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Conserved domains on  [gi|594190961|ref|NP_001277424|]
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pseudouridylate synthase TRUB2, mitochondrial isoform b [Mus musculus]

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 ...
 9-165 4.21e-88

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 cd02868:

Pssm-ID: 469624 [Multi-domain]  Cd Length: 226  Bit Score: 258.85  E-value: 4.21e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961   9 DYTVRGLLGKATDNFCEDGRLIEKTTYDHVTRERLDRILAVIQGSHQ-KALVMYSNLDLkSQEAYEMAVQGVIRPMNKSP 87
Cdd:cd02868   70 VYTIRGLLGKATENFFHTGRVIEKTTYDHITREKIERLLAVIQSGHQqKAFELCSVDDQ-SQQAAELAARGLIRPADKSP 148

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 594190961  88 MLISGIRCLHFAPPEFLLEVQCMHETQQQLRKLVHEIGLELKTSAVCTQVRRTRDGFFGLDDALLRTQWDLHNIQDAI 165
Cdd:cd02868  149 PIIYGIRLLEFRPPEFTLEVQCINETQEYLRKLIHEIGLELRSSAVCTQVRRTRDGPFTVDDALLRKQWNLQNIISNI 226
 
Name Accession Description Interval E-value
PseudoU_synth_hTruB2_like cd02868
Pseudouridine synthase, humanTRUB2_like; This group consists of eukaryotic pseudouridine ...
 9-165 4.21e-88

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: 258.85  E-value: 4.21e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961   9 DYTVRGLLGKATDNFCEDGRLIEKTTYDHVTRERLDRILAVIQGSHQ-KALVMYSNLDLkSQEAYEMAVQGVIRPMNKSP 87
Cdd:cd02868   70 VYTIRGLLGKATENFFHTGRVIEKTTYDHITREKIERLLAVIQSGHQqKAFELCSVDDQ-SQQAAELAARGLIRPADKSP 148

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 594190961  88 MLISGIRCLHFAPPEFLLEVQCMHETQQQLRKLVHEIGLELKTSAVCTQVRRTRDGFFGLDDALLRTQWDLHNIQDAI 165
Cdd:cd02868  149 PIIYGIRLLEFRPPEFTLEVQCINETQEYLRKLIHEIGLELRSSAVCTQVRRTRDGPFTVDDALLRKQWNLQNIISNI 226
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 10-109 1.29e-20

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: 84.07  E-value: 1.29e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961   10 YTVRGLLGKATDNFCEDGRLIEkTTYDHVTRERLDRILAVIQGSHQKALVMYSNLDLKSQEAYEMAVQGVIRPMNKSPML 89
Cdd:pfam01509  44 YVATIRLGVATDTLDAEGEIVE-ESVDHITEEKIEEVLASFTGEIEQVPPMYSAVKVNGKRLYELAREGIEVERPPRPVT 122

                          90       100
                  ....*....|....*....|
gi 594190961   90 ISGIRCLHFAPPEFLLEVQC 109
Cdd:pfam01509 123 IYSLELLEFDLPEVTFRVTC 142
truB PRK02193
tRNA pseudouridine synthase B; Provisional
 10-145 7.86e-11

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 179381 [Multi-domain]  Cd Length: 279  Bit Score: 60.15  E-value: 7.86e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961  10 YTVRGLLGKATDNFCEDGRLIEKTTYDHVTRERLDRILAVIQGSHQKALVMYSNLDLKSQEAYEMAVQGVIRPMNKSPML 89
Cdd:PRK02193  64 YIAKIKFGFISTTYDSEGQIINVSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKVNGKRAYDLARQGKQIELKPIEIK 143

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 594190961  90 ISGIRCLHFAPPEFLLEVQCMHETQQQLRKLVHEIGLELKTSAVCTQVRRTRDGFF 145
Cdd:PRK02193 144 ISKIELLNFDEKLQNCVFMWVVSRGTYIRSLIHDLGKMLKTGAYMSDLERTKIGNL 199
 
Name Accession Description Interval E-value
PseudoU_synth_hTruB2_like cd02868
Pseudouridine synthase, humanTRUB2_like; This group consists of eukaryotic pseudouridine ...
 9-165 4.21e-88

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: 258.85  E-value: 4.21e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961   9 DYTVRGLLGKATDNFCEDGRLIEKTTYDHVTRERLDRILAVIQGSHQ-KALVMYSNLDLkSQEAYEMAVQGVIRPMNKSP 87
Cdd:cd02868   70 VYTIRGLLGKATENFFHTGRVIEKTTYDHITREKIERLLAVIQSGHQqKAFELCSVDDQ-SQQAAELAARGLIRPADKSP 148

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 594190961  88 MLISGIRCLHFAPPEFLLEVQCMHETQQQLRKLVHEIGLELKTSAVCTQVRRTRDGFFGLDDALLRTQWDLHNIQDAI 165
Cdd:cd02868  149 PIIYGIRLLEFRPPEFTLEVQCINETQEYLRKLIHEIGLELRSSAVCTQVRRTRDGPFTVDDALLRKQWNLQNIISNI 226
PseudoU_synth_TruB_like cd00506
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal ...
 9-156 5.09e-46

