1QHT,1D5A,1TGO,1WNS,2JGU


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: 2-Oct-2020
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:
Feature 1                 ####                                                                    
1QHT_A        133 EELTMLAFAIATLYHEGE--EFGTGPILMISYAD------GSEARVITWKKIDLP----YVDVVSTE-------KEMIKR 193  Thermococcus sp.
P52025        173 PELNCIAFDMELYCKKEP--NAKKDPIIMVNLFS------KDYQKVITYKKFENSeyngCVDYVKDE-------KELIQK 237  Methanococcus...
NP_247880     154 PKLKSVAFDMEVYNRDTEp-NPERDPILMASFWD------ENGGKVITYKEFNHP----NIEVVKNE-------KELIKK 215  Methanocaldoc...
NP_987500     145 PDFKTVSFDIEVYCNKEP--NPKKDPIIMASFSS------KDFNTVVSTKKFDHE----KLEYVKDE-------KELIKR 205  Methanococcus...
YP_001324849  149 PDLKAVSFDMEVHFKDREp-EPEKDAILMTSFYShdkkinKKIKKVITYKPFEHE----SVEIVKDE-------KELIKK 216  Methanococcus...
1D5A_A        133 EELRMLAFDIETLAHAGA--AAGAGPILMISYAD------EEGARVITWKNIDLP----YVESVSTE-------KEMIKR 193  Desulfurococc...
1TGO_A        133 EELKMLAFDIETLYHEGE--EFAEGPILMISYAD------EEGARVITWKNIDLP----YVDVVSTE-------KEMIKR 193  Thermococcus ...
1WNS_A        133 EELKMLAFDIETLYHEGE--EFAEGPILMISYAD------EEGARVITWKNVDLP----YVDVVSTE-------REMIKR 193  Thermococcus ...
2JGU_A        133 EELKILAFDIETLYHEGE--EFGKGPIIMISYAD------ENEARVITWKNIDLP----YVESVSTE-------KEMIKR 193  Pyrococcus fu...
NP_614322     162 EDLVVASFDLEVLAEPGTtiKGASGPIIAISFAYstp-dgERRNYVITWKGEDESf---EVDGVETEvivcrseAAALRR 237  Methanopyrus ...
YP_001273614  168 QDFRILSFDLEVRNPHGMp-NSEVDEIIMIGVASn-----FGINQVISTKTNSEDrd-dFVNQVESE-------KEMIET 233  Methanobrevib...
NP_276336     167 HGLDILSFDIEVRNPHGMp-DPEKDEIVMIGVAGn-----MGYESVISTAGDHLD----FVEVVEDE-------RELLER 229  Methanothermo...
YP_448519     166 NQNKILSFDIEVYNAEGMp-SAKKDAIIMMSLCGn-----NGFKKVLSTKKSSKD----FVETLPTE-------EDMLKR 228  Methanosphaer...
Feature 1                        ##  ###                                                          
1QHT_A        194 FLRVVREkdPDVLITYNGDNFDFAYLKKRCEELGIk--FTLGRDg---SEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTI 268  Thermococcus sp.
P52025        238 TIEILKQ--YDVIYTYNGDNFDFPYLKKRANIYEIeldFDNASNsqqpQIIKISKGGINRKSKIPGIIHIDLYPIARKLL 315  Methanococcus...
NP_247880     216 IIETLKE--YDVIYTYNGDNFDFPYLKARAKIYGId--INLGKDg---EELKIKRGGMEYRSYIPGRVHIDLYPISRRLL 288  Methanocaldoc...
NP_987500     206 IIEILKE--YDIIYTYNGDNFDFPYLKKRAESFGLe--LKLGKNd---EKIKITKGGMNSKSYIPGRVHIDLYPIARRLL 278  Methanococcus...
YP_001324849  217 TMELLKQ--YNIIYTYNGDNFDFPYLKRRAEHLKIp--LNFGEN----HKLKLSKGGMNLKSAISGIVHIDLYPIARRTL 288  Methanococcus...
1D5A_A        194 FLKVIQEkdPDVLITYNGDNFDFAYLKKRSEMLGVk--FILGRDg---SEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTI 268  Desulfurococc...
