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Conserved domains on  [gi|21430260|gb|AAM50808|]
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LD32220p [Drosophila melanogaster]

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 ...
 54-227 5.12e-14

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: 68.85  E-value: 5.12e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260  54 DIKDQKIISLLVEPSFYGRHHPTSILVVATCNG-TYIFDIKALGLIFLE--LAKILEADQPRKVIHYSHRIADHLLHRQR 130
Cdd:cd06148   6 HLKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGqIYLFDILKLGSIVFIngLKDILESKKILKVIHDCRRDSDALYHQYG 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260 131 ISLGGIFDTFVA--VCLSSNTR---IPYT----------LPEAISLVFGLPMEKVtggcESQRNFTARPLTHSQMRYLAK 195
Cdd:cd06148  86 IKLNNVFDTQVAdaLLQEQETGgfnPDRVislvqlldkyLYISISLKEDVKKLMR----EDPKFWALRPLTEDMIRYAAL 161

                       170       180       190
                ....*....|....*....|....*....|....*.
gi 21430260 196 ----LVQLQHIMHDHLNYSHIFCAEVYrISLEFSHS 227
Cdd:cd06148 162 dvlcLLPLYYAMLDALISKFLKAVFKY-LNTERNLS 196
 
Name Accession Description Interval E-value
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 54-227 5.12e-14

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: 68.85  E-value: 5.12e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260  54 DIKDQKIISLLVEPSFYGRHHPTSILVVATCNG-TYIFDIKALGLIFLE--LAKILEADQPRKVIHYSHRIADHLLHRQR 130
Cdd:cd06148   6 HLKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGqIYLFDILKLGSIVFIngLKDILESKKILKVIHDCRRDSDALYHQYG 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260 131 ISLGGIFDTFVA--VCLSSNTR---IPYT----------LPEAISLVFGLPMEKVtggcESQRNFTARPLTHSQMRYLAK 195
Cdd:cd06148  86 IKLNNVFDTQVAdaLLQEQETGgfnPDRVislvqlldkyLYISISLKEDVKKLMR----EDPKFWALRPLTEDMIRYAAL 161

                       170       180       190
                ....*....|....*....|....*....|....*.
gi 21430260 196 ----LVQLQHIMHDHLNYSHIFCAEVYrISLEFSHS 227
Cdd:cd06148 162 dvlcLLPLYYAMLDALISKFLKAVFKY-LNTERNLS 196
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 50-203 1.73e-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: 1.73e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260     50 SALKDIKDQKI-ISLLVEPSFYGRHHPTSILVVATCNGTYIFDIKALGL--IFLELAKILEADQPRKVIHYShRIADHLL 126
Cdd:smart00474  12 ELLEKLRAAGGeVALDTETTGLDSYSGKLVLIQISVTGEGAFIIDPLALgdDLEILKDLLEDETITKVGHNA-KFDLHVL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260    127 HRQRISLGGIFDTFVAvclsSNTRIPYtlPEAISL---VFGLPMEKVTGGcESQRNFTARPLTHSQMRYLAK----LVQL 199
Cdd:smart00474  91 ARFGIELENIFDTMLA----AYLLLGG--PSKHGLatlLLGYLGVELDKE-EQKSDWGARPLSEEQLEYAAEdadaLLRL 163


                   ....
gi 21430260    200 QHIM 203
Cdd:smart00474 164 YEKL 167
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
79-207 1.88e-05

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 45.25  E-value: 1.88e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260  79 LV-VATCNGTYIFDIKALGlIFLELAKILEADQPRKVIHYSH---RIadhLLHRQRISLGGIFDTFVA--VClssntrip 152
Cdd:COG0349  39 LIqLADGEEVALIDPLAIG-DLSPLWELLADPAIVKVFHAARedlEI---LYHLFGILPKPLFDTQIAaaLL-------- 106

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21430260 153 yTLPEAISL------VFGLPMEKvtggcESQR-NFTARPLTHSQMRYLAK----LVQLQHIMHDHL 207
Cdd:COG0349 107 -GYGDSVGYaalveeLLGVELDK-----SEQRsDWLRRPLSEEQLEYAAAdvryLLPLYEKLLEEL 166
 
Name Accession Description Interval E-value
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 54-227 5.12e-14

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: 68.85  E-value: 5.12e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260  54 DIKDQKIISLLVEPSFYGRHHPTSILVVATCNG-TYIFDIKALGLIFLE--LAKILEADQPRKVIHYSHRIADHLLHRQR 130
Cdd:cd06148   6 HLKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGqIYLFDILKLGSIVFIngLKDILESKKILKVIHDCRRDSDALYHQYG 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260 131 ISLGGIFDTFVA--VCLSSNTR---IPYT----------LPEAISLVFGLPMEKVtggcESQRNFTARPLTHSQMRYLAK 195
Cdd:cd06148  86 IKLNNVFDTQVAdaLLQEQETGgfnPDRVislvqlldkyLYISISLKEDVKKLMR----EDPKFWALRPLTEDMIRYAAL 161

