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: 17-Jan-2013
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:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1           #### #                                                                       
2F96_A        32 VVVDVETGGfns-atdALLEIAATTvgxdekgflfpeHTYFFRIEPfeganiepaaleftgikldhplrxaVQEE-AALT 109
gi 83816222   67 VFLDTETTGsgp--qdAVIELGVVAaq--------geVLIHTLVAPlapvtrgarrv---hgitdeeladaPPFP-TVAD 132
gi 158335553  11 VAIDFETADyq---rdSACAIGVIRvend-----qivDRSHFLIRPprqkfqftyih----gitwsdvkhhPTFA-ELWP 77
gi 160931331  17 VILDTETTDld----gRIIEISIIDaat-------gtVLMDQLINPqgapicaeartv--hhispddlataPTFT-QVRP 82
gi 153817923  10 IILDTETTGlds--daRIVEVSIIDaqt-------giKLYSSLVNPlcsispevtai---hgitndmvidmPTFD-KVWN 76
gi 75226734  105 LFLDTETTGldn--taEALEIGLTDaa--------gqVVFETRLKPtvaigaqaaav---hgiseqalcgaPSWT-DVAR 170
gi 114778579   5 LVLDTETTGlgd--daEIIEIGIINgs--------geTVMNTLVKPtisipeeatai---hgitdndllnaPVFA-DVVE 70
gi 151937941  31 IIIDTETTGlga--daEIVEFTAICans-------geVIVDELVKPtcsipadatai---hgitnedvkdaPDFHlMFSN 98
gi 110634574  16 VAFDTETTGldt-rtaRVVQVAGVAisrga---vrqdESFESLVHPgmsippdsiri---hgitdgmlreaPAFA-AVWR 87
gi 166833603  14 AAIDFESAGaargetdQPVQIGIAAcprled-epelwTSYIAVEKPvlwsasqvhg------ittemladaPSFP-SLWP 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                              ## ###                                                    
2F96_A       110 EIFRGIRKalkangckrAILVGHNsSFDLGFLNaavartgi-------krnpfhpfSSFDTATLagLAYgqtvlakacqa 182
gi 83816222  133 RLDTVLADa--------ECVWTFGpTYDRRMLLqtaalaecp-----ethrriqdsTWRDLQPDatRVLgdaervaltda 199
gi 158335553  78 NLQPKFAGs--------DFVAAHNaNFDRSVLNaccqaae----------ldpmplPFLCTVKLarEVWnirptklpnv- 138
gi 160931331  83 RLEDVVAD---------RVVMAWNaPFDRERIEaey------------------alAGLDAPAWpwCCLmrleasvmg-- 133
gi 153817923  77 DIKGYLSD---------AVIYVYNlDFDYRMFAqslrpfgyp-----vanlvrffgGGVCVMRWyaNFYgslcgndvtpr 142
gi 75226734  171 QLRHAIGD---------RPVIIFNaRFDIRILKqtaaahsd-------padwleemTVYCAMELaaGYYgatnrygtisl 234
gi 114778579  71 ELEGLIQG---------KILLIYNaDYDLRLLRqsarkskv--------qinlepaEVRCVMLEyaKFFgewnpkyenwk 133
gi 151937941  99 RFLPLLNG---------RPIIIYNsDFDTRLIIqsldkhcnaayvqsvhdlffkfcVPQCAMLWyaEFYgvwneyhedyk 169
gi 110634574  88 SFEMFRGV---------RPLIGYAvGFDLAIIEreaarag----------irrkrpRTLCVRTLsrIVNrdlrghsleal 148
gi 166833603  86 EIRSRLGQ---------AVVVGHNpATERKFLRrfpg---------------hgfgPWLDTLALgrMCVpgladyslssl 141
                        170       180       190
                 ....*....|....*....|....*....|....*.
Feature 1                             #    #         
2F96_A       183 -----------agxefdnreaHSARYDTEKTAELFC 207
gi 83816222  200 ak-------rldvsipteghhHRALYDAKLARRVWT 228
gi 158335553 139 -----------cefldiplqhHQALSDAEACAKIVI 163
gi 160931331 134 ------------cqwrrldgpHRGLGDVIAARRRLI 157
gi 153817923 143 fqrlt-nacyqqdvdtsdltaHRALADCEMTRRLIN 177
gi 75226734  235 ac------aasqagltwegpaHSAIADARMAAGVVN 264
gi 114778579 134 wqslanaarrtgyvpaegmlpHRAIADCVAALHVYR 169
gi 151937941 170 wqslt-nacaqqhvdvsdliaHRALADCEMTRRLIH 204
gi 110634574 149 ----------aawlgfeiigrHQALDDAMAAAKVFT 174
gi 166833603 142 cgal--gltcsveallparrwHDALYDALASLLIVR 175

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