ribonuclease D family protein similar to Haemophilus influenzae ribonuclease D involved in the maturation of small stable RNAs and the 3' maturation of tRNA by catalyzing the exonucleolytic cleavage of extra residues from the 3'-terminus of tRNA, and to the ribonuclease D-like proteins, Bartonella birtlesii nanoRNase NrnC which exhibits oligo RNA degradation (nanoRNase) activity, and Agrobacterium tumefaciens nanoRNase NrnC which degrades dsDNA but leaves dsRNA intact
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
25-361
2.88e-66
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. [Transcription, RNA processing]
Pssm-ID: 130455 [Multi-domain] Cd Length: 367 Bit Score: 214.25 E-value: 2.88e-66
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
12-185
1.88e-55
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: 180.04 E-value: 1.88e-55
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
20-169
1.39e-21
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: 90.44 E-value: 1.39e-21
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
25-361
2.88e-66
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. [Transcription, RNA processing]
Pssm-ID: 130455 [Multi-domain] Cd Length: 367 Bit Score: 214.25 E-value: 2.88e-66
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
12-185
1.88e-55
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: 180.04 E-value: 1.88e-55
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
20-169
1.39e-21
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: 90.44 E-value: 1.39e-21
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
25-163
4.14e-15
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: 72.16 E-value: 4.14e-15
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
39-181
2.47e-13
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: 68.08 E-value: 2.47e-13
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ...
210-277
2.51e-12
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Pssm-ID: 425755 [Multi-domain] Cd Length: 68 Bit Score: 61.40 E-value: 2.51e-12
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ...
24-164
2.38e-10
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: 58.41 E-value: 2.38e-10
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
25-164
4.67e-08
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: 52.68 E-value: 4.67e-08
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
25-153
5.32e-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: 5.32e-08
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
75-172
2.85e-07
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: 50.29 E-value: 2.85e-07
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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