2FC0,1YT3,2E6L,2HBL,3CYM


Conserved Protein Domain Family
RNaseD_like

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cd06129: RNaseD_like 
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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.
Statistics
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PSSM-Id: 176650
View PSSM: cd06129
Aligned: 5 rows
Threshold Bit Score: 223.159
Threshold Setting Gi: 189096244
Created: 26-Mar-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1:catalytic site [active site]
Evidence:
  • Comment:The catalytic site is characterized by the presence of four negatively charged residues (DEDD) that serve as ligands for the two metal ions required for activity.
  • Comment:DEDDy exonucleases contain a conserved tyrosine at the ExoIII motif which is important in catalysis.
  • Structure:1YT3_A; Escherichia coli RNase D binds two Zn ions.
    View structure with Cn3D
  • Structure:2FC0_A; Human WRN exonuclease binds two Mn ions in the catalytic site.
    View structure with Cn3D
  • Citation:PMID 9396823

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                          # #                                                        
2FC0_A     30 DCSFLSEDIsmslsdGDVVGFDMEWPplynrgklgkVALIQLCvsesKCYLFHVssmsv---fpqgLKMLLENkavkKAG 106 human
1YT3_A     11 ALASLCEAVr----aFPAIALDTEFVrtrt--yypqLGLIQLFdg-eHLALIDPlgit----dwspLKAILRDpsitKFL 79  Escherichia coli
2E6L_A     25 DCSFLSEDIsmrlsdGDVVGFDMEWPpiykpgkrsrVAVIQLCvsesKCYLFHIssmsv---fpqgLKMLLENksikKAG 101 house mouse
2HBL_A     95 ELESMLEDLk----nTKEIAVDLEHHdyrs--yygiVCLMQIStr-eRDYLVDTlklre---nlhiLNEVFTNpsivKVF 164 baker's yeast
3CYM_A     26 AFRDYCSELas---sHGSLAADAERAsgfr--ygheDWLVQFKrdgaGIGLLDPqalaaagadwndFNRAVGDa--vWIL 98  Bifidobacterium ad...
Feature 1          #                                                                    #   # 
2FC0_A    107 VGIEGDQWKLLRDFDiklkNFVELTDVANKKlkctetwSLNSLVKHLLgkqllkdksiRCSNWSKFplteDQKLYAATDA 186 human
1YT3_A     80 HAGSEDLEVFLNVFGelpqPLIDTQILAAFCgrp-mswGFASMVEEYSgvtl--dkseSRTDWLARplteRQCEYAAADV 156 Escherichia coli
2E6L_A    102 VGIEGDQWKLLRDFDvkleSFVELTDVANEKlkcaetwSLNGLVKHVLgkqllkdksiRCSNWSNFplteDQKLYAATDA 181 house mouse
2HBL_A    165 HGAFMDIIWLQRDLGlyvvGLFDTYHASKAIglp--rhSLAYLLENFAnfkt--skkyQLADWRIRplskPMTAAARADT 240 baker's yeast
3CYM_A     99 HDSLQDLPGFDELGMep-qRLFDTEIAARLLglk--rfGLAAVTEHFLgltl--akehSAADWSYRplprDWRNYAALDV 173 Bifidobacterium ad...
Feature 1                 
2FC0_A    187 YAGFIIYRNLEI 198 human
1YT3_A    157 WYLLPITAKLMV 168 Escherichia coli
2E6L_A    182 YAGLIIYQKLGN 193 house mouse
2HBL_A    241 HFLLNIYDQLRN 252 baker's yeast
3CYM_A    174 ELLIELETKMRA 185 Bifidobacterium adolescentis L2-32

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