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Conserved domains on  [gi|678246464|ref|NP_001288630|]
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ERI1 exoribonuclease 3 isoform 4 [Homo sapiens]

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 ...
1-146 4.39e-61

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: 186.27  E-value: 4.39e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464   1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGlldpnvKSIFVTCGDWDLKVMLPGQ 80
Cdd:cd06133   36 KEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQ 109
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 678246464  81 CQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTL 146
Cdd:cd06133  110 CKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 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 ...
1-146 4.39e-61

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: 186.27  E-value: 4.39e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464   1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGlldpnvKSIFVTCGDWDLKVMLPGQ 80
Cdd:cd06133   36 KEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQ 109
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 678246464  81 CQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTL 146
Cdd:cd06133  110 CKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
5-156 1.67e-39

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 140.41  E-value: 1.67e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464   5 STFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLD--PNVKSIFVTCGDWDLKVMLPGQ-- 80
Cdd:PTZ00315  95 AEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVYCEALQFLAEAGLGDapPLRSYCVVTCGDWDLKTMLPSQmr 174
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464  81 -CQYLGLPVAdyFKQWINLKKAYS---FAMGCW---------PKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLA 147
Cdd:PTZ00315 175 vSGQQGTPLS--FQRWCNLKKYMSqlgFGNGSGcgggatpplGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELL 252

                 ....*....
gi 678246464 148 YRGFIFKQT 156
Cdd:PTZ00315 253 RRGLVIDPT 261
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
1-143 2.26e-39

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: 130.93  E-value: 2.26e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464    1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQ 80
Cdd:pfam00929  30 NEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNLLVAHNASFDVGFLRYDDKRFLKKP 109
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 678246464   81 CQylglPVADYFKQWINLKKAYSFAMGcwpkNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIM 143
Cdd:pfam00929 110 MP----KLNPVIDTLILDKATYKELPG----RSLDALAEKLGLEHIGRAHRALDDARATAKLF 164
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
2-146 1.33e-36

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 124.20  E-value: 1.33e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464   2 EIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEglldpnvKSIFVTCGDWDLKVMLPgQC 81
Cdd:COG5018   39 EIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAIEDFKKWIGSE-------DYILCSWGDYDRKQLER-NC 110
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 678246464  82 QYLGLPVaDYFKQWINLKKAYSFAMGCwpkNGLLDMNKGLSLQHI---GRPHSGIDDCKNIANIMKTL 146
Cdd:COG5018  111 RFHGVPY-PFGDRHINLKKLFALYFGL---KKRIGLKKALELLGLefeGTHHRALDDARNTAKLFKKI 174
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
2-151 4.70e-31

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 109.70  E-value: 4.70e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464     2 EIESTFHMYVQPvvHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQC 81
Cdd:smart00479  31 EIIEVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQP 108
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464    82 QYlgLPVADYFKqwinLKKAYSFAmgcWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGF 151
Cdd:smart00479 109 PK--LPVIDTLK----LARATNPG---LPKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
 
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 ...
1-146 4.39e-61

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: 186.27  E-value: 4.39e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464   1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGlldpnvKSIFVTCGDWDLKVMLPGQ 80
Cdd:cd06133   36 KEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNG------KYAFVTWGDWDLKDLLQNQ 109
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 678246464  81 CQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTL 146
Cdd:cd06133  110 CKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
5-156 1.67e-39

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 140.41  E-value: 1.67e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464   5 STFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLD--PNVKSIFVTCGDWDLKVMLPGQ-- 80
Cdd:PTZ00315  95 AEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVYCEALQFLAEAGLGDapPLRSYCVVTCGDWDLKTMLPSQmr 174
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464  81 -CQYLGLPVAdyFKQWINLKKAYS---FAMGCW---------PKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLA 147
Cdd:PTZ00315 175 vSGQQGTPLS--FQRWCNLKKYMSqlgFGNGSGcgggatpplGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELL 252

                 ....*....
gi 678246464 148 YRGFIFKQT 156
Cdd:PTZ00315 253 RRGLVIDPT 261
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
1-143 2.26e-39

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: 130.93  E-value: 2.26e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464    1 MEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQ 80
Cdd:pfam00929  30 NEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNLLVAHNASFDVGFLRYDDKRFLKKP 109
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 678246464   81 CQylglPVADYFKQWINLKKAYSFAMGcwpkNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIM 143
Cdd:pfam00929 110 MP----KLNPVIDTLILDKATYKELPG----RSLDALAEKLGLEHIGRAHRALDDARATAKLF 164
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
2-146 1.33e-36

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 124.20  E-value: 1.33e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464   2 EIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEglldpnvKSIFVTCGDWDLKVMLPgQC 81
Cdd:COG5018   39 EIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAIEDFKKWIGSE-------DYILCSWGDYDRKQLER-NC 110
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 678246464  82 QYLGLPVaDYFKQWINLKKAYSFAMGCwpkNGLLDMNKGLSLQHI---GRPHSGIDDCKNIANIMKTL 146
Cdd:COG5018  111 RFHGVPY-PFGDRHINLKKLFALYFGL---KKRIGLKKALELLGLefeGTHHRALDDARNTAKLFKKI 174
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
2-151 4.70e-31

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 109.70  E-value: 4.70e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464     2 EIESTFHMYVQPvvHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQC 81
Cdd:smart00479  31 EIIEVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQP 108
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464    82 QYlgLPVADYFKqwinLKKAYSFAmgcWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGF 151
Cdd:smart00479 109 PK--LPVIDTLK----LARATNPG---LPKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
PRK07748 PRK07748
3'-5' exonuclease KapD;
2-144 4.60e-13

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 63.94  E-value: 4.60e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 678246464   2 EIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEwmakeglLDPNVKSIFVTCGDWDLKVmLPGQC 81
Cdd:PRK07748  41 EVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEELVEKLAE-------YDKRCKPTIVTWGNMDMKV-LKHNC 112
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 678246464  82 QYLGLPVAdyFK-QWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMK 144
Cdd:PRK07748 113 EKAGVPFP--FKgQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFK 174
polC PRK00448
DNA polymerase III PolC; Validated
2-51 1.75e-07

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 49.45  E-value: 1.75e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 678246464    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 2.46e-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: 2.46e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 678246464   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 5.74e-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: 5.74e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 678246464   2 EIESTFHMYVQPvvHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMA 52
Cdd:COG0847   31 RIVETFHTLVNP--ERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
21-50 1.39e-04

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 41.06  E-value: 1.39e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 678246464  21 PFCTELTGIIQAMVDGQPSLQQVLERVDEW 50
Cdd:PRK07883  63 PFITVLTGITTAMVAGAPPIEEVLPAFLEF 92
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
2-47 1.36e-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: 1.36e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 678246464   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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