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Conserved domains on  [gi|1046839940|ref|XP_017444128|]
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tRNA-splicing endonuclease subunit Sen34 isoform X1 [Rattus norvegicus]

Protein Classification

tRNA-intron endonuclease family protein( domain architecture ID 16909852)

tRNA-intron endonuclease family protein similar to Homo sapiens tRNA-splicing endonuclease subunit Sen34, which constitutes one of the two catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron

CATH:  3.40.1170.20
EC:  4.6.1.16
Gene Ontology:  GO:0000214|GO:0000379|GO:0006397|GO:0003676|GO:0016829|GO:0000213
PubMed:  22638584|37544645|35156311

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
tRNA-intron_lyase_C cd22363
catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA ...
 220-308 1.13e-39

catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA intron endonucleases cleaves pre tRNA at the 5' and 3' splice sites to release the intron (EC:3.1.27.9). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


:

Pssm-ID: 411767  Cd Length: 91  Bit Score: 134.15  E-value: 1.13e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 220 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSPQPDG 299
Cdd:cd22363     3 LLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDEELSWLELVRAGRLAHSVKKTLVLAVVDEEG 82


                  ....*....
gi 1046839940 300 KVVYTSLQW 308
Cdd:cd22363    83 EVTYYSIEW 91
 
Name Accession Description Interval E-value
tRNA-intron_lyase_C cd22363
catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA ...
 220-308 1.13e-39

catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA intron endonucleases cleaves pre tRNA at the 5' and 3' splice sites to release the intron (EC:3.1.27.9). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411767  Cd Length: 91  Bit Score: 134.15  E-value: 1.13e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 220 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSPQPDG 299
Cdd:cd22363     3 LLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDEELSWLELVRAGRLAHSVKKTLVLAVVDEEG 82


                  ....*....
gi 1046839940 300 KVVYTSLQW 308
Cdd:cd22363    83 EVTYYSIEW 91
tRNA_int_endo pfam01974
tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA ...
 219-303 1.85e-31

tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.


Pssm-ID: 396521  Cd Length: 85  Bit Score: 112.74  E-value: 1.85e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 219 HELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSPQPD 298
Cdd:pfam01974   1 FWLKYLVYRDLRERGYVVKPGIKFGADFRVYGGGPGKGHSEYLVRVLSEDDPISLLDLLRAVRLAHSVRKELVLAIVDDE 80


                  ....*
gi 1046839940 299 GKVVY 303
Cdd:pfam01974  81 GDVTY 85
endA TIGR00324
tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and ...
 221-309 5.79e-21

tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini. The genes are homologous in Eucarya and Archea. The two yeast genes have been functionally studied and are two subunits of a heterotetramer enzyme in yeast the other two subunits of which have no known homologs. [Transcription, RNA processing]


Pssm-ID: 129424  Cd Length: 170  Bit Score: 87.91  E-value: 5.79e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 221 LRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAH--YIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSPQPD 298
Cdd:TIGR00324  80 RKYLVYKDLRDRGYVVKTGFKFGADFRLYERGPLRDHSHseYLVAIDDHDESIDLIDLSSGVRVAHGVKKKLVIAYVDEE 159

                          90
                  ....*....|.
gi 1046839940 299 GKVVYTSLQWA 309
Cdd:TIGR00324 160 KEIHYLSIEWV 170
SEN2 COG1676
tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; ...
 220-308 6.53e-18

tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; tRNA splicing endonuclease subunit SEN34 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441282  Cd Length: 173  Bit Score: 79.48  E-value: 6.53e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 220 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRF-HAHYIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSPQPD 298
Cdd:COG1676    81 DRKYLVYRDLRDRGYVVKTGFKFGSDFRVYERGPGIEdHSPYLVHVVPEGTEFSPRELSRAVRLAHSVRKRMVFAVVDDE 160

                          90
                  ....*....|
gi 1046839940 299 GKVVYTSLQW 308
Cdd:COG1676   161 GEIEYYKFEW 170
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 220-306 4.31e-07

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 50.74  E-value: 4.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 220 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPG----DPLRfHAHYIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSp 295
Cdd:PRK09300  237 DRKLAVYRDLRERGFVPKTGFKFGSDFRVYEGvesvEKLP-HSEYLVRVIPDDHEFSPRDLSRAVRLAHSVRKKMVFAL- 314

