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Conserved domains on  [gi|430768618|ref|NP_001258914|]
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tRNA pseudouridine(38/39) synthase isoform 2 [Homo sapiens]

Protein Classification

pseudouridine synthase family protein( domain architecture ID 1007)

pseudouridine synthase family protein may catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PseudoU_synth super family cl00130
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to ...
 1-121 5.81e-75

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 cd02569:

Pssm-ID: 469624 [Multi-domain]  Cd Length: 256  Bit Score: 229.09  E-value: 5.81e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   1 MDYAAQKYVGTHDFRNLCKMDVANGVINFQRTILSAQVQLVGQSPgegrwqEPFQLCQFEVTGQAFLYHQVRCMMAILFL 80
Cdd:cd02569  142 MRKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVEPVDQHP------DGDGLYYFEVRGSAFLWHQVRCMMAVLFL 215

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 430768618  81 IGQGMEKPEIIDELLNIEKNPQKPQYSMAVEFPLVLYDCKF 121
Cdd:cd02569  216 IGQGLEPPSVISQLLDVEKNPRKPQYTMASEVPLVLYDCGF 256
 
Name Accession Description Interval E-value
PseudoU_synth_ScPus3 cd02569
Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like; This group consists of eukaryotic ...
 1-121 5.81e-75

Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like; This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya.


Pssm-ID: 211336 [Multi-domain]  Cd Length: 256  Bit Score: 229.09  E-value: 5.81e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   1 MDYAAQKYVGTHDFRNLCKMDVANGVINFQRTILSAQVQLVGQSPgegrwqEPFQLCQFEVTGQAFLYHQVRCMMAILFL 80
Cdd:cd02569  142 MRKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVEPVDQHP------DGDGLYYFEVRGSAFLWHQVRCMMAVLFL 215

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 430768618  81 IGQGMEKPEIIDELLNIEKNPQKPQYSMAVEFPLVLYDCKF 121
Cdd:cd02569  216 IGQGLEPPSVISQLLDVEKNPRKPQYTMASEVPLVLYDCGF 256
PseudoU_synth_1 pfam01416
tRNA pseudouridine synthase; Involved in the formation of pseudouridine at the anticodon stem ...
 4-122 4.39e-43

tRNA pseudouridine synthase; Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis.


Pssm-ID: 460204 [Multi-domain]  Cd Length: 108  Bit Score: 142.29  E-value: 4.39e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618    4 AAQKYVGTHDFRNLCKMDVANGviNFQRTILSAQVQLVGQSPGEgrwqepfqLCQFEVTGQAFLYHQVRCMMAILFLIGQ 83
Cdd:pfam01416   1 AAKLYVGTHDFGNFCKQDQPKK--NTVRTILEAAVSRVGGEDGD--------LIVFEVRGSGFLDHMVRAMVGVLFLVGQ 70

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 430768618   84 GMEKPEIIDELLNIEKnPQKPQYSMAVEFPLVLYDCKFE 122
Cdd:pfam01416  71 GKEPPEWIAELLNAKD-PRKIAGPTAPPVGLYLFHVRYP 108
hisT_truA TIGR00071
tRNA pseudouridine(38-40) synthase; Members of this family are the tRNA modification enzyme ...
 1-109 1.34e-19

tRNA pseudouridine(38-40) synthase; Members of this family are the tRNA modification enzyme TruA, tRNA pseudouridine(38-40) synthase. In a few species (e.g. Bacillus anthracis), TruA is represented by two paralogs. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272889 [Multi-domain]  Cd Length: 227  Bit Score: 84.67  E-value: 1.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618    1 MDYAAQKYVGTHDFRNLCKMDvaNGVINFQRTILSAQVQLVGQSpgegrwqepfqlCQFEVTGQAFLYHQVRCMMAILFL 80
Cdd:TIGR00071 128 MRAAAKQLLGKHDFSNFSKAK--SKSRSPIRTISDIKVSESGEY------------IIFDIIGNSFLWHMVRKIVGALVL 193

                          90       100
                  ....*....|....*....|....*....
gi 430768618   81 IGQGMEKPEIIDELLNIEKNPQKPQYSMA 109
Cdd:TIGR00071 194 VGRGKLPPEWVAKLLDAKKRNLAPTTAPA 222
TruA COG0101
tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]; ...
 1-95 7.85e-12

tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]; tRNA U38,U39,U40 pseudouridine synthase TruA is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439871 [Multi-domain]  Cd Length: 250  Bit Score: 63.58  E-value: 7.85e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   1 MDYAAQKYVGTHDFRNLCKmdVANGVINFQRTILSAQVQLVGQspgegrwqepfqLCQFEVTGQAFLYHQVRCMMAILFL 80
Cdd:COG0101  140 MNEAAQLLLGEHDFSSFRA--AGCQAKSTVRTIYRAEVEREGD------------LIVFEIEANGFLHNMVRNIVGTLVE 205

