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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 157423306 118 ICVVDFEATCEENN-PPDYLHEIIEFPMVLIDTHTLEIVS 156
Cdd:cd06133    1 YLVIDFEATCWEGNsKPDYPNEIIEIGAVLVDVKTKEIID 40

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved 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. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 157423306 118 ICVVDFEATCEENN-PPDYLHEIIEFPMVLIDTHTLEIVS 156
Cdd:cd06133    1 YLVIDFEATCWEGNsKPDYPNEIIEIGAVLVDVKTKEIID 40

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 157423306 116 DYICVVDFEATCEENNPPDYLH-EIIEFPMVLIDTHTlEIVS 156
Cdd:COG5018    2 MKYLVIDLEATCWDGKPPPGFPmEIIEIGAVKVDENG-EIID 42

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;

                           10        20
                   ....*....|....*....|....*...
gi 157423306    69 ELRAKCTELKLDTRGVNDVLRKRLKSYY 96
Cdd:smart00513   8 ELKDELKKRGLSTSGTKAELVDRLLEAL 35

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved 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. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 157423306 118 ICVVDFEATCEENN-PPDYLHEIIEFPMVLIDTHTLEIVS 156
Cdd:cd06133    1 YLVIDFEATCWEGNsKPDYPNEIIEIGAVLVDVKTKEIID 40

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 157423306 116 DYICVVDFEATCEENNPPDYLH-EIIEFPMVLIDTHTlEIVS 156
Cdd:COG5018    2 MKYLVIDLEATCWDGKPPPGFPmEIIEIGAVKVDENG-EIID 42

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;

                           10        20
                   ....*....|....*....|....*...
gi 157423306    69 ELRAKCTELKLDTRGVNDVLRKRLKSYY 96
Cdd:smart00513   8 ELKDELKKRGLSTSGTKAELVDRLLEAL 35