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: 2-Oct-2020
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:
Feature 1                ####                                                          ##  ###   
BAA93703     170 PELKVLAFDIEVYNKYGSPNPRRDPVIIIGVWTkEGGKQFLADk--YDDLRAIREFINFVQTYDPDIIVGYNINNFDWPY 247 Sulfurisphaera ...
NP_148383    182 KGLRVMAFDIEVYSKMRTPDPKKDPVIMIGLQQaGGEIEILEAe-dRSDKKVIAGFVERVKSIDPDVIVGYNQNRFDWPY 260 Aeropyrum perni...
YP_919805    176 PRLKTYAFDIECYNRYGEPDPERDPVLVISRTGeDGTVIFSQDe-gSSEKKLLEEFVNDLVQYDPDVILGYNSNRFDWPY 254 Thermofilum pen...
AAX97697     174 RDLRLMAVDIEVYSEHGSPKPSRDPVIIIGVGVpGGGVKQFTAs-gLDDRNAIAEFVDYVLKYDPDIILGYNSNSFDWPY 252 Sulfophobococcu...
AAY98790     176 PDLRIIAFDIEVYNKSGTPRPQTDPIIIIGIMNnNGDIKQFLAn-kYDDKISVEEFVNYVKTFDPDIIVGYNTDGFDWPY 254 Staphylothermus...
BAA07580     179 PPMRLVAFDIEVYSRRGSPNPARDPVIIVSLRDsEGKERLIEAe-gHDDRRVLREFVEYVRAFDPDIIVGYNSNHFDWPY 257 Pyrodictium occ...
NP_559770    164 PPLRVLAFDIEVYNERGTPDPLRDPVILLAVQAsDGRVEVFEAs-gRDDRSVLRSFIDFVREFDPDVIVGYNSNQFDWPY 242 Pyrobaculum aer...
YP_001434653 170 PKLKTLAFDIEVYNKSGTPRPERDPIISIALAS-EGSVVSKLSq-dKNDKDLIVWFKKEMLERDPDVVVGYNSNSFDWPY 247 Ignicoccus hosp...
YP_254794    174 PRLKTMAFSIEVYNKYGFPNTRRDPIIVIGVYTeNGYKQFISSd--YDDINVIREFIKFVNDFEPDIIFGYNSNSFDWRY 251 Sulfolobus acid...
YP_001541158 166 PRLNYMALDIEVYNPRGTPDPKRDPIIIIALANsNGDVKLLTLdnyKHEREMLNDMMSVIKEWDPDVLFGYNSNKFDMPY 245 Caldivirga maqu...
NP_069333    160 PELKMLVFDCEMLSSFGMPEPEKDPIIVISVKT-NDDDEIILT---GDERKIISDFVKLIKSYDPDIIVGYNQDAFDWPY 235 Archaeoglobus f...
P95979       164 PELRTIGVDFQIYSKYGSLNPRKDPIVVMSLWSkEGPMQFSLDe-gIDDLKIIRRFVDYILNYDPDIIFVYDSDLLPWKY 242 Sulfolobus solf...
YP_001737626 117 EDLKKLFFSGMIYSEDGFPVEGKSPIVAISYSVdDGPIEVISAs-dLDDSVIIREFVSVISKENPDVIVGYGQDADEFKH 195 Candidatus Kora...
Feature 1                                                                    ##                  
BAA93703     248 LLERANIRGIRLDVGRRVNgEPSQGv------yGHYSITGRLNVDLYGFAQSIqe-vKVKTLENIADYLGVlpKEKRTIV 320 Sulfurisphaera ...
NP_148383    261 LVERARVLGVKLAVGRRSV-EPQPGl------yGHYSVSGRLNVDLLDFAEELhe-vKVKTLEEVADYLGVvkIGERVTL 332 Aeropyrum perni...
YP_919805    255 LLQRARVNGVKLSIGRNLG-EPSQSv------yGHFSVVGRANVDLYDYASELqe-vKVKTLENVSEFLGVmkKSERVLI 326 Thermofilum pen...
AAX97697     253 LLERTRVLGIRFDIGRRIGaLPTTSt------yGHISIPGRLSVDLYNYAEEIse-iKLKSLDVVAEYLGVmkRNERVLI 325 Sulfophobococcu...
