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Conserved domains on  [gi|17566950|ref|NP_506056|]
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U6 snRNA-specific terminal uridylyltransferase [Caenorhabditis elegans]

Protein Classification

NT_Pol-beta-like and PAP_assoc domain-containing protein( domain architecture ID 10311142)

NT_Pol-beta-like and PAP_assoc domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
382-437 4.90e-07

Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.


:

Pssm-ID: 427532  Cd Length: 60  Bit Score: 47.18  E-value: 4.90e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566950   382 DYCKFFRELFKYYA-NFDFTNKAI--YGKKAMQKKTLSSA-HGGVEESPLMLMDPMDITH 437
Cdd:pfam03828   1 SLGELLIGFFEYYGrEFDYENVVIsiRTGGILSKKEKGWLrNEGRRPFLLCIEDPFDLDN 60
NT_Pol-beta-like super family cl11966
Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This ...
142-297 6.45e-03

Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism for Rel-Spo enzymes.


The actual alignment was detected with superfamily member cd05402:

Pssm-ID: 472251 [Multi-domain]  Cd Length: 114  Bit Score: 36.77  E-value: 6.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566950 142 RLKILEDgfsfIEQGVSELIQNSACEMFGSFASPVRRNGySDIDInvesvsapgqrvstnvrplnevvanpkCLITHPLT 221
Cdd:cd05402   2 REEVLDR----LQELIKEWFPGAKLYPFGSYVTGLGLPG-SDIDL---------------------------CLLGPNHR 49
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17566950 222 KSeletypQEEIIKILYRCFNENSAFKtkfEMRFLP-ARTPIIVFKNIEvegMNVSYDLSVHNQISVEKASLLHEFI 297
Cdd:cd05402  50 VD------REDFLRKLAKLLKKSGEVV---EVEPIInARVPIIKFVDKP---TGIEVDISFNNLNGIRNTKLLRAYV 114
 
Name Accession Description Interval E-value
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
382-437 4.90e-07

Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.


Pssm-ID: 427532  Cd Length: 60  Bit Score: 47.18  E-value: 4.90e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566950   382 DYCKFFRELFKYYA-NFDFTNKAI--YGKKAMQKKTLSSA-HGGVEESPLMLMDPMDITH 437
Cdd:pfam03828   1 SLGELLIGFFEYYGrEFDYENVVIsiRTGGILSKKEKGWLrNEGRRPFLLCIEDPFDLDN 60
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
142-297 6.45e-03

Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved.


Pssm-ID: 143392 [Multi-domain]  Cd Length: 114  Bit Score: 36.77  E-value: 6.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566950 142 RLKILEDgfsfIEQGVSELIQNSACEMFGSFASPVRRNGySDIDInvesvsapgqrvstnvrplnevvanpkCLITHPLT 221
Cdd:cd05402   2 REEVLDR----LQELIKEWFPGAKLYPFGSYVTGLGLPG-SDIDL---------------------------CLLGPNHR 49
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17566950 222 KSeletypQEEIIKILYRCFNENSAFKtkfEMRFLP-ARTPIIVFKNIEvegMNVSYDLSVHNQISVEKASLLHEFI 297
Cdd:cd05402  50 VD------REDFLRKLAKLLKKSGEVV---EVEPIInARVPIIKFVDKP---TGIEVDISFNNLNGIRNTKLLRAYV 114
 
Name Accession Description Interval E-value
PAP_assoc pfam03828
Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown ...
382-437 4.90e-07

Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.


Pssm-ID: 427532  Cd Length: 60  Bit Score: 47.18  E-value: 4.90e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566950   382 DYCKFFRELFKYYA-NFDFTNKAI--YGKKAMQKKTLSSA-HGGVEESPLMLMDPMDITH 437
Cdd:pfam03828   1 SLGELLIGFFEYYGrEFDYENVVIsiRTGGILSKKEKGWLrNEGRRPFLLCIEDPFDLDN 60
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
142-297 6.45e-03

Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved.


Pssm-ID: 143392 [Multi-domain]  Cd Length: 114  Bit Score: 36.77  E-value: 6.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566950 142 RLKILEDgfsfIEQGVSELIQNSACEMFGSFASPVRRNGySDIDInvesvsapgqrvstnvrplnevvanpkCLITHPLT 221
Cdd:cd05402   2 REEVLDR----LQELIKEWFPGAKLYPFGSYVTGLGLPG-SDIDL---------------------------CLLGPNHR 49
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17566950 222 KSeletypQEEIIKILYRCFNENSAFKtkfEMRFLP-ARTPIIVFKNIEvegMNVSYDLSVHNQISVEKASLLHEFI 297
Cdd:cd05402  50 VD------REDFLRKLAKLLKKSGEVV---EVEPIInARVPIIKFVDKP---TGIEVDISFNNLNGIRNTKLLRAYV 114
 
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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