Conserved Protein Domain Family

cd06125: DnaQ_like_exo 
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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.
PSSM-Id: 176647
View PSSM: cd06125
Aligned: 7 rows
Threshold Bit Score: 53.9819
Threshold Setting Gi: 56965999
Created: 21-Dec-2007
Updated: 2-Oct-2020
Aligned Rows:
Conserved site includes 10 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
  • Structure:1CLQ_A; Enterobacteria phage RB69 family-B DNA polymerase exonuclease domain binds two calcium ions and the 3 'end of primer DNA; defined at 3.5A contacts.
    View structure with Cn3D
  • Structure:2OA8_A; Mus musculus TREX1 binds ssDNA and two Ca ions; defined at 3.5A contacts.
    View structure with Cn3D

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
Feature 1        ####                                                                         
2KFZ_A     29 FAFDTETDsldn--------isanLVGLSFAie-----------------------pgVAAYIPvahdyldapd------ 71  Escherichia coli
1S5J_A    193 VAIDIEVYtpvkgripdsqkaefpIISIALAgs-----------------------dgLKKVLVlnrndvnegsvkldg- 248 Sulfolobus solfata...
2F96_A     32 VVVDVETGgfns--------atdaLLEIAATtvgxdek--------------gflfpeHTYFFRiepfeganiepaalef 89  Pseudomonas aerugi...
2OA8_A     12 IFLDLEATglps--------srpeVTELCLLavhrralentsisqghpppvprpprvvDKLSLCiapgkacspgaseitg 83  house mouse
1YT3_A     25 IALDTEFVrtrt--------yypqLGLIQLFdg------------------------eHLALIDplgit----------- 61  Escherichia coli
1CLQ_A    111 ANFDIEVTspdgfpe--psqakhpIDAITHYdsi----------------------ddRFYVFDllnspygnveewsiei 166 Enterobacteria pha...
1W0H_A     13 CIIDFEATceegnp----pefvheIIEFPVVllnth-----------------tleieDTFQQYvrpeintqlsdfcisl 71  human
Feature 1                                                            ##  ###                  
2KFZ_A     72 ------------------------qisreralelLKPLLEDek-------alKVGQNl-KYD-RGILAnygie------- 111 Escherichia coli
1S5J_A    249 -------------------isverfnteyellgrFFDILLEyp--------iVLTFNgdDFD-LPYIYfralklgyfpee 300 Sulfolobus solfata...
2F96_A     90 tgi-------------kldhplrxavqeeaalteIFRGIRKalkangckraiLVGHNs-SFD-LGFLNaavartgik--- 151 Pseudomonas aerugi...
2OA8_A     84 lsk-------------aelevqgrqrfddnlailLRAFLQRqpq-----pccLVAHNgdRYD-FPLLQtelarlstp--- 141 house mouse
1YT3_A     62 ------------------------------dwspLKAILRDps-------itKFLHAg-SED-LEVFLnvfge------- 95  Escherichia coli
1CLQ_A    167 aaklqeqggdevpseiidkiiympfdnekellmeYLNFWQQktp------viLTGWNveSFD-IPYVYnriknifgesta 239 Enterobacteria pha...
1W0H_A     72 tg--------------itqdqvdradtfpqvlkkVIDWXKLkelgt-kykysLLTDG--SWDxSKFLNiqcqlsrlk--- 131 human
Feature 1                                                                                     
2KFZ_A    112 --------------------------lrgiaFDTMLEsyilnsvagrhdmdslaerwlkhktitfeeiagkgknqltfnq 165 Escherichia coli
1S5J_A    301 ipi-------------dvagkdeakylaglhIDLYKFffnkavrnyafegkyneynldavak--allgtskvkvdtlisf 365 Sulfolobus solfata...
2F96_A    152 ----------------------rnpfhpfssFDTATLaglaygqtvlakac------------------------qaagx 185 Pseudomonas aerugi...
2OA8_A    142 -----------------------spldgtfcVDSIAAlkaleqasspsgngsrksy--------------slgsiytrly 184 house mouse
1YT3_A     96 --------------------------lpqplIDTQILaafcgrpmswgfasmveeysgvt-------ldksesrtdwlar 142 Escherichia coli
1CLQ_A    240 krlsphrktrvkvienmygsreiitlfgisvLDYIDLykkfsftnqpsysldyisefelnv-----gklkydgpisklre 314 Enterobacteria pha...
1W0H_A    132 -----------------------yppfakkwINIRKSygnfykvprsqtklti---------------------xleklg 167 human
Feature 1                 #         
2KFZ_A    166 ialeeagryAAEDADVTLQLHL 187 Escherichia coli
1S5J_A    366 ldveklieyNFRDAEITLQLTT 387 Sulfolobus solfataricus
2F96_A    186 efdnreahsARYDTEKTAELFC 207 Pseudomonas aeruginosa
2OA8_A    185 wqaptdshtAEGDVLTLLSICQ 206 house mouse
1YT3_A    143 plterqceyAAADVWYLLPITA 164 Escherichia coli
1CLQ_A    315 snhqryisyNIIDVYRVLQIDA 336 Enterobacteria phage RB69
1W0H_A    168 xdydgrphcGLDDSKNIARIAV 189 human

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