                         90
                 ....*....|....*
gi 430768618  81 IGQGMEKPEIIDELL 95
Cdd:COG0101  206 VGRGKLSPEWIKEIL 220
truA PRK00021
tRNA pseudouridine(38-40) synthase TruA;
1-96 8.85e-12

tRNA pseudouridine(38-40) synthase TruA;


Pssm-ID: 234577 [Multi-domain]  Cd Length: 244  Bit Score: 63.24  E-value: 8.85e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   1 MDYAAQKYVGTHDFRNLCKM--DVANGVinfqRTILSAqvqlvgqspgegRWQEPFQLCQFEVTGQAFLYHQVRCMMAIL 78
Cdd:PRK00021 140 MNEAAQYLLGEHDFTSFRASgcQSKSPV----RTIYEA------------DVTREGDFIVFDISANGFLHNMVRNIVGTL 203

                         90
                 ....*....|....*...
gi 430768618  79 FLIGQGMEKPEIIDELLN 96
Cdd:PRK00021 204 LEVGKGKRPPEDIKELLE 221
 
Name Accession Description Interval E-value
PseudoU_synth_ScPus3 cd02569
Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like; This group consists of eukaryotic ...
 1-121 5.81e-75

Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like; This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya.


Pssm-ID: 211336 [Multi-domain]  Cd Length: 256  Bit Score: 229.09  E-value: 5.81e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   1 MDYAAQKYVGTHDFRNLCKMDVANGVINFQRTILSAQVQLVGQSPgegrwqEPFQLCQFEVTGQAFLYHQVRCMMAILFL 80
Cdd:cd02569  142 MRKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVEPVDQHP------DGDGLYYFEVRGSAFLWHQVRCMMAVLFL 215

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 430768618  81 IGQGMEKPEIIDELLNIEKNPQKPQYSMAVEFPLVLYDCKF 121
Cdd:cd02569  216 IGQGLEPPSVISQLLDVEKNPRKPQYTMASEVPLVLYDCGF 256
PseudoU_synth_1 pfam01416
tRNA pseudouridine synthase; Involved in the formation of pseudouridine at the anticodon stem ...
 4-122 4.39e-43

tRNA pseudouridine synthase; Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis.


Pssm-ID: 460204 [Multi-domain]  Cd Length: 108  Bit Score: 142.29  E-value: 4.39e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618    4 AAQKYVGTHDFRNLCKMDVANGviNFQRTILSAQVQLVGQSPGEgrwqepfqLCQFEVTGQAFLYHQVRCMMAILFLIGQ 83
Cdd:pfam01416   1 AAKLYVGTHDFGNFCKQDQPKK--NTVRTILEAAVSRVGGEDGD--------LIVFEVRGSGFLDHMVRAMVGVLFLVGQ 70

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 430768618   84 GMEKPEIIDELLNIEKnPQKPQYSMAVEFPLVLYDCKFE 122
Cdd:pfam01416  71 GKEPPEWIAELLNAKD-PRKIAGPTAPPVGLYLFHVRYP 108
PseudoU_synth_TruA_like cd00497
Pseudouridine synthase, TruA family; This group consists of eukaryotic, bacterial and archeal ...
 1-121 1.87e-23

Pseudouridine synthase, TruA family; This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).


Pssm-ID: 211322 [Multi-domain]  Cd Length: 215  Bit Score: 94.76  E-value: 1.87e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   1 MDYAAQKYVGTHDFRNLCKMDVANGVinfqRTILSAQVQlvgqspgegrwqEPFQLCQFEVTGQAFLYHQVRCMMAILFL 80
Cdd:cd00497  113 LKSAASRFLGTHDFTNFSKKDTRNTV----RTIISIECK------------DLNPFVVVEFKAKSFLWHQVRRMVGFLML 176

