Conserved Protein Domain Family
DNA_polB_Kod1_like_exo

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cd05780: DNA_polB_Kod1_like_exo 
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DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases
The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that 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 contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. 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: 99823
View PSSM: cd05780
Aligned: 13 rows
Threshold Bit Score: 258.824
Threshold Setting Gi: 20094475
Created: 1-Oct-2007
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
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                 ####                                                                    
1QHT_A        133 EELTMLAFAIATLYHEGE--EFGTGPILMISYAD------GSEARVITWKKIDLP----YVDVVSTE-------KEMIKR 193
gi 1706513    173 PELNCIAFDMELYCKKEP--NAKKDPIIMVNLFS------KDYQKVITYKKFENSeyngCVDYVKDE-------KELIQK 237
gi 15669075   154 PKLKSVAFDMEVYNRDTEp-NPERDPILMASFWD------ENGGKVITYKEFNHP----NIEVVKNE-------KELIKK 215
gi 45357943   145 PDFKTVSFDIEVYCNKEP--NPKKDPIIMASFSS------KDFNTVVSTKKFDHE----KLEYVKDE-------KELIKR 205
gi 150401083  149 PDLKAVSFDMEVHFKDREp-EPEKDAILMTSFYShdkkinKKIKKVITYKPFEHE----SVEIVKDE-------KELIKK 216
1D5A_A        133 EELRMLAFDIETLAHAGA--AAGAGPILMISYAD------EEGARVITWKNIDLP----YVESVSTE-------KEMIKR 193
1TGO_A        133 EELKMLAFDIETLYHEGE--EFAEGPILMISYAD------EEGARVITWKNIDLP----YVDVVSTE-------KEMIKR 193
1WNS_A        133 EELKMLAFDIETLYHEGE--EFAEGPILMISYAD------EEGARVITWKNVDLP----YVDVVSTE-------REMIKR 193
2JGU_A        133 EELKILAFDIETLYHEGE--EFGKGPIIMISYAD------ENEARVITWKNIDLP----YVESVSTE-------KEMIKR 193
gi 20094475   162 EDLVVASFDLEVLAEPGTtiKGASGPIIAISFAYstp-dgERRNYVITWKGEDESf---EVDGVETEvivcrseAAALRR 237
gi 148643101  168 QDFRILSFDLEVRNPHGMp-NSEVDEIIMIGVASn-----FGINQVISTKTNSEDrd-dFVNQVESE-------KEMIET 233
gi 15679219   167 HGLDILSFDIEVRNPHGMp-DPEKDEIVMIGVAGn-----MGYESVISTAGDHLD----FVEVVEDE-------RELLER 229
gi 84490287   166 NQNKILSFDIEVYNAEGMp-SAKKDAIIMMSLCGn-----NGFKKVLSTKKSSKD----FVETLPTE-------EDMLKR 228
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                        ##  ###                                                          
1QHT_A        194 FLRVVREkdPDVLITYNGDNFDFAYLKKRCEELGIk--FTLGRDg---SEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTI 268
gi 1706513    238 TIEILKQ--YDVIYTYNGDNFDFPYLKKRANIYEIeldFDNASNsqqpQIIKISKGGINRKSKIPGIIHIDLYPIARKLL 315
gi 15669075   216 IIETLKE--YDVIYTYNGDNFDFPYLKARAKIYGId--INLGKDg---EELKIKRGGMEYRSYIPGRVHIDLYPISRRLL 288
gi 45357943   206 IIEILKE--YDIIYTYNGDNFDFPYLKKRAESFGLe--LKLGKNd---EKIKITKGGMNSKSYIPGRVHIDLYPIARRLL 278
gi 150401083  217 TMELLKQ--YNIIYTYNGDNFDFPYLKRRAEHLKIp--LNFGEN----HKLKLSKGGMNLKSAISGIVHIDLYPIARRTL 288
1D5A_A        194 FLKVIQEkdPDVLITYNGDNFDFAYLKKRSEMLGVk--FILGRDg---SEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTI 268
1TGO_A        194 FLKVVKEkdPDVLITYNGDNFDFAYLKKRSEKLGVk--FILGREg---SEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTI 268
1WNS_A        194 FLRVVKEkdPDVLITYNGDNFDFAYLKKRCEKLGIn--FALGRDg---SEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTI 268
2JGU_A        194 FLRIIREkdPDIIVTYNGDSFDFPYLAKRAEKLGIk--LTIGRDg---SEPKMQRIGDMTAVEVKGRIHFDLYHVIRTTI 268
gi 20094475   238 FFDEFRRvdPDVVFTYNGDEFDLPYLQHRAGKLGId-vSPLARPag-kRGIILKHGGGRYASDIFGRAHVDLYHTARKNL 315
gi 148643101  234 FIDIVKKsnVDIIVGYNSDNFDLPYLKDRAKLYGLe--LDLGMDd---SNIKFIRRGFANAASFKGLIHVDLYLVMRRYM 308
gi 15679219   230 FAEIVIDkkPDILVGYNSDNFDFPYITRRAAILGAe--LDLGWDg---SKIRTMRRGFANATAIKGTVHVDLYPVMRRYM 304
gi 84490287   229 FVEIIKEenPDMLVGYNSDNFDLPYIKERADTLNIk--LPLGIDk---SSIKFIKRGFNNAGLIRGRVHVDLYLLVRQYM 303
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
Feature 1              ##                                    #   #           
1QHT_A        269 NLPTYTLEAVYEAVFGKPKEKVYAEEIAQAWESge-gLERVARYSMEDAKVTYELGREF 326
gi 1706513    316 NLTKYKLENVVQELFKINKEAVDYGDIPKMWETe---DTTLLRYAYEDALYTYKMGNYF 371
gi 15669075   289 KLTKYTLEDVVYNLFGIEKLKIPHTKIVDYWANn---DKTLIEYSLQDAKYTYKIGKYF 344
gi 45357943   279 NLTKYRLENVTEALFDVKKVDVGHENIPKMWDNl---DETLVEYSHQDAYYTQRIGEQF 334
gi 150401083  289 NLTKYKLEDVSKELFNIEKLEVGHHNIVPLWNNn---NPKLVEYSLQDAEYTYKIGEYF 344
1D5A_A        269 NLPTYTLETVYEPVFGQPAEKVYAEEIAEAWASge-gLERVARYSMEDAKATYELGKEF 326
1TGO_A        269 NLPTYTLEAVYEAIFGQPKEKVYAEEIAQAWETge-gLERVARYSMEDAKVTYELGKEF 326
1WNS_A        269 NLPTYTLEAVYEAVFGQPKEKVYAEEITTAWETge-nLERVARYSMEDAKVTYELGKEF 326
2JGU_A        269 NLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESge-nLERVAKYSMEDAKATYELGKEF 326
gi 20094475   316 KLERFTLEEAVKDVLGVEKEEMELADINEAWKRg--nLDELMRYSAEDAHYTLELGLEL 372
gi 148643101  309 TLERYTLERVYYELFGEEKIDVPGEHIWEYWDSdsteLDDLFDYSLDDVVSTLKIAQQT 367
gi 15679219   305 NLDRYTLERVYQELFGEEKIDLPGDRLWEYWDRde-lRDELFRYSLDDVVATHRIAEKI 362
gi 84490287   304 NLDRYTLERVYKELFDIEKIDVPGDKIFEYWDSdnelLEKLFDYSMDDAITTTEIADKL 362

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