46
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
22-173
3.55e-16
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: 75.64 E-value: 3.55e-16
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
21-131
4.34e-07
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: 51.01 E-value: 4.34e-07
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
10-163
5.07e-04
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: 41.23 E-value: 5.07e-04
anaerobic sulfatase-maturating enzyme; Members of this protein family are radical SAM family ...
12-392
3.63e-172
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: 485.96 E-value: 3.63e-172
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide ...
1-384
5.53e-53
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: 182.39 E-value: 5.53e-53
Iron-sulfur cluster-binding SPASM domain of anaerobic sulfatase maturating enzyme; Anaerobic sulfatase maturating enzyme (anSME) is a radical S-adenosylmethionine (SAM) enzyme that catalyzes, under anaerobic conditions, the co- or post-translational modification of arylsulfatases to form a catalytically essential formylglycine (FGly) residue to perform their hydrolysis function, removing sulfate groups from a wide array of substrates. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster; anSME contains two auxillary 4Fe-4S clusters in its SPASM domain.
Pssm-ID: 410611 [Multi-domain] Cd Length: 107 Bit Score: 155.90 E-value: 1.26e-46
radical SAM/SPASM domain protein, GRRM system; Members of this protein family are radical SAM ...
22-190
5.17e-42
radical SAM/SPASM domain protein, GRRM system; Members of this protein family are radical SAM/SPASM domain proteins (see pfam04055 and TIGR04085) related to anaeroboic sulfatase maturating enzymes and the peptide modification enzyme PqqE. Members are found primarily in Cyanobacteria adjacent to a short protein, ~150 residues, in which the last ~60 residues tends to be repetitive and highly glycine-rich (see TIGR04260). The arrangement suggests modifications to the repetitive C-terminal region by this radical SAM domain enzyme, but the purpose of this system on the whole is unknown.
Pssm-ID: 211984 [Multi-domain] Cd Length: 363 Bit Score: 151.73 E-value: 5.17e-42
putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are ...
22-366
1.23e-27
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: 112.90 E-value: 1.23e-27
radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055) ...
22-385
2.10e-27
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: 112.13 E-value: 2.10e-27
radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding ...
288-375
5.26e-22
radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by model pfam04055. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulfatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. We name this domain SPASM for Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin.
Pssm-ID: 274968 [Multi-domain] Cd Length: 93 Bit Score: 89.94 E-value: 5.26e-22
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
21-184
4.56e-21
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: 89.19 E-value: 4.56e-21
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
22-173
3.55e-16
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: 75.64 E-value: 3.55e-16
radical SAM peptide maturase, CXXX-repeat target family; Members of this radical SAM domain ...
22-353
5.41e-11
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: 63.75 E-value: 5.41e-11
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
17-169
6.54e-11
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: 61.58 E-value: 6.54e-11
putative geopeptide radical SAM maturase; This family is the radical SAM/SPASM domain putative ...
2-364
1.29e-10
putative geopeptide radical SAM maturase; This family is the radical SAM/SPASM domain putative peptide maturase for geopeptide, described by model TIGR04229. The SPASM domain (see model TIGR04085) frequently marks peptide-modifying radical SAM enzymes.
Pssm-ID: 275100 [Multi-domain] Cd Length: 428 Bit Score: 62.80 E-value: 1.29e-10
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
10-193
2.16e-09
SynChlorMet cassette radical SAM/SPASM protein ScmE; 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 closer in sequence.
Pssm-ID: 211973 [Multi-domain] Cd Length: 358 Bit Score: 58.71 E-value: 2.16e-09
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
21-131
4.34e-07
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: 51.01 E-value: 4.34e-07
Iron-sulfur cluster-binding SPASM domain of antilisterial bacteriocin subtilosin biosynthesis ...
288-357
1.93e-06
Iron-sulfur cluster-binding SPASM domain of antilisterial bacteriocin subtilosin biosynthesis protein AlbA and similar proteins; Bacillus subtilis antilisterial bacteriocin subtilosin biosynthesis protein AlbA is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of three thioether bonds in the post-translational modification of a linear peptide into the cyclic peptide subtilosin A. The thioether bonds formed are between the sulfur of three cysteine residues and the alpha-carbons of two phenylalanines and one threonine to produce a rigid cyclic peptide. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. AlbA appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN.
Pssm-ID: 410616 [Multi-domain] Cd Length: 97 Bit Score: 45.94 E-value: 1.93e-06
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur ...
292-348
3.37e-06
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, pfam04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin.
Pssm-ID: 433020 [Multi-domain] Cd Length: 66 Bit Score: 44.39 E-value: 3.37e-06
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
22-199
1.26e-05
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: 47.14 E-value: 1.26e-05
Iron-sulfur cluster-binding SPASM domain of sactionine bond-forming enzyme CteB and similar ...
288-367
2.59e-04
Iron-sulfur cluster-binding SPASM domain of sactionine bond-forming enzyme CteB and similar proteins; Clostridium thermocellum sactionine bond-forming enzyme CteB is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of the requisite thioether bridge between a cysteine and the alpha-carbon of an opposing amino acid that is required in sactipeptide biosynthesis. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. CteB contains two auxillary 4Fe-4S clusters in its SPASM domain; the auxillary cluster nearest the RS site, called AuxI, exhibits an open coordination site in the absence of peptide substrate, which is coordinated by a peptidyl-cysteine residue in the bound state.
Pssm-ID: 410615 [Multi-domain] Cd Length: 96 Bit Score: 40.03 E-value: 2.59e-04
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
10-163
5.07e-04
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: 41.23 E-value: 5.07e-04
Iron-sulfur cluster-binding SPASM domain; This iron-sulfur cluster-binding domain is named ...
297-347
1.14e-03
Iron-sulfur cluster-binding SPASM domain; This iron-sulfur cluster-binding domain is named SPASM after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. SPASM occurs as an additional C-terminal domain in many peptide-modifying enzymes of the radical S-adenosylmethionine (SAM) superfamily. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster.
Pssm-ID: 410609 [Multi-domain] Cd Length: 65 Bit Score: 37.02 E-value: 1.14e-03
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar ...
288-355
2.64e-03
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar proteins; This group is composed of Mycobacterium tuberculosis putative mycofactocin radical SAM maturase MftC and similar proteins. MftC is a radical S-adenosylmethionine (SAM) enzyme that may function to modify mycofactocin, a conserved polypeptide that might serve as an electron carrier. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster that is similar to the second auxillary 4Fe-4S cluster (AuxII) of Clostridium perfringens anaerobic sulfatase-maturating enzyme (anSME).
Pssm-ID: 410614 [Multi-domain] Cd Length: 91 Bit Score: 36.85 E-value: 2.64e-03
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
21-117
3.00e-03
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: 39.02 E-value: 3.00e-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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