AAY98790     255 LIERSKYIGVKLDVTRRVGaTPRTSt------yGHISVPGRLNTDLYHFAEEIpe-vKVKSLENVAEYLGVmkKSERVII 327 Staphylothermus...
BAA07580     258 LMERARRLGIKLDVTRRVGaEPTTSv------yGHVSVQGRLNVDLYDYAEEMpe-iKMKTLEEVAEYLGVmkKSERVII 330 Pyrodictium occ...
NP_559770    243 LAERARALGIPLKVDRVGG-APQQSv------yGHWSVTGRANVDLYNIVDEFpe-iKLKTLDRVAEYFGVmkREERVLV 314 Pyrobaculum aer...
YP_001434653 248 LIERSKVVGVRLDVGRKVGvIPTTGa------yGHVSVPGRLNVDVYDFAKEVye-vKVKTLENVADYFNVmkKDERPLI 320 Ignicoccus hosp...
YP_254794    252 LVERAELRGIKVAIGRKVNsEPSQGv------yGHYSVTGRLNVDLAGVFCSS----RSKSLIDLADNLGVmpKNKREIL 321 Sulfolobus acid...
YP_001541158 246 LVNRADALNVKLQLSKYGT-PPEQSv------yGHWSIIGRAHIDLYNFIEDMtd-vKRKSLDYVAEYFGVmkRSERVNI 317 Caldivirga maqu...
NP_069333    236 LRKRAERWNIPLDVGRDGSnVVFRG--------GRPKITGRLNVDLYDIAMRIsd-iKIKKLENVAEFLGT--KIEIADI 304 Archaeoglobus f...
P95979       243 ITERASSLGVKIDIGRKIGsEVSVGt------yGHYSISGRLNVDLTGLLVNErs-lGHVDLIDVSNYLGI--SPSRYSF 313 Sulfolobus solf...
YP_001737626 196 LMARSKNLGLRLSIGRDGSePMETGkffrgtiiVENRIRGRANLDLFSVAWRDfpqlPERTWYELADELGVg-RPEVMMK 274 Candidatus Kora...
Feature 1                            #   #           
BAA93703     321 ewydIPKYWDDekKRDILLKYNLDDAKSAYLLGEVF 356 Sulfurisphaera ohwakuensis
NP_148383    333 ewwqIGEYWDDpsKREILRKYLRDDVRSTMGLAEKF 368 Aeropyrum pernix K1
YP_919805    327 dtnkVYEYWDSkdKRSLLLRYAGDDARSTYLLGQVV 362 Thermofilum pendens Hrk 5
AAX97697     326 dyteFPKYWRDpeKKKLLLKYNEDDVVSTLGLADKF 361 Sulfophobococcus zilligii
AAY98790     328 eyidIPKYWDDekLRPKLLQYNIDDVKSTYGLAEKF 363 Staphylothermus marinus
BAA07580     331 ewwrIPEYWDDekKRQLLERYALDDVRATYGLAEKM 366 Pyrodictium occultum
NP_559770    315 pghkIYEYWRDqgKRPLLRQYVIDDVKSTYGLAEKL 350 Pyrobaculum aerophilum str. IM2
YP_001434653 321 phhlIYQYWEDpqKRDVLRKYNEADALSTLMLAELF 356 Ignicoccus hospitalis KIN4/I
YP_254794    322 ewyeVPRYWDDksKREILLKHNLSNIKSIYDIGQSN 357 Sulfolobus acidocaldarius DSM 639
YP_001541158 318 pghrIYQYWDDegKRSQLIKYARDDVLSTLGLGKIL 353 Caldivirga maquilingensis IC-167
NP_069333    305 eakdIYRYWSRg-EKEKVLNYARQDAINTYLIAKEL 339 Archaeoglobus fulgidus DSM 4304
P95979       314 kwyeISRYWDNekNRRIIREYSIENARSIYLLGNYL 349 Sulfolobus solfataricus
YP_001737626 275 f--rVAEAWKL--NRDNALDYMRKKLSTIIGIYSKI 306 Candidatus Korarchaeum cryptofilum OPF8

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