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Conserved domains on  [gi|1831512115|ref|NP_001368344|]
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3'-5' exonuclease eri-1 [Caenorhabditis elegans]

Protein Classification

3'-5' exonuclease( domain architecture ID 10150039)

3'-5' exonuclease catalyzes the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction; similar to human ERI1 exoribonuclease 3

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 2-128 6.71e-39

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


:

Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 136.97  E-value: 6.71e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115   2 QFTKIAQETVDAAPYFREALQRLYTWMRKFNlgqknsRFAFVTDGPHDMWKFMQFQCLLSNIRMPHMFRSFINIKKTFKE 81
Cdd:cd06133    60 ELTGITQEDVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAK 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1831512115  82 KFNglikGNGKSGIENMLERLDLSFVGNKHSGLDDATNIAAIAIQMM 128
Cdd:cd06133   134 FYG----LKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
 
Name Accession Description Interval E-value
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 2-128 6.71e-39

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 136.97  E-value: 6.71e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115   2 QFTKIAQETVDAAPYFREALQRLYTWMRKFNlgqknsRFAFVTDGPHDMWKFMQFQCLLSNIRMPHMFRSFINIKKTFKE 81
Cdd:cd06133    60 ELTGITQEDVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAK 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1831512115  82 KFNglikGNGKSGIENMLERLDLSFVGNKHSGLDDATNIAAIAIQMM 128
Cdd:cd06133   134 FYG----LKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-123 7.13e-21

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 88.18  E-value: 7.13e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115   1 MQFTKIAQETVDAAPYFREALQRLYTWMRKFNLGQKNSRFAFVTDGPHDMWKFMQFQCllsnIRMPHMFRSFINIKKTFK 80
Cdd:pfam00929  53 TKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNLLVAHNASFDVGFLRYDDKRFLKKPM----PKLNPVIDTLILDKATYK 128

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1831512115  81 EKFNglikgngkSGIENMLERLDLSFVGNKHSGLDDATNIAAI 123
Cdd:pfam00929 129 ELPG--------RSLDALAEKLGLEHIGRAHRALDDARATAKL 163
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 1-129 3.02e-20

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 87.22  E-value: 3.02e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115   1 MQFTKIAQETVDAAPYFREALQRLYTWMRKfnlgqknSRFAFVTDGPHDMwKFMQFQCLLSNIRMPhMFRSFINIKKTFK 80
Cdd:COG5018    61 TELTGITQEDVDSAPSFAEAIEDFKKWIGS-------EDYILCSWGDYDR-KQLERNCRFHGVPYP-FGDRHINLKKLFA 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1831512115  81 EKFnglikGNGKS-GIENMLERLDLSFVGNKHSGLDDATNIAAIAIQMMK 129
Cdd:COG5018   132 LYF-----GLKKRiGLKKALELLGLEFEGTHHRALDDARNTAKLFKKILG 176
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-131 5.27e-17

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 77.73  E-value: 5.27e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115    1 MQFTKIAQETVDAAPYFREALQRLYTWMRKFNLgqknsrfaFVTDGPHDMWKFMQFQCLLSNIRMPHMFRsFINIKKTFK 80
Cdd:smart00479  51 TEIHGITPEMLDDAPTFEEVLEELLEFLRGRIL--------VAGNSAHFDLRFLKLEHPRLGIKQPPKLP-VIDTLKLAR 121

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1831512115   81 EKFNGLikgnGKSGIENMLERLDLSFVGNKHSGLDDATNIAAIAIQMMKLK 131
Cdd:smart00479 122 ATNPGL----PKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERL 168
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 2-130 2.63e-08

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 55.67  E-value: 2.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115   2 QFTKIAQETVDAA-PY---FREALQrlytWMRKFNLGQK--NSRFAFVTDGPHDMwKFMqfqcLLSNIRM------PHMF 69
Cdd:PTZ00315  115 ELTGITQSMVSRAdPFpvvYCEALQ----FLAEAGLGDAppLRSYCVVTCGDWDL-KTM----LPSQMRVsgqqgtPLSF 185

