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Conserved domains on  [gi|17560354|ref|NP_505729|]
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Cytoplasmic tRNA 2-thiolation protein 2 [Caenorhabditis elegans]

Protein Classification

tRNA(Ile)-lysidine synthetase( domain architecture ID 1909277)

tRNA(Ile)-lysidine synthetase ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CTU2 super family cl18566
Cytoplasmic tRNA 2-thiolation protein 2; CTU2 is a family of proteins necessary for the ...
 276-328 2.74e-05

Cytoplasmic tRNA 2-thiolation protein 2; CTU2 is a family of proteins necessary for the formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. The family is conserved from plants to humans ]1]. It plays a central role in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine, or the wobble nucleoside. This wobble modification in tRNAs, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U), is required for the proper decoding of NNR codons in eukaryotes. The 2-thio group gives rigidity by largely fixing the C3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing.


The actual alignment was detected with superfamily member pfam10288:

Pssm-ID: 463044  Cd Length: 106  Bit Score: 42.80  E-value: 2.74e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 17560354   276 SVQTLTDAFICTLENEkFYSTINTVLSTAAKIHNTSIGKDDSKCSFCNVEVAD 328
Cdd:pfam10288   1 SIQELTEKFITNLQAD-YPSTVSTVVRTGEKLVAPKISDSSGKCSLCGSPLDD 52
TilS super family cl43000
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 180-254 1.41e-03

tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA(Ile)-lysidine synthase TilS/MesJ is part of the Pathway/BioSystem: tRNA modification


The actual alignment was detected with superfamily member COG0037:

Pssm-ID: 439807 [Multi-domain]  Cd Length: 235  Bit Score: 39.82  E-value: 1.41e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17560354 180 RVLKEKCLQKIACSMGILKCMVPDHADD-----LGRLAidqlclgRGGSISTLVTVTDKRPDFM-LIRPLCDISKKELAV 253
Cdd:COG0037 100 RRARYGALYELARELGADKIATGHHLDDqaetfLLNLL-------RGSGLAGLAGMPPSRGGGVrLIRPLLYVSRKEIEA 172


                .
gi 17560354 254 Y 254
Cdd:COG0037 173 Y 173
 
Name Accession Description Interval E-value
CTU2 pfam10288
Cytoplasmic tRNA 2-thiolation protein 2; CTU2 is a family of proteins necessary for the ...
 276-328 2.74e-05

Cytoplasmic tRNA 2-thiolation protein 2; CTU2 is a family of proteins necessary for the formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. The family is conserved from plants to humans ]1]. It plays a central role in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine, or the wobble nucleoside. This wobble modification in tRNAs, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U), is required for the proper decoding of NNR codons in eukaryotes. The 2-thio group gives rigidity by largely fixing the C3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing.


Pssm-ID: 463044  Cd Length: 106  Bit Score: 42.80  E-value: 2.74e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 17560354   276 SVQTLTDAFICTLENEkFYSTINTVLSTAAKIHNTSIGKDDSKCSFCNVEVAD 328
Cdd:pfam10288   1 SIQELTEKFITNLQAD-YPSTVSTVVRTGEKLVAPKISDSSGKCSLCGSPLDD 52
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 180-254 1.41e-03

tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA(Ile)-lysidine synthase TilS/MesJ is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439807 [Multi-domain]  Cd Length: 235  Bit Score: 39.82  E-value: 1.41e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17560354 180 RVLKEKCLQKIACSMGILKCMVPDHADD-----LGRLAidqlclgRGGSISTLVTVTDKRPDFM-LIRPLCDISKKELAV 253
Cdd:COG0037 100 RRARYGALYELARELGADKIATGHHLDDqaetfLLNLL-------RGSGLAGLAGMPPSRGGGVrLIRPLLYVSRKEIEA 172


                .
gi 17560354 254 Y 254
Cdd:COG0037 173 Y 173
 
Name Accession Description Interval E-value
CTU2 pfam10288
Cytoplasmic tRNA 2-thiolation protein 2; CTU2 is a family of proteins necessary for the ...
 276-328 2.74e-05

Cytoplasmic tRNA 2-thiolation protein 2; CTU2 is a family of proteins necessary for the formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. The family is conserved from plants to humans ]1]. It plays a central role in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine, or the wobble nucleoside. This wobble modification in tRNAs, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U), is required for the proper decoding of NNR codons in eukaryotes. The 2-thio group gives rigidity by largely fixing the C3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing.


Pssm-ID: 463044  Cd Length: 106  Bit Score: 42.80  E-value: 2.74e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 17560354   276 SVQTLTDAFICTLENEkFYSTINTVLSTAAKIHNTSIGKDDSKCSFCNVEVAD 328
Cdd:pfam10288   1 SIQELTEKFITNLQAD-YPSTVSTVVRTGEKLVAPKISDSSGKCSLCGSPLDD 52
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 180-254 1.41e-03

tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA(Ile)-lysidine synthase TilS/MesJ is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439807 [Multi-domain]  Cd Length: 235  Bit Score: 39.82  E-value: 1.41e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17560354 180 RVLKEKCLQKIACSMGILKCMVPDHADD-----LGRLAidqlclgRGGSISTLVTVTDKRPDFM-LIRPLCDISKKELAV 253
Cdd:COG0037 100 RRARYGALYELARELGADKIATGHHLDDqaetfLLNLL-------RGSGLAGLAGMPPSRGGGVrLIRPLLYVSRKEIEA 172


                .
gi 17560354 254 Y 254
Cdd:COG0037 173 Y 173
 
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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