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Conserved domains on  [gi|21356549|ref|NP_650075|]
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exonuclease 3'-5' domain-containing 2, isoform A [Drosophila melanogaster]

Protein Classification

3'-5' exonuclease( domain architecture ID 10150121)

3'-5' exonuclease catalyzes the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction; similar to human exonuclease 3'-5' domain-containing protein 2 that that has both 3'-5' exoribonuclease and exodeoxyribonuclease activities

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 62-226 8.03e-55

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: 183.16  E-value: 8.03e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  62 TTQWVLNELKNHcqtFKVLGFDCEWITVG--GSRRPVALLQLSSHRgLCALFRLCHMKQIPQDLRELLEDDSVIKVGVAP 139
Cdd:cd06141   6 DAEEAVKELLGK---EKVVGFDTEWRPSFrkGKRNKVALLQLATES-RCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549 140 QEDAMKLSHDYGVGVASTLDLRFLCVMAGH--KPEGLGKLSKTHLNYTLDKHWRLACSNWEAKTLEPKQLDYAANDALMA 217
Cdd:cd06141  82 KGDARKLARDFGIEVRGVVDLSHLAKRVGPrrKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYAS 161


                ....*....
gi 21356549 218 VAIYQKLCR 226
Cdd:cd06141 162 LELYRKLLA 170
 
Name Accession Description Interval E-value
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 62-226 8.03e-55

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: 183.16  E-value: 8.03e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  62 TTQWVLNELKNHcqtFKVLGFDCEWITVG--GSRRPVALLQLSSHRgLCALFRLCHMKQIPQDLRELLEDDSVIKVGVAP 139
Cdd:cd06141   6 DAEEAVKELLGK---EKVVGFDTEWRPSFrkGKRNKVALLQLATES-RCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549 140 QEDAMKLSHDYGVGVASTLDLRFLCVMAGH--KPEGLGKLSKTHLNYTLDKHWRLACSNWEAKTLEPKQLDYAANDALMA 217
Cdd:cd06141  82 KGDARKLARDFGIEVRGVVDLSHLAKRVGPrrKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYAS 161


                ....*....
gi 21356549 218 VAIYQKLCR 226
Cdd:cd06141 162 LELYRKLLA 170
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 66-224 1.11e-17

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: 80.86  E-value: 1.11e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549     66 VLNELKNHCqtfKVLGFDCEWITVGGSRRPVALLQLSSHRGLCALFRLCHMKQIPQDLRELLEDDSVIKVGVAPQEDAMK 145
Cdd:smart00474  13 LLEKLRAAG---GEVALDTETTGLDSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGHNAKFDLHV 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549    146 LsHDYGVGVASTLDLRFL--CVMAGHKPEGLGKLSKTHLNYTLDKHWRlaCSNWEAKTLEPKQLDYAANDALMAVAIYQK 223
Cdd:smart00474  90 L-ARFGIELENIFDTMLAayLLLGGPSKHGLATLLLGYLGVELDKEEQ--KSDWGARPLSEEQLEYAAEDADALLRLYEK 166


                   .
gi 21356549    224 L 224
Cdd:smart00474 167 L 167
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 66-229 2.74e-14

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: 71.18  E-value: 2.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549    66 VLNELKNHcqtfKVLGFDCEW----ITVGGSRrpVALLQLSSHRGlCALFRLCHMKQIPQD-LRELLEDDSVIKVGVAPQ 140
Cdd:pfam01612  13 LIEELLNA----PYVAVDTETtsldTYSYYLR--GALIQIGTGEG-AYIIDPLALGDDVLSaLKRLLEDPNITKVGHNAK 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549   141 EDAMKLSHDYGVGVASTLDLRFLCVMAGhKPE--GLGKLSKTHLNYTLDKhwRLACSNWEAKTLEPKQLDYAANDALMAV 218
Cdd:pfam01612  86 FDLEVLARDFGIKLRNLFDTMLAAYLLG-YDRshSLADLAEKYLGVELDK--EEQCSDWQARPLSEEQLRYAALDADYLL 162

                         170
                  ....*....|.
gi 21356549   219 AIYQKLCRDLQ 229
Cdd:pfam01612 163 RLYDKLRKELE 173
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
62-229 3.61e-12

