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Conserved domains on  [gi|1867157823|ref|NP_001371965|]
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piRNA biogenesis protein EXD1 isoform 3 [Homo sapiens]

Protein Classification

3'-5' exonuclease family protein( domain architecture ID 10150270)

3'-5' exonuclease family protein belonging to the DnaQ-like (or DEDD) 3'-5' exonuclease superfamily, similar to human piRNA biogenesis protein EXD1, an RNA-binding component of the PET complex, a multiprotein complex required for the processing of piRNAs during spermatogenesis

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
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 124-322 2.36e-86

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: 265.30  E-value: 2.36e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 124 GAAILHIKKQNVLSVAAEGANVCRHGKLCWLQVAT-NCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCL 202
Cdd:cd06148     1 KEAIIHLKKQKVIGLDCEGVNLGRKGKLCLVQIATrTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 203 SHQYGILLNNVFDTQVADVLQFSMETGGYLPNCITTLQESLIKHLQVAPkylSFLEKRQKLIQENPEVWFIRPVSPSLLK 282
Cdd:cd06148    81 YHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI---SLKEDVKKLMREDPKFWALRPLTEDMIR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1867157823 283 ILALEATYLLPLRLALLDEMMSDLTTLVDGYLNTYREGSA 322
Cdd:cd06148   158 YAALDVLCLLPLYYAMLDALISKFLKAVFKYLNTERNLSE 197
 
Name Accession Description Interval E-value
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 124-322 2.36e-86

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: 265.30  E-value: 2.36e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 124 GAAILHIKKQNVLSVAAEGANVCRHGKLCWLQVAT-NCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCL 202
Cdd:cd06148     1 KEAIIHLKKQKVIGLDCEGVNLGRKGKLCLVQIATrTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 203 SHQYGILLNNVFDTQVADVLQFSMETGGYLPNCITTLQESLIKHLQVAPkylSFLEKRQKLIQENPEVWFIRPVSPSLLK 282
Cdd:cd06148    81 YHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI---SLKEDVKKLMREDPKFWALRPLTEDMIR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1867157823 283 ILALEATYLLPLRLALLDEMMSDLTTLVDGYLNTYREGSA 322
Cdd:cd06148   158 YAALDVLCLLPLYYAMLDALISKFLKAVFKYLNTERNLSE 197
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
150-219 6.53e-12

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 67.20  E-value: 6.53e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1867157823 150 KLCWLQVATNCRVYLFDIFLLGSRAfhnGLQMILEDKRILKVIHDCRwlSD--CLSHQYGILLNNVFDTQVA 219
Cdd:COG0349    36 RLCLIQLADGEEVALIDPLAIGDLS---PLWELLADPAIVKVFHAAR--EDleILYHLFGILPKPLFDTQIA 102
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 135-290 8.79e-10

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: 57.75  E-value: 8.79e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823  135 VLSVAAEGANV-CRHGKLCWLQVATN-CRVYLFDIFLLGSRAfhNGLQMILEDKRILKVIHDCRWLSDCLsHQYGILLNN 212
Cdd:smart00474  23 EVALDTETTGLdSYSGKLVLIQISVTgEGAFIIDPLALGDDL--EILKDLLEDETITKVGHNAKFDLHVL-ARFGIELEN 99

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1867157823  213 VFDTQVADvlqfSMETGGYLPNCITTLQESLIKHlqvapkylsFLEKRQKLiqenpEVWFIRPVSPSLLKILALEATY 290
Cdd:smart00474 100 IFDTMLAA----YLLLGGPSKHGLATLLLGYLGV---------ELDKEEQK-----SDWGARPLSEEQLEYAAEDADA 159
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 149-229 2.29e-08

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: 53.84  E-value: 2.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 149 GKLCWLQVATNCRVYLFDIFLLGSrAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVAD-VLQFSME 227
Cdd:pfam01612  39 LRGALIQIGTGEGAYIIDPLALGD-DVLSALKRLLEDPNITKVGHNAKFDLEVLARDFGIKLRNLFDTMLAAyLLGYDRS 117


                  ..
gi 1867157823 228 TG 229
Cdd:pfam01612 118 HS 119
 
Name Accession Description Interval E-value
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 124-322 2.36e-86

