Conserved Protein Domain Family
DNA_polB_B3_exo

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cd05781: DNA_polB_B3_exo 
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases
The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Statistics
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PSSM-Id: 99824
View PSSM: cd05781
Aligned: 13 rows
Threshold Bit Score: 232.987
Threshold Setting Gi: 170290810
Created: 20-Nov-2007
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
Feature 1:active site [active site]
Evidence:
  • Comment:The active site includes the catalytic site (characterized by four invariant acidic residues, DEDD) and the substrate (ssDNA) binding site.
  • Citation:PMID 9888810

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                ####                                                          ##  ###   
gi 7416107   170 PELKVLAFDIEVYNKYGSPNPRRDPVIIIGVWTkEGGKQFLADk--YDDLRAIREFINFVQTYDPDIIVGYNINNFDWPY 247
gi 118431730 182 KGLRVMAFDIEVYSKMRTPDPKKDPVIMIGLQQaGGEIEILEAe-dRSDKKVIAGFVERVKSIDPDVIVGYNQNRFDWPY 260
gi 119719310 176 PRLKTYAFDIECYNRYGEPDPERDPVLVISRTGeDGTVIFSQDe-gSSEKKLLEEFVNDLVQYDPDVILGYNSNRFDWPY 254
gi 62736742  174 RDLRLMAVDIEVYSEHGSPKPSRDPVIIIGVGVpGGGVKQFTAs-gLDDRNAIAEFVDYVLKYDPDIILGYNSNSFDWPY 252
gi 68525479  176 PDLRIIAFDIEVYNKSGTPRPQTDPIIIIGIMNnNGDIKQFLAn-kYDDKISVEEFVNYVKTFDPDIIVGYNTDGFDWPY 254
gi 807830    179 PPMRLVAFDIEVYSRRGSPNPARDPVIIVSLRDsEGKERLIEAe-gHDDRRVLREFVEYVRAFDPDIIVGYNSNHFDWPY 257
gi 18313103  164 PPLRVLAFDIEVYNERGTPDPLRDPVILLAVQAsDGRVEVFEAs-gRDDRSVLRSFIDFVREFDPDVIVGYNSNQFDWPY 242
gi 156936857 170 PKLKTLAFDIEVYNKSGTPRPERDPIISIALAS-EGSVVSKLSq-dKNDKDLIVWFKKEMLERDPDVVVGYNSNSFDWPY 247
gi 70605924  174 PRLKTMAFSIEVYNKYGFPNTRRDPIIVIGVYTeNGYKQFISSd--YDDINVIREFIKFVNDFEPDIIFGYNSNSFDWRY 251
gi 159041906 166 PRLNYMALDIEVYNPRGTPDPKRDPIIIIALANsNGDVKLLTLdnyKHEREMLNDMMSVIKEWDPDVLFGYNSNKFDMPY 245
gi 11498108  160 PELKMLVFDCEMLSSFGMPEPEKDPIIVISVKT-NDDDEIILT---GDERKIISDFVKLIKSYDPDIIVGYNQDAFDWPY 235
gi 3913515   164 PELRTIGVDFQIYSKYGSLNPRKDPIVVMSLWSkEGPMQFSLDe-gIDDLKIIRRFVDYILNYDPDIIFVYDSDLLPWKY 242
gi 170290810 117 EDLKKLFFSGMIYSEDGFPVEGKSPIVAISYSVdDGPIEVISAs-dLDDSVIIREFVSVISKENPDVIVGYGQDADEFKH 195
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                    ##                  
