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Conserved domains on  [gi|1196928224|ref|NP_001338665|]
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mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 3 [Homo sapiens]

Protein Classification

pseudouridine synthase family protein( domain architecture ID 10120734)

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

CATH:  3.30.2350.10
EC:  5.4.99.-
Gene Ontology:  GO:0003723|GO:0001522|GO:0009982
PubMed:  17113994|12756329|12762017

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 58-210 1.46e-27

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


:

Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 103.19  E-value: 1.46e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196928224  58 LVTLNKPQGLPVTGKPGELTLFSVLPEL-SQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPT 136
Cdd:cd02869     1 LLVVNKPAGLPVHPGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVK 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1196928224 137 ATYCAVTDGIPAASEGKIQAALKLEHIDGVnltvpvkapSRKDILEGVKKTLSHFRVVATGSGCALVQLQPLTG 210
Cdd:cd02869    77 KTYLALVDGKPPEDEGTIDAPLGRKKRKKR---------ARVVVSEDGKPAITHYKVLERFGNVTLVELQLETG 141
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 58-210 1.46e-27

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 103.19  E-value: 1.46e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196928224  58 LVTLNKPQGLPVTGKPGELTLFSVLPEL-SQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPT 136
Cdd:cd02869     1 LLVVNKPAGLPVHPGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVK 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1196928224 137 ATYCAVTDGIPAASEGKIQAALKLEHIDGVnltvpvkapSRKDILEGVKKTLSHFRVVATGSGCALVQLQPLTG 210
Cdd:cd02869    77 KTYLALVDGKPPEDEGTIDAPLGRKKRKKR---------ARVVVSEDGKPAITHYKVLERFGNVTLVELQLETG 141
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 58-210 6.95e-21

RNA pseudouridylate synthase; 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 RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.


Pssm-ID: 459961 [Multi-domain]  Cd Length: 151  Bit Score: 84.76  E-value: 6.95e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196928224  58 LVTLNKPQGLPVTGKPGELTLFSvLPELSQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPTA 137
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLS-LLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLF----PERKIEK 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1196928224 138 TYCAVTDgIPAASEGKIQAALKLEHidgvnltvpVKAPSRKDILEGVKKTLSHFRVVATGS--GCALVQLQPLTG 210
Cdd:pfam00849  76 EYLALVD-KPEEEEGTIKSPIKKEK---------NKSPFRKEEELGGKKAVTHLKVLKSGSkgDYSLLELELVTG 140
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 61-210 4.16e-12

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 62.85  E-value: 4.16e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196928224  61 LNKPQGLPVTGKPGEL--TLFSVLpelsqsLGLREQELQVVRAS-----GKESSGLVLLSSCPQTASRLQKYFtHARRAQ 133
Cdd:COG0564    11 VNKPAGLVVHPGSGGDdgTLVNAL------RAHLGELSGVPRPGlvhrlDRDTSGLLLVAKTRKAARRLSEQF-REREVE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1196928224 134 RptaTYCAVTDGIPAASEGKIQAALKLEHIDGVNLTVPVKAPsrkdilegvKKTLSHFRVVATGSGCALVQLQPLTG 210
Cdd:COG0564    84 K---RYLALVEGKPKEDEGTIDAPLGRDPKDRKKMAVVDEDG---------KPAVTHYRVLERFGGYSLVEVRLETG 148
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 58-210 1.46e-27

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 103.19  E-value: 1.46e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196928224  58 LVTLNKPQGLPVTGKPGELTLFSVLPEL-SQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPT 136
Cdd:cd02869     1 LLVVNKPAGLPVHPGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVK 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1196928224 137 ATYCAVTDGIPAASEGKIQAALKLEHIDGVnltvpvkapSRKDILEGVKKTLSHFRVVATGSGCALVQLQPLTG 210
Cdd:cd02869    77 KTYLALVDGKPPEDEGTIDAPLGRKKRKKR---------ARVVVSEDGKPAITHYKVLERFGNVTLVELQLETG 141
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 58-210 6.95e-21

RNA pseudouridylate synthase; 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 RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.


Pssm-ID: 459961 [Multi-domain]  Cd Length: 151  Bit Score: 84.76  E-value: 6.95e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196928224  58 LVTLNKPQGLPVTGKPGELTLFSvLPELSQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPTA 137
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLS-LLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLF----PERKIEK 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1196928224 138 TYCAVTDgIPAASEGKIQAALKLEHidgvnltvpVKAPSRKDILEGVKKTLSHFRVVATGS--GCALVQLQPLTG 210
Cdd:pfam00849  76 EYLALVD-KPEEEEGTIKSPIKKEK---------NKSPFRKEEELGGKKAVTHLKVLKSGSkgDYSLLELELVTG 140
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 61-210 4.16e-12

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 62.85  E-value: 4.16e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196928224  61 LNKPQGLPVTGKPGEL--TLFSVLpelsqsLGLREQELQVVRAS-----GKESSGLVLLSSCPQTASRLQKYFtHARRAQ 133
Cdd:COG0564    11 VNKPAGLVVHPGSGGDdgTLVNAL------RAHLGELSGVPRPGlvhrlDRDTSGLLLVAKTRKAARRLSEQF-REREVE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1196928224 134 RptaTYCAVTDGIPAASEGKIQAALKLEHIDGVNLTVPVKAPsrkdilegvKKTLSHFRVVATGSGCALVQLQPLTG 210
Cdd:COG0564    84 K---RYLALVEGKPKEDEGTIDAPLGRDPKDRKKMAVVDEDG---------KPAVTHYRVLERFGGYSLVEVRLETG 148
 
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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