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: 265.30  E-value: 2.36e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 124 GAAILHIKKQNVLSVAAEGANVCRHGKLCWLQVAT-NCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCL 202
Cdd:cd06148     1 KEAIIHLKKQKVIGLDCEGVNLGRKGKLCLVQIATrTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 203 SHQYGILLNNVFDTQVADVLQFSMETGGYLPNCITTLQESLIKHLQVAPkylSFLEKRQKLIQENPEVWFIRPVSPSLLK 282
Cdd:cd06148    81 YHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI---SLKEDVKKLMREDPKFWALRPLTEDMIR 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1867157823 283 ILALEATYLLPLRLALLDEMMSDLTTLVDGYLNTYREGSA 322
Cdd:cd06148   158 YAALDVLCLLPLYYAMLDALISKFLKAVFKYLNTERNLSE 197
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
150-219 6.53e-12

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 67.20  E-value: 6.53e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1867157823 150 KLCWLQVATNCRVYLFDIFLLGSRAfhnGLQMILEDKRILKVIHDCRwlSD--CLSHQYGILLNNVFDTQVA 219
Cdd:COG0349    36 RLCLIQLADGEEVALIDPLAIGDLS---PLWELLADPAIVKVFHAAR--EDleILYHLFGILPKPLFDTQIA 102
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 125-219 1.38e-11

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: 63.32  E-value: 1.38e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 125 AAILHIKKQNVLSVAAEGANV-CRHGKLCWLQVATNCRVYLFDIFLLGsrAFHNgLQMILEDKRILKVIHDCRWLSDCLS 203
Cdd:cd06142     4 DLCERLASAGVIAVDTEFMRLnTYYPRLCLIQISTGGEVYLIDPLAIG--DLSP-LKELLADPNIVKVFHAAREDLELLK 80

                          90
                  ....*....|....*.
gi 1867157823 204 HQYGILLNNVFDTQVA 219
Cdd:cd06142    81 RDFGILPQNLFDTQIA 96
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 135-290 8.79e-10

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: 57.75  E-value: 8.79e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823  135 VLSVAAEGANV-CRHGKLCWLQVATN-CRVYLFDIFLLGSRAfhNGLQMILEDKRILKVIHDCRWLSDCLsHQYGILLNN 212
Cdd:smart00474  23 EVALDTETTGLdSYSGKLVLIQISVTgEGAFIIDPLALGDDL--EILKDLLEDETITKVGHNAKFDLHVL-ARFGIELEN 99

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1867157823  213 VFDTQVADvlqfSMETGGYLPNCITTLQESLIKHlqvapkylsFLEKRQKLiqenpEVWFIRPVSPSLLKILALEATY 290
Cdd:smart00474 100 IFDTMLAA----YLLLGGPSKHGLATLLLGYLGV---------ELDKEEQK-----SDWGARPLSEEQLEYAAEDADA 159
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 149-229 2.29e-08

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: 53.84  E-value: 2.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 149 GKLCWLQVATNCRVYLFDIFLLGSrAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVAD-VLQFSME 227
Cdd:pfam01612  39 LRGALIQIGTGEGAYIIDPLALGD-DVLSALKRLLEDPNITKVGHNAKFDLEVLARDFGIKLRNLFDTMLAAyLLGYDRS 117


                  ..
gi 1867157823 228 TG 229
Cdd:pfam01612 118 HS 119
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 148-218 7.55e-08

DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. 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. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.


Pssm-ID: 176653 [Multi-domain]  Cd Length: 170  Bit Score: 52.20  E-value: 7.55e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1867157823 148 HGKLCWLQVATNCRVYLFDIFLLGsrAFHNGLQMILEDKRILKVIHDCRwlSDC--LSHQYGILLNNVFDTQV 218
Cdd:cd06141    36 RNKVALLQLATESRCLLFQLAHMD--KLPPSLKQLLEDPSILKVGVGIK--GDArkLARDFGIEVRGVVDLSH 104
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
 149-219 3.96e-05

DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains 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. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif.


Pssm-ID: 176650 [Multi-domain]  Cd Length: 161  Bit Score: 44.04  E-value: 3.96e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1867157823 149 GKLCWLQVATNC-RVYLFDIflLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQVA 219
Cdd:cd06129    30 GEVALIQLCVSEeKCYLFDP--LSLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIA 99
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
 152-225 3.17e-03

DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins; Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain 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. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.


Pssm-ID: 99850 [Multi-domain]  Cd Length: 192  Bit Score: 39.12  E-value: 3.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1867157823 152 CWLQVATNCRVYLFDIFLLgsraFHNG--LQMILEDKRILKVIH----DCRWLSdclsHQYGILLNNVFDT-QVADVLQF 224
Cdd:cd06147    44 CLMQISTREEDYIVDTLKL----RDDMhiLNEVFTDPNILKVFHgadsDIIWLQ----RDFGLYVVNLFDTgQAARVLNL 115


                  .
gi 1867157823 225 S 225
Cdd:cd06147   116 P 116
 
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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