Conserved Protein Domain Family

cd09018: DEDDy_polA_RNaseD_like_exo 
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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
View PSSM: cd09018
Aligned: 3 rows
Threshold Bit Score: 207.477
Threshold Setting Gi: 75765643
Created: 7-Jan-2008
Updated: 2-Oct-2020
Aligned Rows:
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
  • Comment:The active site includes the catalytic site (characterized by four invariant acidic residues, DEDD) and the substrate (ssDNA or RNA) binding site.
  • Structure:2KFZ_A; Escherichia coli Klenow Fragment exonuclease domain binds two zinc metal ions and ssDNA; defined at 3.5A contacts.
    View structure with Cn3D
  • Citation:PMID 9888810
  • Citation:PMID 1989886

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
Feature 1         ####                                                              ## ###    
2KFZ_A     28 VFAFDTETDsldn--isanLVGLSFAiepgVAAYIPVahdyldapdqisreralelLKPLLEDekalKVGQNLKYDRGIL 105 Escherichia coli
2FC0_A     47 VVGFDMEWPplynrgklgkVALIQLCvsesKCYLFHVssmsv----------fpqgLKMLLENkavkKAGVGIEGDQWKL 116 human
1YT3_A     24 AIALDTEFVrtrt--yypqLGLIQLFdg-eHLALIDPlgit-----------dwspLKAILRDpsitKFLHAGSEDLEVF 89  Escherichia coli
Feature 1                                 ##                                      #   #       
2KFZ_A    106 ANYGIelrgiAFDTMLESYILnsvagrhDMDSLAERWLkhktitfeeiagkgknqltfnqialeeagrYAAEDADVTLQL 185 Escherichia coli
2FC0_A    117 LRDFDiklknFVELTDVANKKlkctetwSLNSLVKHLLgkqllkdksircs----nwskfpltedqklYAATDAYAGFII 192 human
1YT3_A     90 LNVFGelpqpLIDTQILAAFCgrp-mswGFASMVEEYSgvtldksesrtd------wlarplterqceYAAADVWYLLPI 162 Escherichia coli
Feature 1           
2KFZ_A    186 HLKMWP 191 Escherichia coli
2FC0_A    193 YRNLEI 198 human
1YT3_A    163 TAKLMV 168 Escherichia coli

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