                          90
                  ....*....|.
gi 1046839940 296 QPDGKVVYTSL 306
Cdd:PRK09300  315 IDDGGIRYLSI 325
 
Name Accession Description Interval E-value
tRNA-intron_lyase_C cd22363
catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA ...
 220-308 1.13e-39

catalytic C-terminal domain of the tRNA-intron lyase; This C-terminal catalytic domain of tRNA intron endonucleases cleaves pre tRNA at the 5' and 3' splice sites to release the intron (EC:3.1.27.9). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411767  Cd Length: 91  Bit Score: 134.15  E-value: 1.13e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 220 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSPQPDG 299
Cdd:cd22363     3 LLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDEELSWLELVRAGRLAHSVKKTLVLAVVDEEG 82


                  ....*....
gi 1046839940 300 KVVYTSLQW 308
Cdd:cd22363    83 EVTYYSIEW 91
tRNA_int_endo pfam01974
tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA ...
 219-303 1.85e-31

tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.


Pssm-ID: 396521  Cd Length: 85  Bit Score: 112.74  E-value: 1.85e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 219 HELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSPQPD 298
Cdd:pfam01974   1 FWLKYLVYRDLRERGYVVKPGIKFGADFRVYGGGPGKGHSEYLVRVLSEDDPISLLDLLRAVRLAHSVRKELVLAIVDDE 80


                  ....*
gi 1046839940 299 GKVVY 303
Cdd:pfam01974  81 GDVTY 85
endA TIGR00324
tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and ...
 221-309 5.79e-21

tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini. The genes are homologous in Eucarya and Archea. The two yeast genes have been functionally studied and are two subunits of a heterotetramer enzyme in yeast the other two subunits of which have no known homologs. [Transcription, RNA processing]


Pssm-ID: 129424  Cd Length: 170  Bit Score: 87.91  E-value: 5.79e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 221 LRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAH--YIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSPQPD 298
Cdd:TIGR00324  80 RKYLVYKDLRDRGYVVKTGFKFGADFRLYERGPLRDHSHseYLVAIDDHDESIDLIDLSSGVRVAHGVKKKLVIAYVDEE 159

                          90
                  ....*....|.
gi 1046839940 299 GKVVYTSLQWA 309
Cdd:TIGR00324 160 KEIHYLSIEWV 170
SEN2 COG1676
tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; ...
 220-308 6.53e-18

tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; tRNA splicing endonuclease subunit SEN34 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441282  Cd Length: 173  Bit Score: 79.48  E-value: 6.53e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 220 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRF-HAHYIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSPQPD 298
Cdd:COG1676    81 DRKYLVYRDLRDRGYVVKTGFKFGSDFRVYERGPGIEdHSPYLVHVVPEGTEFSPRELSRAVRLAHSVRKRMVFAVVDDE 160

                          90
                  ....*....|
gi 1046839940 299 GKVVYTSLQW 308
Cdd:COG1676   161 GEIEYYKFEW 170
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 220-306 4.31e-07

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 50.74  E-value: 4.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1046839940 220 ELRYSIYRDLWERGFFLSAAGKFGGDFLVYPG----DPLRfHAHYIAQCWSAEDPIPLQDLVSAGRLGTSVRKTLLLCSp 295
Cdd:PRK09300  237 DRKLAVYRDLRERGFVPKTGFKFGSDFRVYEGvesvEKLP-HSEYLVRVIPDDHEFSPRDLSRAVRLAHSVRKKMVFAL- 314

                          90
                  ....*....|.
gi 1046839940 296 QPDGKVVYTSL 306
Cdd:PRK09300  315 IDDGGIRYLSI 325
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 214-282 3.71e-06

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 47.66  E-value: 3.71e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1046839940 214 AGRPAHELRYSIYRDLWERGFFLSAAgkfGGDFLVYP--GDPLRFHAHYIAQCWSAEDPIPLQDLVSAGRL 282
Cdd:PRK09300   66 SLRPNFELRYLVYKDLRERGYYVQPG---DADFRVYPrgSGPGDGESKYRVRVVSERDPLPFSDLIERKQL 133
 
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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