ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the ...
11-441
0e+00
ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the methylthiotransferase RimO, which modifies a conserved Asp residue in ribosomal protein S12. This clade of radical SAM family proteins is closely related to the tRNA modification bifunctional enzyme MiaB (see TIGR01574), and it catalyzes the same two types of reactions: a radical-mechanism sulfur insertion, and a methylation of the inserted sulfur. This clade spans alpha and gamma proteobacteria, cyano bacteria, Deinococcus, Porphyromonas, Aquifex, Helicobacter, Campylobacter, Thermotoga, Chlamydia, Streptococcus coelicolor and Clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes. [Protein synthesis, Ribosomal proteins: synthesis and modification]
The actual alignment was detected with superfamily member TIGR01125:
Pssm-ID: 273453 [Multi-domain] Cd Length: 426 Bit Score: 582.86 E-value: 0e+00
ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the ...
11-441
0e+00
ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the methylthiotransferase RimO, which modifies a conserved Asp residue in ribosomal protein S12. This clade of radical SAM family proteins is closely related to the tRNA modification bifunctional enzyme MiaB (see TIGR01574), and it catalyzes the same two types of reactions: a radical-mechanism sulfur insertion, and a methylation of the inserted sulfur. This clade spans alpha and gamma proteobacteria, cyano bacteria, Deinococcus, Porphyromonas, Aquifex, Helicobacter, Campylobacter, Thermotoga, Chlamydia, Streptococcus coelicolor and Clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273453 [Multi-domain] Cd Length: 426 Bit Score: 582.86 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: 552.77 E-value: 0e+00
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
143-366
1.27e-49
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: 167.96 E-value: 1.27e-49
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
11-104
2.61e-27
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: 104.52 E-value: 2.61e-27
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
147-359
1.61e-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: 63.51 E-value: 1.61e-11
ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the ...
11-441
0e+00
ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the methylthiotransferase RimO, which modifies a conserved Asp residue in ribosomal protein S12. This clade of radical SAM family proteins is closely related to the tRNA modification bifunctional enzyme MiaB (see TIGR01574), and it catalyzes the same two types of reactions: a radical-mechanism sulfur insertion, and a methylation of the inserted sulfur. This clade spans alpha and gamma proteobacteria, cyano bacteria, Deinococcus, Porphyromonas, Aquifex, Helicobacter, Campylobacter, Thermotoga, Chlamydia, Streptococcus coelicolor and Clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273453 [Multi-domain] Cd Length: 426 Bit Score: 582.86 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: 552.77 E-value: 0e+00
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
11-442
1.08e-123
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: 366.18 E-value: 1.08e-123
MiaB-like tRNA modifying enzyme; This clade of sequences is closely related to MiaB, a ...
14-423
9.82e-66
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: 216.47 E-value: 9.82e-66
tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents ...
11-393
2.47e-64
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: 213.52 E-value: 2.47e-64
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to ...
11-445
3.83e-54
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: 186.14 E-value: 3.83e-54
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
143-366
1.27e-49
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: 167.96 E-value: 1.27e-49
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
11-104
2.61e-27
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: 104.52 E-value: 2.61e-27
TRAM domain; This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) ...
383-445
2.20e-26
TRAM domain; This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) domain found in the methylthiotransferases RimO enzymes that catalyze the conversion of aspartate to 2-methylthio-aspartate (msD) in the S12 protein near the decoding center in prokaryotic ribosomes. The TRAM domain in RimO, contains five anti-parallel beta-strands and docks on the surface of the Radical-SAM domain at the distal edge of its open TIM-barrel from its conserved [4Fe-4S] cluster.
Pssm-ID: 465832 [Multi-domain] Cd Length: 63 Bit Score: 101.00 E-value: 2.20e-26
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
149-320
1.21e-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: 79.88 E-value: 1.21e-17
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
147-359
1.61e-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: 63.51 E-value: 1.61e-11
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.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
where hash marks (#) above the aligned sequences show the location of the conserved feature residues.
The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
Click here to see more details.
This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
(labeled illustration) or all hits
(labeled illustration).
Domains are color coded according to superfamilies
to which they have been assigned. Hits with scores that pass a domain-specific threshold
(specific hits) are drawn in bright colors.
Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
with the same color and shade of the domain or superfamily that provides the annotation. Mouse over the colored bars or triangles to see descriptions of the domains and features.
click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
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.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
mapped to the query sequence.
Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
(CDART).
Modify your query to search against a different database and/or use advanced search options
