2F96,1W0H,2IGI,2O4G,2QXF,2P1J,2GUI,1WLJ,2OA8


Conserved Protein Domain Family
DEDDh

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cd06127: DEDDh 
Click on image for an interactive view with Cn3D
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.
Statistics
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PSSM-Id: 176648
View PSSM: cd06127
Aligned: 398 rows
Threshold Bit Score: 63.4736
Threshold Setting Gi: 158428766
Created: 10-Mar-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1           #### #                                                                       
2F96_A        32 VVVDVETGGfns-atdALLEIAATTvgxdekgflfpeHTYFFRIEPfeganiepaaleftgikldhplrxaVQEE-AALT 109 Pseudomonas aer...
YP_444853     67 VFLDTETTGsgp--qdAVIELGVVAaq--------geVLIHTLVAPlapvtrgarrv---hgitdeeladaPPFP-TVAD 132 Salinibacter ru...
YP_001516725  11 VAIDFETADyq---rdSACAIGVIRvend-----qivDRSHFLIRPprqkfqftyih----gitwsdvkhhPTFA-ELWP 77  Acaryochloris m...
ZP_02078731   17 VILDTETTDld----gRIIEISIIDaat-------gtVLMDQLINPqgapicaeartv--hhispddlataPTFT-QVRP 82  Clostridium lep...
ZP_01970590   10 IILDTETTGlds--daRIVEVSIIDaqt-------giKLYSSLVNPlcsispevtai---hgitndmvidmPTFD-KVWN 76  Vibrio cholerae...
ZP_00713690  105 LFLDTETTGldn--taEALEIGLTDaa--------gqVVFETRLKPtvaigaqaaav---hgiseqalcgaPSWT-DVAR 170 Escherichia col...
ZP_01453406    5 LVLDTETTGlgd--daEIIEIGIINgs--------geTVMNTLVKPtisipeeatai---hgitdndllnaPVFA-DVVE 70  Mariprofundus f...
EDN56786      31 IIIDTETTGlga--daEIVEFTAICans-------geVIVDELVKPtcsipadatai---hgitnedvkdaPDFHlMFSN 98  Vibrio sp. Ex25
YP_674782     16 VAFDTETTGldt-rtaRVVQVAGVAisrga---vrqdESFESLVHPgmsippdsiri---hgitdgmlreaPAFA-AVWR 87  Mesorhizobium s...
ZP_02251179   14 AAIDFESAGaargetdQPVQIGIAAcprled-epelwTSYIAVEKPvlwsasqvhg------ittemladaPSFP-SLWP 85  Akkermansia muc...
Feature 1                              ## ###                                                    
2F96_A       110 EIFRGIRKalkangckrAILVGHNsSFDLGFLNaavartgi-------krnpfhpfSSFDTATLagLAYgqtvlakacqa 182 Pseudomonas aer...
YP_444853    133 RLDTVLADa--------ECVWTFGpTYDRRMLLqtaalaecp-----ethrriqdsTWRDLQPDatRVLgdaervaltda 199 Salinibacter ru...
YP_001516725  78 NLQPKFAGs--------DFVAAHNaNFDRSVLNaccqaae----------ldpmplPFLCTVKLarEVWnirptklpnv- 138 Acaryochloris m...
ZP_02078731   83 RLEDVVAD---------RVVMAWNaPFDRERIEaey------------------alAGLDAPAWpwCCLmrleasvmg-- 133 Clostridium lep...
ZP_01970590   77 DIKGYLSD---------AVIYVYNlDFDYRMFAqslrpfgyp-----vanlvrffgGGVCVMRWyaNFYgslcgndvtpr 142 Vibrio cholerae...
ZP_00713690  171 QLRHAIGD---------RPVIIFNaRFDIRILKqtaaahsd-------padwleemTVYCAMELaaGYYgatnrygtisl 234 Escherichia col...
ZP_01453406   71 ELEGLIQG---------KILLIYNaDYDLRLLRqsarkskv--------qinlepaEVRCVMLEyaKFFgewnpkyenwk 133 Mariprofundus f...
EDN56786      99 RFLPLLNG---------RPIIIYNsDFDTRLIIqsldkhcnaayvqsvhdlffkfcVPQCAMLWyaEFYgvwneyhedyk 169 Vibrio sp. Ex25
YP_674782     88 SFEMFRGV---------RPLIGYAvGFDLAIIEreaarag----------irrkrpRTLCVRTLsrIVNrdlrghsleal 148 Mesorhizobium s...
ZP_02251179   86 EIRSRLGQ---------AVVVGHNpATERKFLRrfpg---------------hgfgPWLDTLALgrMCVpgladyslssl 141 Akkermansia muc...
Feature 1                             #    #         
2F96_A       183 -----------agxefdnreaHSARYDTEKTAELFC 207 Pseudomonas aeruginosa
YP_444853    200 ak-------rldvsipteghhHRALYDAKLARRVWT 228 Salinibacter ruber DSM 13855
YP_001516725 139 -----------cefldiplqhHQALSDAEACAKIVI 163 Acaryochloris marina MBIC11017
ZP_02078731  134 ------------cqwrrldgpHRGLGDVIAARRRLI 157 Clostridium leptum DSM 753
ZP_01970590  143 fqrlt-nacyqqdvdtsdltaHRALADCEMTRRLIN 177 Vibrio cholerae NCTC 8457
ZP_00713690  235 ac------aasqagltwegpaHSAIADARMAAGVVN 264 Escherichia coli B7A
ZP_01453406  134 wqslanaarrtgyvpaegmlpHRAIADCVAALHVYR 169 Mariprofundus ferrooxydans PV-1
EDN56786     170 wqslt-nacaqqhvdvsdliaHRALADCEMTRRLIH 204 Vibrio sp. Ex25
YP_674782    149 ----------aawlgfeiigrHQALDDAMAAAKVFT 174 Mesorhizobium sp. BNC1
ZP_02251179  142 cgal--gltcsveallparrwHDALYDALASLLIVR 175 Akkermansia muciniphila ATCC BAA-835

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