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Conserved domains on  [gi|2046363465|ref|NP_001136019|]
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mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 2 [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 ...
 80-252 1.28e-26

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: 103.57  E-value: 1.28e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465  80 GKPGELTLFSVLPEL-SQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPTATYCAVTDGIPAA 158
Cdd:cd02869    14 PGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVKKTYLALVDGKPPE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465 159 SEGKIQAALKLEHIDGVnltvpvkapSRKDILEGVKKTLSHFRVVATGSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGD 238
Cdd:cd02869    90 DEGTIDAPLGRKKRKKR---------ARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160

                         170
                  ....*....|....
gi 2046363465 239 HMYSARVGTVLGQR 252
Cdd:cd02869   161 PKYGGKASDSPGLK 174
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 80-252 1.28e-26

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: 103.57  E-value: 1.28e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465  80 GKPGELTLFSVLPEL-SQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPTATYCAVTDGIPAA 158
Cdd:cd02869    14 PGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVKKTYLALVDGKPPE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465 159 SEGKIQAALKLEHIDGVnltvpvkapSRKDILEGVKKTLSHFRVVATGSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGD 238
Cdd:cd02869    90 DEGTIDAPLGRKKRKKR---------ARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160

                         170
                  ....*....|....
gi 2046363465 239 HMYSARVGTVLGQR 252
Cdd:cd02869   161 PKYGGKASDSPGLK 174
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 82-228 3.72e-16

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: 74.36  E-value: 3.72e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465  82 PGELTLFSVLPELSQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPTATYCAVTDgIPAASEG 161
Cdd:pfam00849  15 TDSLTKLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLF----PERKIEKEYLALVD-KPEEEEG 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2046363465 162 KIQAALKLEHidgvnltvpVKAPSRKDILEGVKKTLSHFRVVATGS--GCALVQLQPLTVFSSQLQVHM 228
Cdd:pfam00849  90 TIKSPIKKEK---------NKSPFRKEEELGGKKAVTHLKVLKSGSkgDYSLLELELVTGRKHQIRAHL 149
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
 112-323 1.94e-07

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 51.55  E-value: 1.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465 112 GKESSGLVLLSSCPQTASRLQKYFtHARRAQRptaTYCAVTDGIPAASEGKIQAALKLehiDGVNLTVPVKAPSrkdilE 191
Cdd:TIGR00005 127 DRDTSGLMVVAKTPLALRELQRQL-KNRTVTK---EYVALVHGQFDSGGGTVDAPLGR---VPNNRGLMAVHPS-----S 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465 192 GVKKTLSHFRVVATGSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGDHMYSARvgTVLGQrflLPAENNKPQRQVLDEAL 271
Cdd:TIGR00005 195 EGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQYLGHPLAGDPLYGNK--PVPGN---NLNGLLNFDRQALHAYE 269

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2046363465 272 LRRLHLTPSQaaqlplhlhlhrlllpgtrardtPVELLAPLPPYFSRTLQCL 323
Cdd:TIGR00005 270 LGFIHPATGE-----------------------ILEFEAPLPADLVLLLEAL 298
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
115-258 2.64e-06

bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 47.68  E-value: 2.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465 115 SSGLVLLSSCPQTASRLQKYFtharRAQRPTATYCAVTDGIPAASEGKIQAALKlehIDGVNltvpvkAPSRKDILEGVK 194
Cdd:PRK10158   67 TSGVIVVALTKAAERELKRQF----REREPKKQYVARVWGHPSPAEGLVDLPLI---CDWPN------RPKQKVCYETGK 133

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2046363465 195 KTLSHFRVVATGS-GCALVQLQPLTVFSSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAE 258
Cdd:PRK10158  134 PAQTEYEVVEYAAdNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAE 198
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 80-252 1.28e-26

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: 103.57  E-value: 1.28e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465  80 GKPGELTLFSVLPEL-SQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPTATYCAVTDGIPAA 158
Cdd:cd02869    14 PGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVKKTYLALVDGKPPE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465 159 SEGKIQAALKLEHIDGVnltvpvkapSRKDILEGVKKTLSHFRVVATGSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGD 238
Cdd:cd02869    90 DEGTIDAPLGRKKRKKR---------ARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160

                         170
                  ....*....|....
gi 2046363465 239 HMYSARVGTVLGQR 252
Cdd:cd02869   161 PKYGGKASDSPGLK 174
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 82-228 3.72e-16

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: 74.36  E-value: 3.72e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465  82 PGELTLFSVLPELSQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPTATYCAVTDgIPAASEG 161
Cdd:pfam00849  15 TDSLTKLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLF----PERKIEKEYLALVD-KPEEEEG 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2046363465 162 KIQAALKLEHidgvnltvpVKAPSRKDILEGVKKTLSHFRVVATGS--GCALVQLQPLTVFSSQLQVHM 228
Cdd:pfam00849  90 TIKSPIKKEK---------NKSPFRKEEELGGKKAVTHLKVLKSGSkgDYSLLELELVTGRKHQIRAHL 149
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
 112-323 1.94e-07

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 51.55  E-value: 1.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465 112 GKESSGLVLLSSCPQTASRLQKYFtHARRAQRptaTYCAVTDGIPAASEGKIQAALKLehiDGVNLTVPVKAPSrkdilE 191
Cdd:TIGR00005 127 DRDTSGLMVVAKTPLALRELQRQL-KNRTVTK---EYVALVHGQFDSGGGTVDAPLGR---VPNNRGLMAVHPS-----S 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465 192 GVKKTLSHFRVVATGSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGDHMYSARvgTVLGQrflLPAENNKPQRQVLDEAL 271
Cdd:TIGR00005 195 EGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQYLGHPLAGDPLYGNK--PVPGN---NLNGLLNFDRQALHAYE 269

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2046363465 272 LRRLHLTPSQaaqlplhlhlhrlllpgtrardtPVELLAPLPPYFSRTLQCL 323
Cdd:TIGR00005 270 LGFIHPATGE-----------------------ILEFEAPLPADLVLLLEAL 298
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
115-258 2.64e-06

bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 47.68  E-value: 2.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363465 115 SSGLVLLSSCPQTASRLQKYFtharRAQRPTATYCAVTDGIPAASEGKIQAALKlehIDGVNltvpvkAPSRKDILEGVK 194
Cdd:PRK10158   67 TSGVIVVALTKAAERELKRQF----REREPKKQYVARVWGHPSPAEGLVDLPLI---CDWPN------RPKQKVCYETGK 133

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2046363465 195 KTLSHFRVVATGS-GCALVQLQPLTVFSSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAE 258
Cdd:PRK10158  134 PAQTEYEVVEYAAdNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAE 198
 
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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