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Conserved domains on  [gi|2462543001|ref|XP_054233382|]
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piRNA biogenesis protein EXD1 isoform X6 [Homo sapiens]

Protein Classification

3'-5' exonuclease family protein( domain architecture ID 1085)

3'-5' exonuclease family protein may cleave nucleotides one at a time from the end (exo) of a polynucleotide chain

CATH:  3.30.420.10
Gene Ontology:  GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaQ_like_exo super family cl10012
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 1-142 3.74e-57

DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.


The actual alignment was detected with superfamily member cd06148:

Pssm-ID: 447876  Cd Length: 197  Bit Score: 184.80  E-value: 3.74e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462543001   1 MILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVADVLQFSMETGGYLPNCITTLQESLIKHLQVAPkylSFLEKR 80
Cdd:cd06148    59 DILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI---SLKEDV 135

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462543001  81 QKLIQENPEVWFIRPVSPSLLKILALEATYLLPLRLALLDEMMSDLTTLVDGYLNTYREGSA 142
Cdd:cd06148   136 KKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISKFLKAVFKYLNTERNLSE 197
 
Name Accession Description Interval E-value
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 1-142 3.74e-57

DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.


Pssm-ID: 99851  Cd Length: 197  Bit Score: 184.80  E-value: 3.74e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462543001   1 MILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVADVLQFSMETGGYLPNCITTLQESLIKHLQVAPkylSFLEKR 80
Cdd:cd06148    59 DILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI---SLKEDV 135

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462543001  81 QKLIQENPEVWFIRPVSPSLLKILALEATYLLPLRLALLDEMMSDLTTLVDGYLNTYREGSA 142
Cdd:cd06148   136 KKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISKFLKAVFKYLNTERNLSE 197
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
2-39 3.97e-07

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 51.41  E-value: 3.97e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2462543001   2 ILEDKRILKVIHDCRwlSD--CLSHQYGILLNNVFDTQVA 39
Cdd:COG0349    65 LLADPAIVKVFHAAR--EDleILYHLFGILPKPLFDTQIA 102
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 1-110 2.36e-05

3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes


Pssm-ID: 214681 [Multi-domain]  Cd Length: 172  Bit Score: 44.27  E-value: 2.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462543001    1 MILEDKRILKVIHDCRWLSDCLsHQYGILLNNVFDTQVADvlqfSMETGGYLPNCITTLQESLIKHlqvapkylsFLEKR 80
Cdd:smart00474  69 DLLEDETITKVGHNAKFDLHVL-ARFGIELENIFDTMLAA----YLLLGGPSKHGLATLLLGYLGV---------ELDKE 134

                           90       100       110
                   ....*....|....*....|....*....|
gi 2462543001   81 QKLiqenpEVWFIRPVSPSLLKILALEATY 110
Cdd:smart00474 135 EQK-----SDWGARPLSEEQLEYAAEDADA 159
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 1-49 2.37e-05

3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.


Pssm-ID: 396266 [Multi-domain]  Cd Length: 173  Bit Score: 44.21  E-value: 2.37e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2462543001   1 MILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVAD-VLQFSMETG 49
Cdd:pfam01612  70 RLLEDPNITKVGHNAKFDLEVLARDFGIKLRNLFDTMLAAyLLGYDRSHS 119
 
Name Accession Description Interval E-value
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 1-142 3.74e-57

DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.


Pssm-ID: 99851  Cd Length: 197  Bit Score: 184.80  E-value: 3.74e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462543001   1 MILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVADVLQFSMETGGYLPNCITTLQESLIKHLQVAPkylSFLEKR 80
Cdd:cd06148    59 DILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI---SLKEDV 135

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462543001  81 QKLIQENPEVWFIRPVSPSLLKILALEATYLLPLRLALLDEMMSDLTTLVDGYLNTYREGSA 142
Cdd:cd06148   136 KKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISKFLKAVFKYLNTERNLSE 197
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 2-39 1.34e-07

DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.


Pssm-ID: 176654 [Multi-domain]  Cd Length: 178  Bit Score: 50.99  E-value: 1.34e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2462543001   2 ILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVA 39
Cdd:cd06142    59 LLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIA 96
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
2-39 3.97e-07

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 51.41  E-value: 3.97e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2462543001   2 ILEDKRILKVIHDCRwlSD--CLSHQYGILLNNVFDTQVA 39
Cdd:COG0349    65 LLADPAIVKVFHAAR--EDleILYHLFGILPKPLFDTQIA 102
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 1-110 2.36e-05

3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes


Pssm-ID: 214681 [Multi-domain]  Cd Length: 172  Bit Score: 44.27  E-value: 2.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462543001    1 MILEDKRILKVIHDCRWLSDCLsHQYGILLNNVFDTQVADvlqfSMETGGYLPNCITTLQESLIKHlqvapkylsFLEKR 80
Cdd:smart00474  69 DLLEDETITKVGHNAKFDLHVL-ARFGIELENIFDTMLAA----YLLLGGPSKHGLATLLLGYLGV---------ELDKE 134

                           90       100       110
                   ....*....|....*....|....*....|
gi 2462543001   81 QKLiqenpEVWFIRPVSPSLLKILALEATY 110
Cdd:smart00474 135 EQK-----SDWGARPLSEEQLEYAAEDADA 159
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 1-49 2.37e-05

3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.


Pssm-ID: 396266 [Multi-domain]  Cd Length: 173  Bit Score: 44.21  E-value: 2.37e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2462543001   1 MILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVAD-VLQFSMETG 49
Cdd:pfam01612  70 RLLEDPNITKVGHNAKFDLEVLARDFGIKLRNLFDTMLAAyLLGYDRSHS 119
 
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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