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Conserved domains on  [gi|157821169|ref|NP_001102111|]
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mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 2 [Rattus norvegicus]

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 ...
 72-244 2.98e-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: 105.11  E-value: 2.98e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169  72 GRPGELTLLSVLPWL-SQALGLEHQELQVVRAPGKEASGLVLLSSCPQTTSHLQKFFthsrRAQRPTATYCAITDGVPEP 150
Cdd:cd02869   14 PGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVKKTYLALVDGKPPE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169 151 SEGTVHIALRLERmdgidlavpVTSPSRKDIQEGVKRTLSHFHVTATGCGCALVQLQPLTVFPSQLQVHMALQLCPILGD 230
Cdd:cd02869   90 DEGTIDAPLGRKK---------RKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160

                        170
                 ....*....|....
gi 157821169 231 HTYAARVGSVLGQR 244
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 ...
 72-244 2.98e-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: 105.11  E-value: 2.98e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169  72 GRPGELTLLSVLPWL-SQALGLEHQELQVVRAPGKEASGLVLLSSCPQTTSHLQKFFthsrRAQRPTATYCAITDGVPEP 150
Cdd:cd02869   14 PGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVKKTYLALVDGKPPE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169 151 SEGTVHIALRLERmdgidlavpVTSPSRKDIQEGVKRTLSHFHVTATGCGCALVQLQPLTVFPSQLQVHMALQLCPILGD 230
Cdd:cd02869   90 DEGTIDAPLGRKK---------RKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160

                        170
                 ....*....|....
gi 157821169 231 HTYAARVGSVLGQR 244
Cdd:cd02869  161 PKYGGKASDSPGLK 174
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 86-236 4.01e-13

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: 67.47  E-value: 4.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169  86 LSQALGLEHQELQVVRAPG------KEASGLVLLSSCPQTTSHLQKFFtHSRRAQRptaTYCAITDGVPEPSEGTVHIAL 159
Cdd:COG0564   30 LVNALRAHLGELSGVPRPGlvhrldRDTSGLLLVAKTRKAARRLSEQF-REREVEK---RYLALVEGKPKEDEGTIDAPL 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157821169 160 RLERMDGIDLAVPvtspsrkdiQEGVKRTLSHFHVTATGCGCALVQLQPLTVFPSQLQVHMALQLCPILGDHTYAAR 236
Cdd:COG0564  106 GRDPKDRKKMAVV---------DEDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAHIGHPIVGDPLYGGD 173
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 105-221 1.17e-12

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: 64.73  E-value: 1.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169  105 KEASGLVLLSSCPQTTSHLQKFFthsrRAQRPTATYCAITDGvPEPSEGTVHIALRLERMDgidlavpvtSPSRKDIQEG 184
Cdd:pfam00849  46 KNTSGLLLLAKDGEAANKLNKLF----PERKIEKEYLALVDK-PEEEEGTIKSPIKKEKNK---------SPFRKEEELG 111

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 157821169  185 VKRTLSHFHVTATGC--GCALVQLQPLTVFPSQLQVHMA 221
Cdd:pfam00849 112 GKKAVTHLKVLKSGSkgDYSLLELELVTGRKHQIRAHLA 150
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
108-255 2.77e-05

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


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 44.60  E-value: 2.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169 108 SGLVLLSSCPQTTSHLQKFFthsrRAQRPTATYCAITDGVPEPSEGTVHIALRLERMDgidlavpvtSPSRKDIQEGVKR 187
Cdd:PRK10158  68 SGVIVVALTKAAERELKRQF----REREPKKQYVARVWGHPSPAEGLVDLPLICDWPN---------RPKQKVCYETGKP 134

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157821169 188 TLSHFHVTATGC-GCALVQLQPLTVFPSQLQVHMALQLCPILGDHTYAARVGSVLGQRFLWPAET---TKPQ 255
Cdd:PRK10158 135 AQTEYEVVEYAAdNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMltiTHPA 206
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 72-244 2.98e-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: 105.11  E-value: 2.98e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169  72 GRPGELTLLSVLPWL-SQALGLEHQELQVVRAPGKEASGLVLLSSCPQTTSHLQKFFthsrRAQRPTATYCAITDGVPEP 150
Cdd:cd02869   14 PGPGHLTGTLVNALLkLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQF----KERKVKKTYLALVDGKPPE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169 151 SEGTVHIALRLERmdgidlavpVTSPSRKDIQEGVKRTLSHFHVTATGCGCALVQLQPLTVFPSQLQVHMALQLCPILGD 230
Cdd:cd02869   90 DEGTIDAPLGRKK---------RKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160

