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Conserved domains on  [gi|1907154176|ref|XP_036019564|]
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ERI1 exoribonuclease 3 isoform X16 [Mus musculus]

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 ...
 1-114 1.28e-38

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: 128.11  E-value: 1.28e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176   1 MVDGQPSLQQVLERVDEWMAKEGlldpnvKSIFVTCGDWDLKVMLPGQCHYLGLPVADYFKQWINLKKAYSFAMGCWPKN 80
Cdd:cd06133    68 DVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRT 141

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907154176  81 GLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTL 114
Cdd:cd06133   142 GLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175
 
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 ...
 1-114 1.28e-38

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: 128.11  E-value: 1.28e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176   1 MVDGQPSLQQVLERVDEWMAKEGlldpnvKSIFVTCGDWDLKVMLPGQCHYLGLPVADYFKQWINLKKAYSFAMGCWPKN 80
Cdd:cd06133    68 DVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRT 141

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907154176  81 GLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTL 114
Cdd:cd06133   142 GLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 1-124 5.83e-24

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 95.35  E-value: 5.83e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176   1 MVDGQPSLQQVLERVDEWMAKEGLLD--PNVKSIFVTCGDWDLKVMLPGQ---CHYLGLPVAdyFKQWINLKKAYS---F 72
Cdd:PTZ00315  123 MVSRADPFPVVYCEALQFLAEAGLGDapPLRSYCVVTCGDWDLKTMLPSQmrvSGQQGTPLS--FQRWCNLKKYMSqlgF 200

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907154176  73 AMGCW---------PKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGFIFKQT 124
Cdd:PTZ00315  201 GNGSGcgggatpplGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPT 261
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-111 3.09e-22

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: 85.87  E-value: 3.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176   1 MVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQChylgLPVADYFKQWINLKKAYSFAMGcwpkN 80
Cdd:pfam00929  62 MLDNKPSFEEVLEEFLEFLRKGNLLVAHNASFDVGFLRYDDKRFLKKPM----PKLNPVIDTLILDKATYKELPG----R 133

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907154176  81 GLLDMNKGLSLQHIGRPHSGIDDCKNIANIM 111
Cdd:pfam00929 134 SLDALAEKLGLEHIGRAHRALDDARATAKLF 164
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-119 1.94e-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: 73.49  E-value: 1.94e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176    1 MVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCHYLglPVADYFKqwinLKKAYSFAmgcWPKN 80
Cdd:smart00479  60 MLDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKL--PVIDTLK----LARATNPG---LPKY 130

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1907154176   81 GLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGF 119
Cdd:smart00479 131 SLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 1-114 4.55e-16

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 70.27  E-value: 4.55e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176   1 MVDGQPSLQQVLERVDEWMAKEglldpnvKSIFVTCGDWDLKVMLPgQCHYLGLPVaDYFKQWINLKKAYSFAMGCwpkN 80
Cdd:COG5018    70 DVDSAPSFAEAIEDFKKWIGSE-------DYILCSWGDYDRKQLER-NCRFHGVPY-PFGDRHINLKKLFALYFGL---K 137

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1907154176  81 GLLDMNKGLSLQHI---GRPHSGIDDCKNIANIMKTL 114
Cdd:COG5018   138 KRIGLKKALELLGLefeGTHHRALDDARNTAKLFKKI 174
 
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 ...
 1-114 1.28e-38

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: 128.11  E-value: 1.28e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176   1 MVDGQPSLQQVLERVDEWMAKEGlldpnvKSIFVTCGDWDLKVMLPGQCHYLGLPVADYFKQWINLKKAYSFAMGCWPKN 80
Cdd:cd06133    68 DVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRT 141

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907154176  81 GLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTL 114
Cdd:cd06133   142 GLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 1-124 5.83e-24

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 95.35  E-value: 5.83e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176   1 MVDGQPSLQQVLERVDEWMAKEGLLD--PNVKSIFVTCGDWDLKVMLPGQ---CHYLGLPVAdyFKQWINLKKAYS---F 72
Cdd:PTZ00315  123 MVSRADPFPVVYCEALQFLAEAGLGDapPLRSYCVVTCGDWDLKTMLPSQmrvSGQQGTPLS--FQRWCNLKKYMSqlgF 200

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907154176  73 AMGCW---------PKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGFIFKQT 124
Cdd:PTZ00315  201 GNGSGcgggatpplGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPT 261
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-111 3.09e-22

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: 85.87  E-value: 3.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176   1 MVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQChylgLPVADYFKQWINLKKAYSFAMGcwpkN 80
Cdd:pfam00929  62 MLDNKPSFEEVLEEFLEFLRKGNLLVAHNASFDVGFLRYDDKRFLKKPM----PKLNPVIDTLILDKATYKELPG----R 133

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907154176  81 GLLDMNKGLSLQHIGRPHSGIDDCKNIANIM 111
Cdd:pfam00929 134 SLDALAEKLGLEHIGRAHRALDDARATAKLF 164
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-119 1.94e-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: 73.49  E-value: 1.94e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176    1 MVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCHYLglPVADYFKqwinLKKAYSFAmgcWPKN 80
Cdd:smart00479  60 MLDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKL--PVIDTLK----LARATNPG---LPKY 130

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1907154176   81 GLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGF 119
Cdd:smart00479 131 SLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 1-114 4.55e-16

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 70.27  E-value: 4.55e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907154176   1 MVDGQPSLQQVLERVDEWMAKEglldpnvKSIFVTCGDWDLKVMLPgQCHYLGLPVaDYFKQWINLKKAYSFAMGCwpkN 80
Cdd:COG5018    70 DVDSAPSFAEAIEDFKKWIGSE-------DYILCSWGDYDRKQLER-NCRFHGVPY-PFGDRHINLKKLFALYFGL---K 137

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1907154176  81 GLLDMNKGLSLQHI---GRPHSGIDDCKNIANIMKTL 114
Cdd:COG5018   138 KRIGLKKALELLGLefeGTHHRALDDARNTAKLFKKI 174
 
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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