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Conserved domains on  [gi|2046363897|ref|NP_775930|]
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mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 1 [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

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 ...
82-267 1.39e-33

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: 122.45  E-value: 1.39e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897  82 LVTLNKPQGLPVTGKPGELTLFSVLPEL-SQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPT 160
Cdd:cd02869     1 LLVVNKPAGLPVHPGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVK 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 161 ATYCAVTDGIPAASEGKIQAALKLEHIDGVnltvpvkapSRKDILEGVKKTLSHFRVVATGSGCALVQLQPLTVFSSQLQ 240
Cdd:cd02869    77 KTYLALVDGKPPEDEGTIDAPLGRKKRKKR---------ARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIR 147
                         170       180
                  ....*....|....*....|....*..
gi 2046363897 241 VHMVLQLCPVLGDHMYSARVGTVLGQR 267
Cdd:cd02869   148 VHLASIGHPIVGDPKYGGKASDSPGLK 174
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
82-267 1.39e-33

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: 122.45  E-value: 1.39e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897  82 LVTLNKPQGLPVTGKPGELTLFSVLPEL-SQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPT 160
Cdd:cd02869     1 LLVVNKPAGLPVHPGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVK 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 161 ATYCAVTDGIPAASEGKIQAALKLEHIDGVnltvpvkapSRKDILEGVKKTLSHFRVVATGSGCALVQLQPLTVFSSQLQ 240
Cdd:cd02869    77 KTYLALVDGKPPEDEGTIDAPLGRKKRKKR---------ARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIR 147
                         170       180
                  ....*....|....*....|....*..
gi 2046363897 241 VHMVLQLCPVLGDHMYSARVGTVLGQR 267
Cdd:cd02869   148 VHLASIGHPIVGDPKYGGKASDSPGLK 174
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
82-243 3.39e-22

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: 90.93  E-value: 3.39e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897  82 LVTLNKPQGLPVTGKPGELTLFSvLPELSQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPTA 161
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLS-LLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLF----PERKIEK 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 162 TYCAVTDgIPAASEGKIQAALKLEHidgvnltvpVKAPSRKDILEGVKKTLSHFRVVATGS--GCALVQLQPLTVFSSQL 239
Cdd:pfam00849  76 EYLALVD-KPEEEEGTIKSPIKKEK---------NKSPFRKEEELGGKKAVTHLKVLKSGSkgDYSLLELELVTGRKHQI 145

                  ....
gi 2046363897 240 QVHM 243
Cdd:pfam00849 146 RAHL 149
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
82-338 3.56e-09

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: 56.95  E-value: 3.56e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897  82 LVTLNKPQGLPVTGKPGEL--TLFSVLPELSQSLGLREQeLQVVRASGKESSGLVLLSSCPQTASRLQKYFtHARRAQRp 159
Cdd:TIGR00005  81 IIVINKPSGLVVHPGGGNPfgTVLNALLAHCPPIAGVER-VGIVHRLDRDTSGLMVVAKTPLALRELQRQL-KNRTVTK- 157
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 160 taTYCAVTDGIPAASEGKIQAALKLehiDGVNLTVPVKAPSrkdilEGVKKTLSHFRVVATGSGCALVQLQPLTVFSSQL 239
Cdd:TIGR00005 158 --EYVALVHGQFDSGGGTVDAPLGR---VPNNRGLMAVHPS-----SEGKPAVTHFRVLERFGNASLVECELETGRTHQI 227
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 240 QVHMVLQLCPVLGDHMYSARvgTVLGQrflLPAENNKPQRQVLDEALLRRLHLTPSQaaqlplhlhlhrlllpgtrardt 319
Cdd:TIGR00005 228 RVHLQYLGHPLAGDPLYGNK--PVPGN---NLNGLLNFDRQALHAYELGFIHPATGE----------------------- 279
                         250
                  ....*....|....*....
gi 2046363897 320 PVELLAPLPPYFSRTLQCL 338
Cdd:TIGR00005 280 ILEFEAPLPADLVLLLEAL 298
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
82-273 5.07e-07