                        170
                 ....*....|....
gi 157821169 231 HTYAARVGSVLGQR 244
Cdd:cd02869  161 PKYGGKASDSPGLK 174
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 86-236 4.01e-13

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: 67.47  E-value: 4.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169  86 LSQALGLEHQELQVVRAPG------KEASGLVLLSSCPQTTSHLQKFFtHSRRAQRptaTYCAITDGVPEPSEGTVHIAL 159
Cdd:COG0564   30 LVNALRAHLGELSGVPRPGlvhrldRDTSGLLLVAKTRKAARRLSEQF-REREVEK---RYLALVEGKPKEDEGTIDAPL 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157821169 160 RLERMDGIDLAVPvtspsrkdiQEGVKRTLSHFHVTATGCGCALVQLQPLTVFPSQLQVHMALQLCPILGDHTYAAR 236
Cdd:COG0564  106 GRDPKDRKKMAVV---------DEDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAHIGHPIVGDPLYGGD 173
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 105-221 1.17e-12

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: 64.73  E-value: 1.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169  105 KEASGLVLLSSCPQTTSHLQKFFthsrRAQRPTATYCAITDGvPEPSEGTVHIALRLERMDgidlavpvtSPSRKDIQEG 184
Cdd:pfam00849  46 KNTSGLLLLAKDGEAANKLNKLF----PERKIEKEYLALVDK-PEEEEGTIKSPIKKEKNK---------SPFRKEEELG 111

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 157821169  185 VKRTLSHFHVTATGC--GCALVQLQPLTVFPSQLQVHMA 221
Cdd:pfam00849 112 GKKAVTHLKVLKSGSkgDYSLLELELVTGRKHQIRAHLA 150
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
108-255 2.77e-05

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


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 44.60  E-value: 2.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169 108 SGLVLLSSCPQTTSHLQKFFthsrRAQRPTATYCAITDGVPEPSEGTVHIALRLERMDgidlavpvtSPSRKDIQEGVKR 187
Cdd:PRK10158  68 SGVIVVALTKAAERELKRQF----REREPKKQYVARVWGHPSPAEGLVDLPLICDWPN---------RPKQKVCYETGKP 134

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157821169 188 TLSHFHVTATGC-GCALVQLQPLTVFPSQLQVHMALQLCPILGDHTYAARVGSVLGQRFLWPAET---TKPQ 255
Cdd:PRK10158 135 AQTEYEVVEYAAdNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMltiTHPA 206
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
 108-233 1.26e-04

tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.


Pssm-ID: 211333 [Multi-domain]  Cd Length: 223  Bit Score: 42.71  E-value: 1.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169 108 SGLVLLSSCPQTTSHLQKFFThsrrAQRPTATYCAITDGVPePSEGTVHIALRLERMDGIDLAVPVTSP--------SRK 179
Cdd:cd02563   57 SGVLLFALSSEVARKLGEQFT----EHRVHKTYLAVVRGYV-PESGTIDYPLSEELDKLADKFASDDKApqaatthyRLL 131

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 157821169 180 DIQEGVKRTLSHFHVTAtgcgcALVQLQPLTVFPSQLQVHMALQLCPILGDHTY 233
Cdd:cd02563  132 AVEELPVVVGKYPTSRY-----SLVELTPHTGRKHQLRRHLAHIRHPIIGDTTH 180
PSRA_1 cd02558
Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial ...
 105-233 8.25e-04

Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.


Pssm-ID: 211332 [Multi-domain]  Cd Length: 246  Bit Score: 40.33  E-value: 8.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821169 105 KEASGLVLLSSCPQTTSHLQKFFtHSRRAQRptaTYCAITDGVPEPSEGTVHiALRLERMDGIDLAVPVtspsrkdiqEG 184
Cdd:cd02558   91 RLTAGLVLFSKRPETRGAYQTLF-ARREVSK---TYEAVAPYVPALTFPLTV-RSRIVKGRGFFQAREV---------EG 156

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 157821169 185 VKRTLSHFHVTATGCGCALVQLQPLTVFPSQLQVHMALQLCPILGDHTY 233
Cdd:cd02558  157 EPNAETRIELLARRGGWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFY 205
 
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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