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Conserved domains on  [gi|1622915789|ref|XP_028697228|]
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ERI1 exoribonuclease 2 isoform X3 [Macaca mulatta]

Protein Classification

ERI1 exoribonuclease 2( domain architecture ID 10150091)

ERI1 exoribonuclease 2 is a 3'-5' exonuclease family protein containing a GRF zinc finger; and may catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676|GO:0008270
PubMed:  11988770|11222749|17210253|12665246
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 ...
 2-137 2.79e-43

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: 152.76  E-value: 2.79e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   2 ELTGIKQAQVDEGVPLKICLSQFCKWIHKIQQqkniifatgvsepstsevklCAFVTWSDWDLGVCLEYECKRKQLLKPV 81
Cdd:cd06133    60 ELTGITQEDVDNAPSFPEVLKEFLEWLGKNGK--------------------YAFVTWGDWDLKDLLQNQCKYKIINLPP 119

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622915789  82 FLNSWIDLRATYKLFYRR-KPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMI 137
Cdd:cd06133   120 FFRQWIDLKKEFAKFYGLkKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 501-549 1.61e-17

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


:

Pssm-ID: 462017  Cd Length: 45  Bit Score: 76.29  E-value: 1.61e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1622915789 501 PLCKCGRRSKRLVVSNNGPNHGKVFYCCPIGKYqenrKCCGYFKWEQTL 549
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGRE----KQCGFFQWADEV 45
 
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 ...
 2-137 2.79e-43

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: 152.76  E-value: 2.79e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   2 ELTGIKQAQVDEGVPLKICLSQFCKWIHKIQQqkniifatgvsepstsevklCAFVTWSDWDLGVCLEYECKRKQLLKPV 81
Cdd:cd06133    60 ELTGITQEDVDNAPSFPEVLKEFLEWLGKNGK--------------------YAFVTWGDWDLKDLLQNQCKYKIINLPP 119

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622915789  82 FLNSWIDLRATYKLFYRR-KPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMI 137
Cdd:cd06133   120 FFRQWIDLKKEFAKFYGLkKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 1-140 1.33e-25

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 103.79  E-value: 1.33e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   1 MELTGIKQAQVDEGVPLKICLSQFCKWIHKiqqqkniifatgvsepstsevKLCAFVTWSDWDLGVcLEYECKRKQLlKP 80
Cdd:COG5018    61 TELTGITQEDVDSAPSFAEAIEDFKKWIGS---------------------EDYILCSWGDYDRKQ-LERNCRFHGV-PY 117

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622915789  81 VFLNSWIDLRATYKLFYR-RKPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMIRDG 140
Cdd:COG5018   118 PFGDRHINLKKLFALYFGlKKRIGLKKALELLGLEFEGTHHRALDDARNTAKLFKKILGDK 178
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 501-549 1.61e-17

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 76.29  E-value: 1.61e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1622915789 501 PLCKCGRRSKRLVVSNNGPNHGKVFYCCPIGKYqenrKCCGYFKWEQTL 549
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGRE----KQCGFFQWADEV 45
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-132 7.20e-11

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: 60.83  E-value: 7.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   1 MELTGIKQAQVDEGVPLKICLSQFCKWIHKIQ--QQKNIIFatgvsepstsevklcaFVTWSDWDLGVCLEYECKRKqll 78
Cdd:pfam00929  53 TKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNllVAHNASF----------------DVGFLRYDDKRFLKKPMPKL--- 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622915789  79 kPVFLNSWIDLRATYKLFYRRkpkGLSGALQEVGIEFSGREHSGLDDSRNTALL 132
Cdd:pfam00929 114 -NPVIDTLILDKATYKELPGR---SLDALAEKLGLEHIGRAHRALDDARATAKL 163
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-140 1.99e-10

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 60.01  E-value: 1.99e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789    1 MELTGIKQAQVDEGVPLKICLSQFCKWIHKiqqqkNIIFATgvsepstsevklcafvTWSDWDLGVcLEYECKRKQLLKP 80
Cdd:smart00479  51 TEIHGITPEMLDDAPTFEEVLEELLEFLRG-----RILVAG----------------NSAHFDLRF-LKLEHPRLGIKQP 108

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622915789   81 vFLNSWID-LRATYKLFYRRKPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMIRDG 140
Cdd:smart00479 109 -PKLPVIDtLKLARATNPGLPKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERL 168
PRK07748 PRK07748
3'-5' exonuclease KapD;
4-140 6.13e-10

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 59.32  E-value: 6.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   4 TGIKQAQVDEGvplkICLSQFckwIHKIQQQKniifatgvsEPSTSEVklcafVTWSDWDLGVcLEYECKRKQLLKPvFL 83
Cdd:PRK07748   66 LGITQEDVDKG----ISFEEL---VEKLAEYD---------KRCKPTI-----VTWGNMDMKV-LKHNCEKAGVPFP-FK 122