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 430768618  81 IGQGMEKPEIIDELLNIEKNPQKpqYSMAVEFPLVLYDCKF 121
Cdd:cd00497  177 VGEGLHSPSSVSRLLAGPAPPIP--MVPAPAEGLLLVDVKY 215
hisT_truA TIGR00071
tRNA pseudouridine(38-40) synthase; Members of this family are the tRNA modification enzyme ...
 1-109 1.34e-19

tRNA pseudouridine(38-40) synthase; Members of this family are the tRNA modification enzyme TruA, tRNA pseudouridine(38-40) synthase. In a few species (e.g. Bacillus anthracis), TruA is represented by two paralogs. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272889 [Multi-domain]  Cd Length: 227  Bit Score: 84.67  E-value: 1.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618    1 MDYAAQKYVGTHDFRNLCKMDvaNGVINFQRTILSAQVQLVGQSpgegrwqepfqlCQFEVTGQAFLYHQVRCMMAILFL 80
Cdd:TIGR00071 128 MRAAAKQLLGKHDFSNFSKAK--SKSRSPIRTISDIKVSESGEY------------IIFDIIGNSFLWHMVRKIVGALVL 193

                          90       100
                  ....*....|....*....|....*....
gi 430768618   81 IGQGMEKPEIIDELLNIEKNPQKPQYSMA 109
Cdd:TIGR00071 194 VGRGKLPPEWVAKLLDAKKRNLAPTTAPA 222
PseudoU_synth_EcTruA cd02570
Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; This group consists ...
 1-96 5.97e-13

Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators.


Pssm-ID: 211337 [Multi-domain]  Cd Length: 239  Bit Score: 66.73  E-value: 5.97e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   1 MDYAAQKYVGTHDFRNLCKmdVANGVINFQRTILSAQVQlvgqsPGEGRWQepfqlcqFEVTGQAFLYHQVRCMMAILFL 80
Cdd:cd02570  135 MQEAAKLLLGTHDFSSFRA--AGCQSKSTVRTIYRADVY-----REGDLIV-------FEIRANGFLYHMVRNIVGTLLE 200

                         90
                 ....*....|....*.
gi 430768618  81 IGQGMEKPEIIDELLN 96
Cdd:cd02570  201 VGRGKLSPEDIKEILE 216
TruA COG0101
tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]; ...
 1-95 7.85e-12

tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]; tRNA U38,U39,U40 pseudouridine synthase TruA is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439871 [Multi-domain]  Cd Length: 250  Bit Score: 63.58  E-value: 7.85e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   1 MDYAAQKYVGTHDFRNLCKmdVANGVINFQRTILSAQVQLVGQspgegrwqepfqLCQFEVTGQAFLYHQVRCMMAILFL 80
Cdd:COG0101  140 MNEAAQLLLGEHDFSSFRA--AGCQAKSTVRTIYRAEVEREGD------------LIVFEIEANGFLHNMVRNIVGTLVE 205

                         90
                 ....*....|....*
gi 430768618  81 IGQGMEKPEIIDELL 95
Cdd:COG0101  206 VGRGKLSPEWIKEIL 220
truA PRK00021
tRNA pseudouridine(38-40) synthase TruA;
1-96 8.85e-12

tRNA pseudouridine(38-40) synthase TruA;


Pssm-ID: 234577 [Multi-domain]  Cd Length: 244  Bit Score: 63.24  E-value: 8.85e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   1 MDYAAQKYVGTHDFRNLCKM--DVANGVinfqRTILSAqvqlvgqspgegRWQEPFQLCQFEVTGQAFLYHQVRCMMAIL 78
Cdd:PRK00021 140 MNEAAQYLLGEHDFTSFRASgcQSKSPV----RTIYEA------------DVTREGDFIVFDISANGFLHNMVRNIVGTL 203

                         90
                 ....*....|....*...
gi 430768618  79 FLIGQGMEKPEIIDELLN 96
Cdd:PRK00021 204 LEVGKGKRPPEDIKELLE 221
PseudoU_synth_PUS1_PUS2 cd02568
Pseudouridine synthase, PUS1/ PUS2 like; This group consists of eukaryotic pseudouridine ...
 6-121 1.65e-08

Pseudouridine synthase, PUS1/ PUS2 like; This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).


Pssm-ID: 211335 [Multi-domain]  Cd Length: 245  Bit Score: 53.77  E-value: 1.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 430768618   6 QKYVGTHDFRNLCK----MDVANgvinfQRTILSAQVQLVGQSPGEgrwqepFQLCQFEVTGQAFLYHQVRCMMAILFLI 81
Cdd:cd02568  140 KEYVGTHNFHNFTVkkkfEDPSA-----NRFIKSFYVSEPFVIEEG------LEWISIKIHGQSFMLHQIRKMIGLAIAI 208

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 430768618  82 GQGMEKPEIIDELLNIEKNPQKPqysMAVEFPLVLYDCKF 121
Cdd:cd02568  209 VRGGAPESLIELSFNKDKIIIIP---LAPGLGLLLERPHF 245
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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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