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: 151.54  E-value: 5.09e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961   9 DYTVRGLLGKATDNFCEDGRLIEKTTYDHVTRERLDRILAVIQGSHQKALVMYSNLDLKSQEAYEMAVQGVIRPMNKSPM 88
Cdd:cd00506   63 DYTAIGRLGQATDTFDATGQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKRQGQRAYELARRGLLVPDEARPP 142

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 594190961  89 LISGIRCLHFAPPEFLLEVQCMHETQQQLRKLVHEIGLELKTSAVCTQVRRTRDGFFGLDDALLRTQW 156
Cdd:cd00506  143 TIYELLCIRFNPPHFLLEVEVVCETGTYIRTLIHDLGLELGVGAHVTELRRTRVGPFKVENAVTLHHL 210
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 10-109 1.29e-20

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: 84.07  E-value: 1.29e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961   10 YTVRGLLGKATDNFCEDGRLIEkTTYDHVTRERLDRILAVIQGSHQKALVMYSNLDLKSQEAYEMAVQGVIRPMNKSPML 89
Cdd:pfam01509  44 YVATIRLGVATDTLDAEGEIVE-ESVDHITEEKIEEVLASFTGEIEQVPPMYSAVKVNGKRLYELAREGIEVERPPRPVT 122

                          90       100
                  ....*....|....*....|
gi 594190961   90 ISGIRCLHFAPPEFLLEVQC 109
Cdd:pfam01509 123 IYSLELLEFDLPEVTFRVTC 142
PseudoU_synth_EcTruB cd02573
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
 10-151 1.49e-13

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: 66.70  E-value: 1.49e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961  10 YTVRGLLGKATDNFCEDGRLIEKTTYDHVTRERLDRILAVIQGSHQKALVMYSNLDLKSQEAYEMAVQGVIRPMNKSPML 89
Cdd:cd02573   64 YRATVRLGEATDTDDAEGEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKVDGKRLYELARAGEEVERPPRKVT 143

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 594190961  90 ISGIRCLHFAP--PEFLLEVQCMHETqqQLRKLVHEIGLELKTSAVCTQVRRTRDGFFGLDDAL 151
Cdd:cd02573  144 IYSLELLSFDPenPEADFEVHCSKGT--YIRSLARDLGKALGCGAHLSALRRTRSGPFTLEQAI 205
truB PRK02193
tRNA pseudouridine synthase B; Provisional
 10-145 7.86e-11

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 179381 [Multi-domain]  Cd Length: 279  Bit Score: 60.15  E-value: 7.86e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961  10 YTVRGLLGKATDNFCEDGRLIEKTTYDHVTRERLDRILAVIQGSHQKALVMYSNLDLKSQEAYEMAVQGVIRPMNKSPML 89
Cdd:PRK02193  64 YIAKIKFGFISTTYDSEGQIINVSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKVNGKRAYDLARQGKQIELKPIEIK 143

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 594190961  90 ISGIRCLHFAPPEFLLEVQCMHETQQQLRKLVHEIGLELKTSAVCTQVRRTRDGFF 145
Cdd:PRK02193 144 ISKIELLNFDEKLQNCVFMWVVSRGTYIRSLIHDLGKMLKTGAYMSDLERTKIGNL 199
PseudoU_synth_TruB_4 cd02867
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
 10-154 1.68e-09

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: 56.29  E-value: 1.68e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961  10 YTVRGLLGKATDNFCEDGRLIEKTTYDHVTRERLDRILAVIQGSHQKALVMYSNLDLKSQEAYEMAVQG--VIRPMNKSP 87
Cdd:cd02867   93 YEATGLFGASTTTYDREGKILKKKPYSHITREDIEEVLAKFRGDIKQVPPLYSALKMDGKRLYEYAREGkpLPRPIERRQ 172

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 594190961  88 MLISGIRcLHFAP---PEFLLEVQCmhETQQQLRKLVHEIGLELKTSAVCTQVRRTRDGFFGLDDALLRT 154
Cdd:cd02867  173 VVVSELL-VKDWIepgPLFTRTVEE--EGKQYERSVVKMLGKELKTFAEVTELTATAEGDPVEEVEATHE 239
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
104-165 3.48e-04

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 40.61  E-value: 3.48e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 594190961 104 LLEVQCmhETQQQLRKLVHEIGLELKTSAVCTQVRRTRDGFFglDDALLRTqwdLHNIQDAI 165
Cdd:PRK04270 145 LFRVRC--ESGTYIRKLCHDIGLALGTGAHMQELRRTRTGPF--TEEDLVT---LQDLADAY 199
TruB_C_2 pfam16198
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset ...
 118-178 9.26e-04

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: 36.30  E-value: 9.26e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 594190961  118 RKLVHEIGLELKTSAVCTQVRRTRDGFFGLDDAllrtqWDLHNIQDAIQAAAPRVAAELQK 178
Cdd:pfam16198   1 RTLCEDIGEALGCGAHMAELRRTRVGPFDEADM-----VTLHDLLDAYLLYKEGDESYLRR 56
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 104-164 1.73e-03

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: 38.01  E-value: 1.73e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 594190961 104 LLEVQCmhETQQQLRKLVHEIGLELKTSAVCTQVRRTRDGFFGLDDALLrtqwDLHNIQDA 164
Cdd:cd02572  127 LFRVSC--EAGTYIRTLCVHIGLLLGVGAHMQELRRTRSGPFSEEDNMV----TLHDVLDA 181
 
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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