1TGO_A        194 FLKVVKEkdPDVLITYNGDNFDFAYLKKRSEKLGVk--FILGREg---SEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTI 268  Thermococcus ...
1WNS_A        194 FLRVVKEkdPDVLITYNGDNFDFAYLKKRCEKLGIn--FALGRDg---SEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTI 268  Thermococcus ...
2JGU_A        194 FLRIIREkdPDIIVTYNGDSFDFPYLAKRAEKLGIk--LTIGRDg---SEPKMQRIGDMTAVEVKGRIHFDLYHVIRTTI 268  Pyrococcus fu...
NP_614322     238 FFDEFRRvdPDVVFTYNGDEFDLPYLQHRAGKLGId-vSPLARPag-kRGIILKHGGGRYASDIFGRAHVDLYHTARKNL 315  Methanopyrus ...
YP_001273614  234 FIDIVKKsnVDIIVGYNSDNFDLPYLKDRAKLYGLe--LDLGMDd---SNIKFIRRGFANAASFKGLIHVDLYLVMRRYM 308  Methanobrevib...
NP_276336     230 FAEIVIDkkPDILVGYNSDNFDFPYITRRAAILGAe--LDLGWDg---SKIRTMRRGFANATAIKGTVHVDLYPVMRRYM 304  Methanothermo...
YP_448519     229 FVEIIKEenPDMLVGYNSDNFDLPYIKERADTLNIk--LPLGIDk---SSIKFIKRGFNNAGLIRGRVHVDLYLLVRQYM 303  Methanosphaer...
Feature 1              ##                                    #   #           
1QHT_A        269 NLPTYTLEAVYEAVFGKPKEKVYAEEIAQAWESge-gLERVARYSMEDAKVTYELGREF 326  Thermococcus sp.
P52025        316 NLTKYKLENVVQELFKINKEAVDYGDIPKMWETe---DTTLLRYAYEDALYTYKMGNYF 371  Methanococcus voltae
NP_247880     289 KLTKYTLEDVVYNLFGIEKLKIPHTKIVDYWANn---DKTLIEYSLQDAKYTYKIGKYF 344  Methanocaldococcus jannaschii DSM ...
NP_987500     279 NLTKYRLENVTEALFDVKKVDVGHENIPKMWDNl---DETLVEYSHQDAYYTQRIGEQF 334  Methanococcus maripaludis S2
YP_001324849  289 NLTKYKLEDVSKELFNIEKLEVGHHNIVPLWNNn---NPKLVEYSLQDAEYTYKIGEYF 344  Methanococcus aeolicus Nankai-3
1D5A_A        269 NLPTYTLETVYEPVFGQPAEKVYAEEIAEAWASge-gLERVARYSMEDAKATYELGKEF 326  Desulfurococcus sp. Tok
1TGO_A        269 NLPTYTLEAVYEAIFGQPKEKVYAEEIAQAWETge-gLERVARYSMEDAKVTYELGKEF 326  Thermococcus gorgonarius
1WNS_A        269 NLPTYTLEAVYEAVFGQPKEKVYAEEITTAWETge-nLERVARYSMEDAKVTYELGKEF 326  Thermococcus kodakarensis
2JGU_A        269 NLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESge-nLERVAKYSMEDAKATYELGKEF 326  Pyrococcus furiosus
NP_614322     316 KLERFTLEEAVKDVLGVEKEEMELADINEAWKRg--nLDELMRYSAEDAHYTLELGLEL 372  Methanopyrus kandleri AV19
YP_001273614  309 TLERYTLERVYYELFGEEKIDVPGEHIWEYWDSdsteLDDLFDYSLDDVVSTLKIAQQT 367  Methanobrevibacter smithii ATCC 35061
NP_276336     305 NLDRYTLERVYQELFGEEKIDLPGDRLWEYWDRde-lRDELFRYSLDDVVATHRIAEKI 362  Methanothermobacter thermautotroph...
YP_448519     304 NLDRYTLERVYKELFDIEKIDVPGDKIFEYWDSdnelLEKLFDYSMDDAITTTEIADKL 362  Methanosphaera stadtmanae DSM 3091

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