Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to ...
37-264
1.75e-96
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
The actual alignment was detected with superfamily member cd02867:
Pssm-ID: 469624 [Multi-domain] Cd Length: 312 Bit Score: 286.64 E-value: 1.75e-96
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
37-264
1.75e-96
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Pssm-ID: 211344 [Multi-domain] Cd Length: 312 Bit Score: 286.64 E-value: 1.75e-96
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
49-251
9.25e-83
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal structure and biogenesis]; tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 439900 [Multi-domain] Cd Length: 288 Bit Score: 250.74 E-value: 9.25e-83
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
45-194
4.47e-67
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.
Pssm-ID: 426297 Cd Length: 148 Bit Score: 205.79 E-value: 4.47e-67
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to ...
45-226
2.82e-59
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop of most tRNAs in all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific functions. The trusted cutoff is set above the scores for the archaeal homologs of unknown function, so yeast Pus4p scores between trusted and noise. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 129523 Cd Length: 209 Bit Score: 187.96 E-value: 2.82e-59
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
37-264
1.75e-96
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Pssm-ID: 211344 [Multi-domain] Cd Length: 312 Bit Score: 286.64 E-value: 1.75e-96
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
49-251
9.25e-83
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal structure and biogenesis]; tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 439900 [Multi-domain] Cd Length: 288 Bit Score: 250.74 E-value: 9.25e-83
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
45-241
7.70e-75
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Pssm-ID: 211339 [Multi-domain] Cd Length: 213 Bit Score: 227.71 E-value: 7.70e-75
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal ...
37-234
9.25e-74
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dyskerin cause X-linked dyskeratosis congenitas.
Pssm-ID: 211323 [Multi-domain] Cd Length: 210 Bit Score: 225.11 E-value: 9.25e-74
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
45-194
4.47e-67
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.
Pssm-ID: 426297 Cd Length: 148 Bit Score: 205.79 E-value: 4.47e-67
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to ...
45-226
2.82e-59
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop of most tRNAs in all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific functions. The trusted cutoff is set above the scores for the archaeal homologs of unknown function, so yeast Pus4p scores between trusted and noise. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 129523 Cd Length: 209 Bit Score: 187.96 E-value: 2.82e-59
Pseudouridine synthase, humanTRUB2_like; This group consists of eukaryotic pseudouridine ...
59-243
8.68e-31
Pseudouridine synthase, humanTRUB2_like; This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Pssm-ID: 211345 [Multi-domain] Cd Length: 226 Bit Score: 114.79 E-value: 8.68e-31
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
43-223
7.02e-27
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl results in miniflies that suffer abnormalities.
Pssm-ID: 211338 Cd Length: 182 Bit Score: 103.50 E-value: 7.02e-27
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset ...
195-254
7.84e-05
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset of TruB_B protein family members pfam01509. It is found from bacteria and archaea to fungi, plants and human.
Pssm-ID: 465060 [Multi-domain] Cd Length: 65 Bit Score: 39.77 E-value: 7.84e-05
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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