                       170       180       190
                ....*....|....*....|....*....|....*.
gi 21430260 196 ----LVQLQHIMHDHLNYSHIFCAEVYrISLEFSHS 227
Cdd:cd06148 162 dvlcLLPLYYAMLDALISKFLKAVFKY-LNTERNLS 196
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 49-207 4.23e-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: 48.68  E-value: 4.23e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260  49 HSALKDIKDQKIISLLVEpsFYGRHH---PTSILVVATCNGTYIFDIKALGlIFLELAKILEADQPRKVIHYSHRIADHL 125
Cdd:cd06142   3 EDLCERLASAGVIAVDTE--FMRLNTyypRLCLIQISTGGEVYLIDPLAIG-DLSPLKELLADPNIVKVFHAAREDLELL 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260 126 LHRQRISLGGIFDTFVAVCLSsNTRIPYTLPEAISLVFGLPMEKvtggcESQR-NFTARPLTHSQMRYLAK----LVQLQ 200
Cdd:cd06142  80 KRDFGILPQNLFDTQIAARLL-GLGDSVGLAALVEELLGVELDK-----GEQRsDWSKRPLTDEQLEYAALdvryLLPLY 153


                ....*..
gi 21430260 201 HIMHDHL 207
Cdd:cd06142 154 EKLKEEL 160
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 50-203 1.73e-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: 1.73e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260     50 SALKDIKDQKI-ISLLVEPSFYGRHHPTSILVVATCNGTYIFDIKALGL--IFLELAKILEADQPRKVIHYShRIADHLL 126
Cdd:smart00474  12 ELLEKLRAAGGeVALDTETTGLDSYSGKLVLIQISVTGEGAFIIDPLALgdDLEILKDLLEDETITKVGHNA-KFDLHVL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260    127 HRQRISLGGIFDTFVAvclsSNTRIPYtlPEAISL---VFGLPMEKVTGGcESQRNFTARPLTHSQMRYLAK----LVQL 199
Cdd:smart00474  91 ARFGIELENIFDTMLA----AYLLLGG--PSKHGLatlLLGYLGVELDKE-EQKSDWGARPLSEEQLEYAAEdadaLLRL 163


                   ....
gi 21430260    200 QHIM 203
Cdd:smart00474 164 YEKL 167
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
79-207 1.88e-05

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 45.25  E-value: 1.88e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260  79 LV-VATCNGTYIFDIKALGlIFLELAKILEADQPRKVIHYSH---RIadhLLHRQRISLGGIFDTFVA--VClssntrip 152
Cdd:COG0349  39 LIqLADGEEVALIDPLAIG-DLSPLWELLADPAIVKVFHAARedlEI---LYHLFGILPKPLFDTQIAaaLL-------- 106

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21430260 153 yTLPEAISL------VFGLPMEKvtggcESQR-NFTARPLTHSQMRYLAK----LVQLQHIMHDHL 207
Cdd:COG0349 107 -GYGDSVGYaalveeLLGVELDK-----SEQRsDWLRRPLSEEQLEYAAAdvryLLPLYEKLLEEL 166
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 47-194 2.55e-05

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: 43.72  E-value: 2.55e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260  47 TYHSALKDIK-DQKIISLLVE--PSFY-GRHHPTSILVVATCNGTYIFDIKALGLIFLELAKILEADQPRKVIHYSHRIA 122
Cdd:cd06141   6 DAEEAVKELLgKEKVVGFDTEwrPSFRkGKRNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGIKGDA 85

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21430260 123 DHLLHRQRISLGGIFDTFVAVCLSSNTRIPYTLPEAISLVFGLPMEKVTGGCESqrNFTARPLTHSQMRYLA 194
Cdd:cd06141  86 RKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCS--NWEARPLSKEQILYAA 155
DNA_polA_I_Bacillus_like_exo cd06140
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and ...
 79-157 6.00e-04

inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.


Pssm-ID: 176652 [Multi-domain]  Cd Length: 178  Bit Score: 39.56  E-value: 6.00e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21430260  79 LVVATCNGTYIFDIKALGLIFLELAKILEADQPRKVIHYSHRIAdHLLHRQRISLGGI-FDTFVAVCLSSNTRIPYTLPE 157
Cdd:cd06140  25 LALANGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAY-VALKRHGIELAGVaFDTMLAAYLLDPTRSSYDLAD 103
 
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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