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Conserved domains on  [gi|1039766605|ref|XP_017175460|]
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ERI1 exoribonuclease 3 isoform X13 [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

 Zoom to residue level

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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 ...
 1-133 3.03e-53

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: 167.78  E-value: 3.03e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGlldpnvKSIFVTCGDWDLKVMLPGQ 80
Cdd:cd06133    36 KEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQ 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1039766605  81 CHYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGI 133
Cdd:cd06133   110 CKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGL 162
 
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 ...
 1-133 3.03e-53

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: 167.78  E-value: 3.03e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGlldpnvKSIFVTCGDWDLKVMLPGQ 80
Cdd:cd06133    36 KEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQ 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1039766605  81 CHYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGI 133
Cdd:cd06133   110 CKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGL 162
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-133 2.24e-33

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: 117.07  E-value: 2.24e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQ 80
Cdd:pfam00929  30 NEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNLLVAHNASFDVGFLRYDDKRFLKKP 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1039766605  81 ChylgLPVADYFKQWINLKKAYSFAMGcwpkNGLLDMNKGLSLQHIGRPHSGI 133
Cdd:pfam00929 110 M----PKLNPVIDTLILDKATYKELPG----RSLDALAEKLGLEHIGRAHRAL 154
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 5-133 8.70e-30

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 114.99  E-value: 8.70e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   5 STFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLD--PNVKSIFVTCGDWDLKVMLPGQ-- 80
Cdd:PTZ00315   95 AEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVYCEALQFLAEAGLGDapPLRSYCVVTCGDWDLKTMLPSQmr 174

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039766605  81 -CHYLGLPVAdyFKQWINLKKAYS---FAMGCW---------PKNGLLDMNKGLSLQHIGRPHSGI 133
Cdd:PTZ00315  175 vSGQQGTPLS--FQRWCNLKKYMSqlgFGNGSGcgggatpplGPSDMPDMLQMLGLPLQGRHHSGI 238
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 2-133 1.86e-29

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 107.25  E-value: 1.86e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   2 EIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEglldpnvKSIFVTCGDWDLKVMLPgQC 81
Cdd:COG5018    39 EIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAIEDFKKWIGSE-------DYILCSWGDYDRKQLER-NC 110

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1039766605  82 HYLGLPVaDYFKQWINLKKAYSFAMGCwpkNGLLDMNKGLSLQHI---GRPHSGI 133
Cdd:COG5018   111 RFHGVPY-PFGDRHINLKKLFALYFGL---KKRIGLKKALELLGLefeGTHHRAL 161
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 2-133 4.41e-24

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 93.13  E-value: 4.41e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605    2 EIESTFHMYVQPvvHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQC 81
Cdd:smart00479  31 EIIEVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQP 108

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039766605   82 HYlgLPVADYFKqwinLKKAYSFAmgcWPKNGLLDMNKGLSLQHIGRPHSGI 133
Cdd:smart00479 109 PK--LPVIDTLK----LARATNPG---LPKYSLKKLAKRLLLEVIQRAHRAL 151
 
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 ...
 1-133 3.03e-53

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: 167.78  E-value: 3.03e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGlldpnvKSIFVTCGDWDLKVMLPGQ 80
Cdd:cd06133    36 KEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQ 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1039766605  81 CHYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGI 133
Cdd:cd06133   110 CKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGL 162
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-133 2.24e-33

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: 117.07  E-value: 2.24e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQ 80
Cdd:pfam00929  30 NEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNLLVAHNASFDVGFLRYDDKRFLKKP 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1039766605  81 ChylgLPVADYFKQWINLKKAYSFAMGcwpkNGLLDMNKGLSLQHIGRPHSGI 133
Cdd:pfam00929 110 M----PKLNPVIDTLILDKATYKELPG----RSLDALAEKLGLEHIGRAHRAL 154
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 5-133 8.70e-30

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 114.99  E-value: 8.70e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   5 STFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLD--PNVKSIFVTCGDWDLKVMLPGQ-- 80
Cdd:PTZ00315   95 AEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVYCEALQFLAEAGLGDapPLRSYCVVTCGDWDLKTMLPSQmr 174

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039766605  81 -CHYLGLPVAdyFKQWINLKKAYS---FAMGCW---------PKNGLLDMNKGLSLQHIGRPHSGI 133
Cdd:PTZ00315  175 vSGQQGTPLS--FQRWCNLKKYMSqlgFGNGSGcgggatpplGPSDMPDMLQMLGLPLQGRHHSGI 238
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 2-133 1.86e-29

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 107.25  E-value: 1.86e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   2 EIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEglldpnvKSIFVTCGDWDLKVMLPgQC 81
Cdd:COG5018    39 EIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAIEDFKKWIGSE-------DYILCSWGDYDRKQLER-NC 110

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1039766605  82 HYLGLPVaDYFKQWINLKKAYSFAMGCwpkNGLLDMNKGLSLQHI---GRPHSGI 133
Cdd:COG5018   111 RFHGVPY-PFGDRHINLKKLFALYFGL---KKRIGLKKALELLGLefeGTHHRAL 161
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 2-133 4.41e-24

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 93.13  E-value: 4.41e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605    2 EIESTFHMYVQPvvHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQC 81
Cdd:smart00479  31 EIIEVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQP 108

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039766605   82 HYlgLPVADYFKqwinLKKAYSFAmgcWPKNGLLDMNKGLSLQHIGRPHSGI 133
Cdd:smart00479 109 PK--LPVIDTLK----LARATNPG---LPKYSLKKLAKRLLLEVIQRAHRAL 151
PRK07748 PRK07748
3'-5' exonuclease KapD;
2-101 1.58e-09

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 55.08  E-value: 1.58e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039766605   2 EIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEwmakeglLDPNVKSIFVTCGDWDLKVM----- 76
Cdd:PRK07748   41 EVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEELVEKLAE-------YDKRCKPTIVTWGNMDMKVLkhnce 113

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1039766605  77 ---LP----GQCHYLGLPVADYF--KQWINLKKA 101
Cdd:PRK07748  114 kagVPfpfkGQCRDLSLEYKKFFgeRNQTGLWKA 147
polC PRK00448
DNA polymerase III PolC; Validated
 2-51 3.43e-07

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 49.84  E-value: 3.43e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039766605    2 EIESTFHMYVQPvvHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWM 51
Cdd:PRK00448   450 EIIDKFEFFIKP--GHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFC 497
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 2-51 4.67e-07

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 47.83  E-value: 4.67e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1039766605   2 EIESTFHMYVQPvvHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWM 51
Cdd:COG2176    39 EIVDRFSTLVNP--GRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFL 86
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-52 9.63e-05

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 40.93  E-value: 9.63e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1039766605   2 EIESTFHMYVQPvvHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMA 52
Cdd:COG0847    31 RIVETFHTLVNP--ERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
21-50 2.66e-04

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 41.06  E-value: 2.66e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 1039766605  21 PFCTELTGIIQAMVDGQPSLQQVLERVDEW 50
Cdd:PRK07883   63 PFITVLTGITTAMVAGAPPIEEVLPAFLEF 92
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 2-47 2.51e-03

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 38.01  E-value: 2.51e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1039766605   2 EIESTFHMYVQPVVhpQLTPFCTELTGIIQAMVDGQPSLQQVLERV 47
Cdd:PRK08074   35 EILERFSSFVNPER--PIPPFITELTGISEEMVKQAPLFEDVAPEI 78
 
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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