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


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 49.99  E-value: 5.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897  82 LVTLNKPQGLpvtgkpgeLTLFSVLPELSQSLGLREQ----ELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQ 157
Cdd:PRK10158   23 IMVVNKPSGL--------LSVPGRLEEHKDSVMTRIQrdypQAESVHRLDMATSGVIVVALTKAAERELKRQF----RER 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 158 RPTATYCAVTDGIPAASEGKIQAALKlehIDGVNltvpvkAPSRKDILEGVKKTLSHFRVVATGS-GCALVQLQPLTVFS 236
Cdd:PRK10158   91 EPKKQYVARVWGHPSPAEGLVDLPLI---CDWPN------RPKQKVCYETGKPAQTEYEVVEYAAdNTARVVLKPITGRS 161
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2046363897 237 SQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAE 273
Cdd:PRK10158  162 HQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAE 198
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
82-267 1.39e-33

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: 122.45  E-value: 1.39e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897  82 LVTLNKPQGLPVTGKPGELTLFSVLPEL-SQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPT 160
Cdd:cd02869     1 LLVVNKPAGLPVHPGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVK 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 161 ATYCAVTDGIPAASEGKIQAALKLEHIDGVnltvpvkapSRKDILEGVKKTLSHFRVVATGSGCALVQLQPLTVFSSQLQ 240
Cdd:cd02869    77 KTYLALVDGKPPEDEGTIDAPLGRKKRKKR---------ARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIR 147
                         170       180
                  ....*....|....*....|....*..
gi 2046363897 241 VHMVLQLCPVLGDHMYSARVGTVLGQR 267
Cdd:cd02869   148 VHLASIGHPIVGDPKYGGKASDSPGLK 174
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
82-243 3.39e-22

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: 90.93  E-value: 3.39e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897  82 LVTLNKPQGLPVTGKPGELTLFSvLPELSQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQRPTA 161
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLS-LLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLF----PERKIEK 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 162 TYCAVTDgIPAASEGKIQAALKLEHidgvnltvpVKAPSRKDILEGVKKTLSHFRVVATGS--GCALVQLQPLTVFSSQL 239
Cdd:pfam00849  76 EYLALVD-KPEEEEGTIKSPIKKEK---------NKSPFRKEEELGGKKAVTHLKVLKSGSkgDYSLLELELVTGRKHQI 145

                  ....
gi 2046363897 240 QVHM 243
Cdd:pfam00849 146 RAHL 149
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
82-338 3.56e-09

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: 56.95  E-value: 3.56e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897  82 LVTLNKPQGLPVTGKPGEL--TLFSVLPELSQSLGLREQeLQVVRASGKESSGLVLLSSCPQTASRLQKYFtHARRAQRp 159
Cdd:TIGR00005  81 IIVINKPSGLVVHPGGGNPfgTVLNALLAHCPPIAGVER-VGIVHRLDRDTSGLMVVAKTPLALRELQRQL-KNRTVTK- 157
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 160 taTYCAVTDGIPAASEGKIQAALKLehiDGVNLTVPVKAPSrkdilEGVKKTLSHFRVVATGSGCALVQLQPLTVFSSQL 239
Cdd:TIGR00005 158 --EYVALVHGQFDSGGGTVDAPLGR---VPNNRGLMAVHPS-----SEGKPAVTHFRVLERFGNASLVECELETGRTHQI 227
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 240 QVHMVLQLCPVLGDHMYSARvgTVLGQrflLPAENNKPQRQVLDEALLRRLHLTPSQaaqlplhlhlhrlllpgtrardt 319
Cdd:TIGR00005 228 RVHLQYLGHPLAGDPLYGNK--PVPGN---NLNGLLNFDRQALHAYELGFIHPATGE----------------------- 279
                         250
                  ....*....|....*....
gi 2046363897 320 PVELLAPLPPYFSRTLQCL 338
Cdd:TIGR00005 280 ILEFEAPLPADLVLLLEAL 298
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
82-273 5.07e-07

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


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 49.99  E-value: 5.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897  82 LVTLNKPQGLpvtgkpgeLTLFSVLPELSQSLGLREQ----ELQVVRASGKESSGLVLLSSCPQTASRLQKYFtharRAQ 157
Cdd:PRK10158   23 IMVVNKPSGL--------LSVPGRLEEHKDSVMTRIQrdypQAESVHRLDMATSGVIVVALTKAAERELKRQF----RER 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046363897 158 RPTATYCAVTDGIPAASEGKIQAALKlehIDGVNltvpvkAPSRKDILEGVKKTLSHFRVVATGS-GCALVQLQPLTVFS 236
Cdd:PRK10158   91 EPKKQYVARVWGHPSPAEGLVDLPLI---CDWPN------RPKQKVCYETGKPAQTEYEVVEYAAdNTARVVLKPITGRS 161
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2046363897 237 SQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAE 273
Cdd:PRK10158  162 HQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAE 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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