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 67.97  E-value: 3.61e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  62 TTQWVLNELKNHCQTFKVLGFDCEwiTVG-GSRRP-VALLQLSSHRGlCALFR-LChmkqiPQD---LRELLEDDSVIKV 135
Cdd:COG0349   3 TTDEELAALCARLAQAPAVAVDTE--FMReRTYYPrLCLIQLADGEE-VALIDpLA-----IGDlspLWELLADPAIVKV 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549 136 GVAPQEDAMKLSHDYGVGVASTLDLRFLCVMAGHKPE-GLGKLSKTHLNYTLDKHWRLacSNWEAKTLEPKQLDYAANDA 214
Cdd:COG0349  75 FHAAREDLEILYHLFGILPKPLFDTQIAAALLGYGDSvGYAALVEELLGVELDKSEQR--SDWLRRPLSEEQLEYAAADV 152

                       170
                ....*....|....*
gi 21356549 215 LMAVAIYQKLCRDLQ 229
Cdd:COG0349 153 RYLLPLYEKLLEELE 167
 
Name Accession Description Interval E-value
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 62-226 8.03e-55

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: 183.16  E-value: 8.03e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  62 TTQWVLNELKNHcqtFKVLGFDCEWITVG--GSRRPVALLQLSSHRgLCALFRLCHMKQIPQDLRELLEDDSVIKVGVAP 139
Cdd:cd06141   6 DAEEAVKELLGK---EKVVGFDTEWRPSFrkGKRNKVALLQLATES-RCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549 140 QEDAMKLSHDYGVGVASTLDLRFLCVMAGH--KPEGLGKLSKTHLNYTLDKHWRLACSNWEAKTLEPKQLDYAANDALMA 217
Cdd:cd06141  82 KGDARKLARDFGIEVRGVVDLSHLAKRVGPrrKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYAS 161


                ....*....
gi 21356549 218 VAIYQKLCR 226
Cdd:cd06141 162 LELYRKLLA 170
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
 77-224 5.16e-20

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: 87.18  E-value: 5.16e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  77 FKVLGFDCEWITVGGSRRPVALLQLSSHRGLCALFRLCHMKQIPQDLRELLEDDSVIKVGVAPQEDAMKLSHDYGVGVAS 156
Cdd:cd06129  13 GDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQR 92

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549 157 TLDLRFLCVMAGhKPE--GLGKLSKTHLNYTLDKHWRlaCSNWEAKTLEPKQLDYAANDALMAVAIYQKL 224
Cdd:cd06129  93 LFDTTIAANLKG-LPErwSLASLVEHFLGKTLDKSIS--CADWSYRPLTEDQKLYAAADVYALLIIYTKL 159
DEDDy_polA_RNaseD_like_exo cd09018
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ...
 79-224 3.03e-18

DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity.


Pssm-ID: 176656 [Multi-domain]  Cd Length: 150  Bit Score: 81.90  E-value: 3.03e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  79 VLGFDCEWITVGGSRRPVALLQLSSHRGLCALFRLCHMKQIPQDLRELLEDDSVIKVGVAPQEDAMKLSHDYGVGVASTL 158
Cdd:cd09018   1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAF 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21356549 159 DLRFLCVMAGHKPE--GLGKLSKTHLNYTLDKHWRLACSNWEAKTLEPKQLDYAANDALMAVAIYQKL 224
Cdd:cd09018  81 DTMLEAYILNSVAGrwDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKL 148
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 66-224 1.11e-17

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: 80.86  E-value: 1.11e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549     66 VLNELKNHCqtfKVLGFDCEWITVGGSRRPVALLQLSSHRGLCALFRLCHMKQIPQDLRELLEDDSVIKVGVAPQEDAMK 145
Cdd:smart00474  13 LLEKLRAAG---GEVALDTETTGLDSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGHNAKFDLHV 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549    146 LsHDYGVGVASTLDLRFL--CVMAGHKPEGLGKLSKTHLNYTLDKHWRlaCSNWEAKTLEPKQLDYAANDALMAVAIYQK 223
Cdd:smart00474  90 L-ARFGIELENIFDTMLAayLLLGGPSKHGLATLLLGYLGVELDKEEQ--KSDWGARPLSEEQLEYAAEDADALLRLYEK 166


                   .
gi 21356549    224 L 224
Cdd:smart00474 167 L 167
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
 79-226 9.32e-17

DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. 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.