gi 7416107   248 LLERANIRGIRLDVGRRVNgEPSQGv------yGHYSITGRLNVDLYGFAQSIqe-vKVKTLENIADYLGVlpKEKRTIV 320
gi 118431730 261 LVERARVLGVKLAVGRRSV-EPQPGl------yGHYSVSGRLNVDLLDFAEELhe-vKVKTLEEVADYLGVvkIGERVTL 332
gi 119719310 255 LLQRARVNGVKLSIGRNLG-EPSQSv------yGHFSVVGRANVDLYDYASELqe-vKVKTLENVSEFLGVmkKSERVLI 326
gi 62736742  253 LLERTRVLGIRFDIGRRIGaLPTTSt------yGHISIPGRLSVDLYNYAEEIse-iKLKSLDVVAEYLGVmkRNERVLI 325
gi 68525479  255 LIERSKYIGVKLDVTRRVGaTPRTSt------yGHISVPGRLNTDLYHFAEEIpe-vKVKSLENVAEYLGVmkKSERVII 327
gi 807830    258 LMERARRLGIKLDVTRRVGaEPTTSv------yGHVSVQGRLNVDLYDYAEEMpe-iKMKTLEEVAEYLGVmkKSERVII 330
gi 18313103  243 LAERARALGIPLKVDRVGG-APQQSv------yGHWSVTGRANVDLYNIVDEFpe-iKLKTLDRVAEYFGVmkREERVLV 314
gi 156936857 248 LIERSKVVGVRLDVGRKVGvIPTTGa------yGHVSVPGRLNVDVYDFAKEVye-vKVKTLENVADYFNVmkKDERPLI 320
gi 70605924  252 LVERAELRGIKVAIGRKVNsEPSQGv------yGHYSVTGRLNVDLAGVFCSS----RSKSLIDLADNLGVmpKNKREIL 321
gi 159041906 246 LVNRADALNVKLQLSKYGT-PPEQSv------yGHWSIIGRAHIDLYNFIEDMtd-vKRKSLDYVAEYFGVmkRSERVNI 317
gi 11498108  236 LRKRAERWNIPLDVGRDGSnVVFRG--------GRPKITGRLNVDLYDIAMRIsd-iKIKKLENVAEFLGT--KIEIADI 304
gi 3913515   243 ITERASSLGVKIDIGRKIGsEVSVGt------yGHYSISGRLNVDLTGLLVNErs-lGHVDLIDVSNYLGI--SPSRYSF 313
gi 170290810 196 LMARSKNLGLRLSIGRDGSePMETGkffrgtiiVENRIRGRANLDLFSVAWRDfpqlPERTWYELADELGVg-RPEVMMK 274
                        170       180       190
                 ....*....|....*....|....*....|....*.
Feature 1                            #   #           
gi 7416107   321 ewydIPKYWDDekKRDILLKYNLDDAKSAYLLGEVF 356
gi 118431730 333 ewwqIGEYWDDpsKREILRKYLRDDVRSTMGLAEKF 368
gi 119719310 327 dtnkVYEYWDSkdKRSLLLRYAGDDARSTYLLGQVV 362
gi 62736742  326 dyteFPKYWRDpeKKKLLLKYNEDDVVSTLGLADKF 361
gi 68525479  328 eyidIPKYWDDekLRPKLLQYNIDDVKSTYGLAEKF 363
gi 807830    331 ewwrIPEYWDDekKRQLLERYALDDVRATYGLAEKM 366
gi 18313103  315 pghkIYEYWRDqgKRPLLRQYVIDDVKSTYGLAEKL 350
gi 156936857 321 phhlIYQYWEDpqKRDVLRKYNEADALSTLMLAELF 356
gi 70605924  322 ewyeVPRYWDDksKREILLKHNLSNIKSIYDIGQSN 357
gi 159041906 318 pghrIYQYWDDegKRSQLIKYARDDVLSTLGLGKIL 353
gi 11498108  305 eakdIYRYWSRg-EKEKVLNYARQDAINTYLIAKEL 339
gi 3913515   314 kwyeISRYWDNekNRRIIREYSIENARSIYLLGNYL 349
gi 170290810 275 f--rVAEAWKL--NRDNALDYMRKKLSTIIGIYSKI 306

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