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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080358426   3 PRLEDVVADRVVMAWNAPFDRERIEAEYALAGLDAPAWPWCCLMRLEASVMGCQWRR-------------LDGPHRGLGD 69
Cdd:cd06127    71 PEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHrlglllaerygipLEGAHRALAD 150

                  ....*.
gi 1080358426  70 VIAARR 75
Cdd:cd06127   151 ALATAE 156

DEDDh 3'-5' exonuclease domain family; DEDDh 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. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080358426   3 PRLEDVVADRVVMAWNAPFDRERIEAEYALAGLDAPAWPWCCLMRLEASVMGCQWRR-------------LDGPHRGLGD 69
Cdd:cd06127    71 PEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHrlglllaerygipLEGAHRALAD 150

                  ....*.
gi 1080358426  70 VIAARR 75
Cdd:cd06127   151 ALATAE 156

DEDDh family exonuclease;

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                  ....*....|....*....|....*....|....*.
gi 1080358426   3 PRLEDVVADRVVMAWNAPFDRERIEAEYALAGLDAP 38
Cdd:PRK06063   86 GEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELP 121

DEDDh 3'-5' exonuclease domain family; DEDDh 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. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080358426   3 PRLEDVVADRVVMAWNAPFDRERIEAEYALAGLDAPAWPWCCLMRLEASVMGCQWRR-------------LDGPHRGLGD 69
Cdd:cd06127    71 PEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHrlglllaerygipLEGAHRALAD 150

                  ....*.
gi 1080358426  70 VIAARR 75
Cdd:cd06127   151 ALATAE 156

an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains 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. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.

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                  ....*....|....*....|....*....|....*....|....*.
gi 1080358426   3 PRLEDVVADRVVMAWNAPFDRERIEAEYALAGLDAPAWPWCCLMRL 48
Cdd:cd06130    69 PEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRL 114

DEDDh family exonuclease;

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                  ....*....|....*....|....*....|....*.
gi 1080358426   3 PRLEDVVADRVVMAWNAPFDRERIEAEYALAGLDAP 38
Cdd:PRK06063   86 GEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELP 121