MiaB/RimO family radical SAM methylthiotransferase similar to ribosomal protein S12 methylthiotransferase RimO, which catalyzes the methylthiolation of the residue Asp-89 of ribosomal protein S12, and tRNA-i(6)A37 methylthiotransferase (MiaB), which catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A) at position 37 in tRNAs
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: 535.43 E-value: 0e+00
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: 535.43 E-value: 0e+00
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
101-571
1.11e-147
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.
Pssm-ID: 272900 [Multi-domain] Cd Length: 429 Bit Score: 432.44 E-value: 1.11e-147
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
248-487
8.71e-47
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: 163.34 E-value: 8.71e-47
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
101-204
9.45e-39
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.
Pssm-ID: 459997 [Multi-domain] Cd Length: 98 Bit Score: 137.26 E-value: 9.45e-39
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: 535.43 E-value: 0e+00
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
101-571
1.11e-147
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.
Pssm-ID: 272900 [Multi-domain] Cd Length: 429 Bit Score: 432.44 E-value: 1.11e-147
tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents ...
101-574
1.14e-138
tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents homologs of the MiaB enzyme responsible for the modification of the isopentenylated adenine-37 base of most bacterial and eukaryotic tRNAs that read codons beginning with uracil (all except tRNA(I,V) Ser). Adenine-37 is next to the anticodon on the 3' side in these tRNA's, and lack of modification at this site leads to an increased spontaneous mutation frequency. Isopentenylated A-37 is modified by methylthiolation at position 2, either by MiaB alone or in concert with a separate methylase yet to be discovered (MiaC?). MiaB contains a 4Fe-4S cluster which is labile under oxidizing conditions. Additionally, the sequence is homologous (via PSI-BLAST searches) to the biotin synthetase, BioB, which utilizes both an iron-sulfur cluster and S-adenosym methionine (SAM) to generate a radical which is responsible for initiating the insertion of sulfur into the substrate. It is reasonable to surmise that the methyl group of SAM becomes the methyl group of the product, but this has not been shown, and the possibility of a separate methylase exists. This equivalog is a member of a subfamily (TIGR00089) which contains several other hypothetical equivalogs which are all probably enzymes with similar function acting on different substrates. These enzymes contain a TRAM domain (pfam01938) which is believed to be responsible for binding to tRNAs. Hits to this model span all major groups of bacteria and eukaryotes, but not archaea, which are known to lack this particular tRNA modification. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterized and shown to complement the E. coli MiaB enzyme. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 273700 [Multi-domain] Cd Length: 438 Bit Score: 409.97 E-value: 1.14e-138
MiaB-like tRNA modifying enzyme; This clade of sequences is closely related to MiaB, a ...
104-550
2.19e-72
MiaB-like tRNA modifying enzyme; This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans low GC Gram positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 273704 [Multi-domain] Cd Length: 414 Bit Score: 238.04 E-value: 2.19e-72
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to ...
101-574
1.13e-63
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by this model as well as ones falling within the scope of the MiaB equivalog model. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 273703 [Multi-domain] Cd Length: 420 Bit Score: 215.03 E-value: 1.13e-63
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
248-487
8.71e-47
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: 163.34 E-value: 8.71e-47
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
101-204
9.45e-39
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.
Pssm-ID: 459997 [Multi-domain] Cd Length: 98 Bit Score: 137.26 E-value: 9.45e-39
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
254-443
5.71e-21
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: 89.89 E-value: 5.71e-21
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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