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1831512115  70 RSFINIKKTFKE--KFNGLIKGNGK------SGIENMLERLDLSFVGNKHSGLDDATNIAAIAIQMMKL 130
Cdd:PTZ00315  186 QRWCNLKKYMSQlgFGNGSGCGGGAtpplgpSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRR 254
 
Name Accession Description Interval E-value
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 2-128 6.71e-39

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 136.97  E-value: 6.71e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115   2 QFTKIAQETVDAAPYFREALQRLYTWMRKFNlgqknsRFAFVTDGPHDMWKFMQFQCLLSNIRMPHMFRSFINIKKTFKE 81
Cdd:cd06133    60 ELTGITQEDVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAK 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1831512115  82 KFNglikGNGKSGIENMLERLDLSFVGNKHSGLDDATNIAAIAIQMM 128
Cdd:cd06133   134 FYG----LKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-123 7.13e-21

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 88.18  E-value: 7.13e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115   1 MQFTKIAQETVDAAPYFREALQRLYTWMRKFNLGQKNSRFAFVTDGPHDMWKFMQFQCllsnIRMPHMFRSFINIKKTFK 80
Cdd:pfam00929  53 TKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNLLVAHNASFDVGFLRYDDKRFLKKPM----PKLNPVIDTLILDKATYK 128

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1831512115  81 EKFNglikgngkSGIENMLERLDLSFVGNKHSGLDDATNIAAI 123
Cdd:pfam00929 129 ELPG--------RSLDALAEKLGLEHIGRAHRALDDARATAKL 163
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 1-129 3.02e-20

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 87.22  E-value: 3.02e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115   1 MQFTKIAQETVDAAPYFREALQRLYTWMRKfnlgqknSRFAFVTDGPHDMwKFMQFQCLLSNIRMPhMFRSFINIKKTFK 80
Cdd:COG5018    61 TELTGITQEDVDSAPSFAEAIEDFKKWIGS-------EDYILCSWGDYDR-KQLERNCRFHGVPYP-FGDRHINLKKLFA 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1831512115  81 EKFnglikGNGKS-GIENMLERLDLSFVGNKHSGLDDATNIAAIAIQMMK 129
Cdd:COG5018   132 LYF-----GLKKRiGLKKALELLGLEFEGTHHRALDDARNTAKLFKKILG 176
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-131 5.27e-17

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 77.73  E-value: 5.27e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115    1 MQFTKIAQETVDAAPYFREALQRLYTWMRKFNLgqknsrfaFVTDGPHDMWKFMQFQCLLSNIRMPHMFRsFINIKKTFK 80
Cdd:smart00479  51 TEIHGITPEMLDDAPTFEEVLEELLEFLRGRIL--------VAGNSAHFDLRFLKLEHPRLGIKQPPKLP-VIDTLKLAR 121

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1831512115   81 EKFNGLikgnGKSGIENMLERLDLSFVGNKHSGLDDATNIAAIAIQMMKLK 131
Cdd:smart00479 122 ATNPGL----PKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERL 168
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 2-130 2.63e-08

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 55.67  E-value: 2.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831512115   2 QFTKIAQETVDAA-PY---FREALQrlytWMRKFNLGQK--NSRFAFVTDGPHDMwKFMqfqcLLSNIRM------PHMF 69
Cdd:PTZ00315  115 ELTGITQSMVSRAdPFpvvYCEALQ----FLAEAGLGDAppLRSYCVVTCGDWDL-KTM----LPSQMRVsgqqgtPLSF 185

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1831512115  70 RSFINIKKTFKE--KFNGLIKGNGK------SGIENMLERLDLSFVGNKHSGLDDATNIAAIAIQMMKL 130
Cdd:PTZ00315  186 QRWCNLKKYMSQlgFGNGSGCGGGAtpplgpSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRR 254
 
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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