Pssm-ID: 176655  Cd Length: 193  Bit Score: 78.87  E-value: 9.32e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  79 VLGFDCEW--ITVGGSRRPVALLQLSSHRG-----LCALFRLChmkqiPQDLRE----LLEDDSVIKVGVAPQEDAMKLS 147
Cdd:cd06146  24 VVGIDSEWkpSFLGDSDPRVAILQLATEDEvflldLLALENLE-----SEDWDRllkrLFEDPDVLKLGFGFKQDLKALS 98

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549 148 HDYGVGVASTLDL-RFLCVMAGHK-----------------PEGLGKLSKTHLNYTLDKHWRlaCSNWEAKTLEPKQLDY 209
Cdd:cd06146  99 ASYPALKCMFERVqNVLDLQNLAKelqksdmgrlkgnlpskTKGLADLVQEVLGKPLDKSEQ--CSNWERRPLREEQILY 176

                       170
                ....*....|....*..
gi 21356549 210 AANDALMAVAIYQKLCR 226
Cdd:cd06146 177 AALDAYCLLEVFDKLLE 193
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 67-229 1.08e-16

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: 77.96  E-value: 1.08e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  67 LNELKNHCQTFKVLGFDCEWITVGGSRRPVALLQLSShRGLCALFRLCHMKQIPqDLRELLEDDSVIKVGVAPQEDAMKL 146
Cdd:cd06142   2 LEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQIST-GGEVYLIDPLAIGDLS-PLKELLADPNIVKVFHAAREDLELL 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549 147 SHDYGVGVASTLDLRFLCVMAGHKPE-GLGKLSKTHLNYTLDKHWRlaCSNWEAKTLEPKQLDYAANDALMAVAIYQKLC 225
Cdd:cd06142  80 KRDFGILPQNLFDTQIAARLLGLGDSvGLAALVEELLGVELDKGEQ--RSDWSKRPLTDEQLEYAALDVRYLLPLYEKLK 157


                ....
gi 21356549 226 RDLQ 229
Cdd:cd06142 158 EELE 161
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 66-229 2.74e-14

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: 71.18  E-value: 2.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549    66 VLNELKNHcqtfKVLGFDCEW----ITVGGSRrpVALLQLSSHRGlCALFRLCHMKQIPQD-LRELLEDDSVIKVGVAPQ 140
Cdd:pfam01612  13 LIEELLNA----PYVAVDTETtsldTYSYYLR--GALIQIGTGEG-AYIIDPLALGDDVLSaLKRLLEDPNITKVGHNAK 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549   141 EDAMKLSHDYGVGVASTLDLRFLCVMAGhKPE--GLGKLSKTHLNYTLDKhwRLACSNWEAKTLEPKQLDYAANDALMAV 218
Cdd:pfam01612  86 FDLEVLARDFGIKLRNLFDTMLAAYLLG-YDRshSLADLAEKYLGVELDK--EEQCSDWQARPLSEEQLRYAALDADYLL 162

                         170
                  ....*....|.
gi 21356549   219 AIYQKLCRDLQ 229
Cdd:pfam01612 163 RLYDKLRKELE 173
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
62-229 3.61e-12

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 67.97  E-value: 3.61e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  62 TTQWVLNELKNHCQTFKVLGFDCEwiTVG-GSRRP-VALLQLSSHRGlCALFR-LChmkqiPQD---LRELLEDDSVIKV 135
Cdd:COG0349   3 TTDEELAALCARLAQAPAVAVDTE--FMReRTYYPrLCLIQLADGEE-VALIDpLA-----IGDlspLWELLADPAIVKV 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549 136 GVAPQEDAMKLSHDYGVGVASTLDLRFLCVMAGHKPE-GLGKLSKTHLNYTLDKHWRLacSNWEAKTLEPKQLDYAANDA 214
Cdd:COG0349  75 FHAAREDLEILYHLFGILPKPLFDTQIAAALLGYGDSvGYAALVEELLGVELDKSEQR--SDWLRRPLSEEQLEYAAADV 152

                       170
                ....*....|....*
gi 21356549 215 LMAVAIYQKLCRDLQ 229
Cdd:COG0349 153 RYLLPLYEKLLEELE 167
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 78-234 2.57e-06

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: 48.43  E-value: 2.57e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549  78 KVLGFDCEWITVG--GsrrPVALLQLSSHRGLCALFRLCHMKQIPQD--LRELLEDDSVIKVGVAPQEDAMKLSHDYGV- 152
Cdd:cd06148  11 KVIGLDCEGVNLGrkG---KLCLVQIATRTGQIYLFDILKLGSIVFIngLKDILESKKILKVIHDCRRDSDALYHQYGIk 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356549 153 -------------------------GVASTLDLRflcvmAGHKPEGLGKLSKTHLNYTLDkhwrlaCSNWEAKTLEPKQL 207
Cdd:cd06148  88 lnnvfdtqvadallqeqetggfnpdRVISLVQLL-----DKYLYISISLKEDVKKLMRED------PKFWALRPLTEDMI 156

                       170       180
                ....*....|....*....|....*..
gi 21356549 208 DYAANDALMAVAIYQKLCRDLQPKHFW 234
Cdd:cd06148 157 RYAALDVLCLLPLYYAMLDALISKFLK 183
 
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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