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622915789  84 NSWIDLRATYKLFY-RRKPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMIRDG 140
Cdd:PRK07748  123 GQCRDLSLEYKKFFgERNQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKDK 180
 
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 ...
 2-137 2.79e-43

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: 152.76  E-value: 2.79e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   2 ELTGIKQAQVDEGVPLKICLSQFCKWIHKIQQqkniifatgvsepstsevklCAFVTWSDWDLGVCLEYECKRKQLLKPV 81
Cdd:cd06133    60 ELTGITQEDVDNAPSFPEVLKEFLEWLGKNGK--------------------YAFVTWGDWDLKDLLQNQCKYKIINLPP 119

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622915789  82 FLNSWIDLRATYKLFYRR-KPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMI 137
Cdd:cd06133   120 FFRQWIDLKKEFAKFYGLkKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 1-140 1.33e-25

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 103.79  E-value: 1.33e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   1 MELTGIKQAQVDEGVPLKICLSQFCKWIHKiqqqkniifatgvsepstsevKLCAFVTWSDWDLGVcLEYECKRKQLlKP 80
Cdd:COG5018    61 TELTGITQEDVDSAPSFAEAIEDFKKWIGS---------------------EDYILCSWGDYDRKQ-LERNCRFHGV-PY 117

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622915789  81 VFLNSWIDLRATYKLFYR-RKPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMIRDG 140
Cdd:COG5018   118 PFGDRHINLKKLFALYFGlKKRIGLKKALELLGLEFEGTHHRALDDARNTAKLFKKILGDK 178
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 501-549 1.61e-17

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 76.29  E-value: 1.61e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1622915789 501 PLCKCGRRSKRLVVSNNGPNHGKVFYCCPIGKYqenrKCCGYFKWEQTL 549
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGRE----KQCGFFQWADEV 45
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 1-132 7.20e-11

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: 60.83  E-value: 7.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   1 MELTGIKQAQVDEGVPLKICLSQFCKWIHKIQ--QQKNIIFatgvsepstsevklcaFVTWSDWDLGVCLEYECKRKqll 78
Cdd:pfam00929  53 TKFTGITQAMLDNKPSFEEVLEEFLEFLRKGNllVAHNASF----------------DVGFLRYDDKRFLKKPMPKL--- 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622915789  79 kPVFLNSWIDLRATYKLFYRRkpkGLSGALQEVGIEFSGREHSGLDDSRNTALL 132
Cdd:pfam00929 114 -NPVIDTLILDKATYKELPGR---SLDALAEKLGLEHIGRAHRALDDARATAKL 163
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 1-140 1.99e-10

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 60.01  E-value: 1.99e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789    1 MELTGIKQAQVDEGVPLKICLSQFCKWIHKiqqqkNIIFATgvsepstsevklcafvTWSDWDLGVcLEYECKRKQLLKP 80
Cdd:smart00479  51 TEIHGITPEMLDDAPTFEEVLEELLEFLRG-----RILVAG----------------NSAHFDLRF-LKLEHPRLGIKQP 108

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622915789   81 vFLNSWID-LRATYKLFYRRKPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMIRDG 140
Cdd:smart00479 109 -PKLPVIDtLKLARATNPGLPKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERL 168
PRK07748 PRK07748
3'-5' exonuclease KapD;
4-140 6.13e-10

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 59.32  E-value: 6.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   4 TGIKQAQVDEGvplkICLSQFckwIHKIQQQKniifatgvsEPSTSEVklcafVTWSDWDLGVcLEYECKRKQLLKPvFL 83
Cdd:PRK07748   66 LGITQEDVDKG----ISFEEL---VEKLAEYD---------KRCKPTI-----VTWGNMDMKV-LKHNCEKAGVPFP-FK 122

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622915789  84 NSWIDLRATYKLFY-RRKPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMIRDG 140
Cdd:PRK07748  123 GQCRDLSLEYKKFFgERNQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKDK 180
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 2-161 3.62e-09

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 59.52  E-value: 3.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789   2 ELTGIKQAQVDEGVPLKIClsqFCKWIHKIQQQkniifATGVSEPSTSEVklcaFVTWSDWDLGVCLEYECK-RKQLLKP 80
Cdd:PTZ00315  115 ELTGITQSMVSRADPFPVV---YCEALQFLAEA-----GLGDAPPLRSYC----VVTCGDWDLKTMLPSQMRvSGQQGTP 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622915789  81 VFLNSWIDLRATYKLFY-------------RRKPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMIRDGCVMKITR 147
Cdd:PTZ00315  183 LSFQRWCNLKKYMSQLGfgngsgcgggatpPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTF 262

                         170
                  ....*....|....
gi 1622915789 148 SLNKVPTKNSSILA 161
Cdd:PTZ00315  263 DTAPFRRWHAPTEA 276
 
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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