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Conserved domains on  [gi|1785365587|ref|XP_031757139|]
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tRNA-splicing endonuclease subunit Sen2 [Xenopus tropicalis]

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 ...
 313-400 6.58e-27

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: 103.33  E-value: 6.58e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 313 FSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIVELVNDkcegaplrPLSWRSLAGLHRTTANVSKEL 392
Cdd:cd22363     2 FLLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDE--------ELSWLELVRAGRLAHSVKKTL 73


                  ....*...
gi 1785365587 393 LFCYLIKP 400
Cdd:cd22363    74 VLAVVDEE 81
 
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 ...
 313-400 6.58e-27

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: 103.33  E-value: 6.58e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 313 FSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIVELVNDkcegaplrPLSWRSLAGLHRTTANVSKEL 392
Cdd:cd22363     2 FLLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDE--------ELSWLELVRAGRLAHSVKKTL 73


                  ....*...
gi 1785365587 393 LFCYLIKP 400
Cdd:cd22363    74 VLAVVDEE 81
tRNA_int_endo pfam01974
tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA ...
 313-396 3.65e-15

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: 70.36  E-value: 3.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 313 FSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIVELVNDkcegaplrPLSWRSLAGLHRTTANVSKEL 392
Cdd:pfam01974   1 FWLKYLVYRDLRERGYVVKPGIKFGADFRVYGGGPGKGHSEYLVRVLSEDD--------PISLLDLLRAVRLAHSVRKEL 72


                  ....
gi 1785365587 393 LFCY 396
Cdd:pfam01974  73 VLAI 76
endA TIGR00324
tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and ...
 295-397 2.11e-13

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: 67.88  E-value: 2.11e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 295 EPLTILKLWEVFSAAQASFSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYRKGP--PFYHASYSVIVELVNDkcegaplrP 372
Cdd:TIGR00324  60 EPLSREELSDLARKVERGFMRKYLVYKDLRDRGYVVKTGFKFGADFRLYERGPlrDHSHSEYLVAIDDHDE--------S 131

                          90       100
                  ....*....|....*....|....*
gi 1785365587 373 LSWRSLAGLHRTTANVSKELLFCYL 397
Cdd:TIGR00324 132 IDLIDLSSGVRVAHGVKKKLVIAYV 156
SEN2 COG1676
tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; ...
 287-395 3.03e-10

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: 59.07  E-value: 3.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 287 YLQLSREEEPLTILKLWEVFSAAQASFSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYRKGP-PFYHASYSVIVeLVNDKc 365
Cdd:COG1676    54 KLEVYDDGKELSFEELLEIARKVDPEFDRKYLVYRDLRDRGYVVKTGFKFGSDFRVYERGPgIEDHSPYLVHV-VPEGT- 131

                          90       100       110
                  ....*....|....*....|....*....|
gi 1785365587 366 egaplrPLSWRSLAGLHRTTANVSKELLFC 395
Cdd:COG1676   132 ------EFSPRELSRAVRLAHSVRKRMVFA 155
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 286-426 3.50e-03

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 39.18  E-value: 3.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 286 EYLQLS-------REEEPLTILKL-----WEVFSAAQASFSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYR------KGP 347
Cdd:PRK09300  197 RRLQLSlveaaylLERGVLSVEILdadefVERAREVEGEFDRKLAVYRDLRERGFVPKTGFKFGSDFRVYEgvesveKLP 276

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1785365587 348 pfyHASYsvIVELVNDKCEgaplrpLSWRSLAGLHRTTANVSKELLFcylikpagftdtdlmspACINRIKVQELIVSR 426
Cdd:PRK09300  277 ---HSEY--LVRVIPDDHE------FSPRDLSRAVRLAHSVRKKMVF-----------------ALIDDGGIRYLSIER 327
 
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 ...
 313-400 6.58e-27

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: 103.33  E-value: 6.58e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 313 FSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIVELVNDkcegaplrPLSWRSLAGLHRTTANVSKEL 392
Cdd:cd22363     2 FLLKYLVYKDLRSRGYVVKSGFKFGADFLVYPRGPGLYHAKYLVHVVPEDE--------ELSWLELVRAGRLAHSVKKTL 73


                  ....*...
gi 1785365587 393 LFCYLIKP 400
Cdd:cd22363    74 VLAVVDEE 81
tRNA_int_endo pfam01974
tRNA intron endonuclease, catalytic C-terminal domain; Members of this family cleave pre tRNA ...
 313-396 3.65e-15

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: 70.36  E-value: 3.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 313 FSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIVELVNDkcegaplrPLSWRSLAGLHRTTANVSKEL 392
Cdd:pfam01974   1 FWLKYLVYRDLRERGYVVKPGIKFGADFRVYGGGPGKGHSEYLVRVLSEDD--------PISLLDLLRAVRLAHSVRKEL 72


                  ....
gi 1785365587 393 LFCY 396
Cdd:pfam01974  73 VLAI 76
endA TIGR00324
tRNA-intron lyase; The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and ...
 295-397 2.11e-13

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: 67.88  E-value: 2.11e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 295 EPLTILKLWEVFSAAQASFSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYRKGP--PFYHASYSVIVELVNDkcegaplrP 372
Cdd:TIGR00324  60 EPLSREELSDLARKVERGFMRKYLVYKDLRDRGYVVKTGFKFGADFRLYERGPlrDHSHSEYLVAIDDHDE--------S 131

                          90       100
                  ....*....|....*....|....*
gi 1785365587 373 LSWRSLAGLHRTTANVSKELLFCYL 397
Cdd:TIGR00324 132 IDLIDLSSGVRVAHGVKKKLVIAYV 156
SEN2 COG1676
tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]; ...
 287-395 3.03e-10

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: 59.07  E-value: 3.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 287 YLQLSREEEPLTILKLWEVFSAAQASFSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYRKGP-PFYHASYSVIVeLVNDKc 365
Cdd:COG1676    54 KLEVYDDGKELSFEELLEIARKVDPEFDRKYLVYRDLRDRGYVVKTGFKFGSDFRVYERGPgIEDHSPYLVHV-VPEGT- 131

                          90       100       110
                  ....*....|....*....|....*....|
gi 1785365587 366 egaplrPLSWRSLAGLHRTTANVSKELLFC 395
Cdd:COG1676   132 ------EFSPRELSRAVRLAHSVRKRMVFA 155
PRK09300 PRK09300
tRNA splicing endonuclease; Reviewed
 286-426 3.50e-03

tRNA splicing endonuclease; Reviewed


Pssm-ID: 236460 [Multi-domain]  Cd Length: 330  Bit Score: 39.18  E-value: 3.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1785365587 286 EYLQLS-------REEEPLTILKL-----WEVFSAAQASFSTTYMAYHHFRSKGWVPKVGLKYGTDLLLYR------KGP 347
Cdd:PRK09300  197 RRLQLSlveaaylLERGVLSVEILdadefVERAREVEGEFDRKLAVYRDLRERGFVPKTGFKFGSDFRVYEgvesveKLP 276

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1785365587 348 pfyHASYsvIVELVNDKCEgaplrpLSWRSLAGLHRTTANVSKELLFcylikpagftdtdlmspACINRIKVQELIVSR 426
Cdd:PRK09300  277 ---HSEY--LVRVIPDDHE------FSPRDLSRAVRLAHSVRKKMVF-----------------ALIDDGGIRYLSIER 327
 
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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