Conserved Protein Domain Family
DNA_polB_delta_exo

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cd05777: DNA_polB_delta_exo 
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase
The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The 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 contain four conserved acidic residues necessary for metal binding and catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation.
Statistics
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PSSM-Id: 99820
View PSSM: cd05777
Aligned: 29 rows
Threshold Bit Score: 333.389
Threshold Setting Gi: 116503123
Created: 1-Oct-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                     ####                                                                
NP_001087694  309 WQKIAPQRVLSFDIECAGRKGv-------FPEPDKD-PVIQIANMVLr----QGEKDPFIRNVFTLGTCASIVGSQVLCF 376  African clawe...
EDO80217      266 YAVNAPIRVLSFDIESVSLQGg-------FPDAASD-YIITICSSLYil-tqSTADAPHANVALVLKSCAPIVGADVFCF 336  Giardia lambl...
EAU86018      253 LPEIAPLRVLSFDVETMVFRPtppatrapFPHPTTS-EVLQISNIISrrygkDQSMELSSRVIFTLGKCAAISGAQVFWF 331  Coprinopsis c...
P30315        296 YQQIPKLRILSFDIECIKLDGk------gFPEAKND-PIIQISSILYf---qGEPIDNCTKFIFTLLECASIPGSNVIWF 365  Plasmodium fa...
XP_627772     288 WATLPPIRILSFDIECITESGv------gFPEPHKD-SVIQISSVVTl----LDSPESICNVIFTLKECASVAEAFVFWF 356  Cryptosporidi...
XP_001032353  294 WADIAPLRIFSFDIECLAKSGg-------FPNASKDdPIIQIATVLKi----HDQQEDIVRTVFTMDTCSNIPGCIVKSF 362  Tetrahymena t...
XP_001326973  241 YMKIPPMRILSFDIEVGGSPEn-------FPTADND-PVIQICCYVAv----QGEEHSRFSAAFILNTCTPIVGSALFQF 308  Trichomonas v...
XP_001610797  264 WQSIGPIRTLSFDIECVKFTGp------gFPNANND-PVIQIASVLHt---hGDSLDSAQKFVFTLDTCDNLHGAHVLSF 333  Babesia bovis...
XP_001443230  153 KSEIAPLRILSFDIECAAEKG--------FPNEEHD-PIIQIACIVKv----HNRNEELIRVVFTLGDCEKIPGAWVKSF 219  Paramecium te...
XP_955596     187 YVVLPPLKVLSIDIECVSAGNg-------FPSSKCD-PIIQIGNTLMl----FGDNSYASQDIFCLKETTGIPGVNVHWY 254  Encephalitozo...
Feature 1                                 ##  ###                                                 
NP_001087694  377 EREDALLKAWAEFVRIIDPDIITGYNIQNFDMPYLINRAQTLKvs---------tFPFLGRIRSLKsvi----------- 436  African clawe...
EDO80217      337 ETEQELLLAFNYLIQLFDPDLFTGYNIDGFDFSYIFKRAEVSQvlvqslpgsmgtDQLLSRMVRKGssayastlpralss 416  Giardia lambl...
EAU86018      332 DTEEELLLSWHQFVKSIDPDVITGYNMGRFDLPFLLARAKILGiq--------dtFGRLGRLEGGMlll----------- 392  Coprinopsis c...
P30315        366 NDEKTLLEAWNEFIIRIDPDFLTGYNIINFDLPYILNRGTALNlk---------kLKFLGRIKNVAstv----------- 425  Plasmodium fa...
XP_627772     357 ESEKDMLLAWKDFLLALDPDVITGYNCINFDMNYLLERAKLFQln---------dFFFFTRLAKTKits----------- 416  Cryptosporidi...
XP_001032353  363 KTETELLLEWEKFLQNVDPDIFLGYNITNFDFPYILERGKQLKinn-------gkYGFMGRIKNTItri----------- 424  Tetrahymena t...
XP_001326973  309 ENEKDLLINFQRFIQWVDPEIITGYNICGFDIPYLVERSIAIKan---------eFCELGRYVKEFstc----------- 368  Trichomonas v...
XP_001610797  334 ANEAALLMAWKQFFIAVDPDFLTGYNIINFDIPYLINRANALKlp---------eFTQLPRITRSKssv----------- 393  Babesia bovis...
XP_001443230  220 QKEEDLLNEFQVFFQGLDPDIIIGYNIQNFDIPYILNRAQNLKlk---------nYGKFGRIPTDQsti----------- 279  Paramecium te...
XP_955596     255 ETEKELLESWKKYFMELDPDVIVGYNVKGFDIPYILSRGEILGie---------sFSVLGRSRKKArtr----------- 314  Encephalitozo...
Feature 1                                                                          ##             
NP_001087694  437 ----rdsSFQSKQMGRREn----------------KVINTE-GRVQFDLLQVLLRDYK---LRSYTLNAVSFHFLQEQKE 492  African clawe...
EDO80217      417 pmtiavsHLQSKQLGKRDt----------------YEIECP-GRISMDILPNIIHDYK---LRSYTLNSVCARFLNEQKD 476  Giardia lambl...
EAU86018      393 ----saeSWSFMRVCVPDpclhfspwdanapqnewKDMPIVpGRITFDASNYIARNKFalgLASARLGDVALQLLGEAKL 468  Coprinopsis c...
P30315        426 ----kdsSFSSKQFGTHEt----------------KEINIF-GRIQFDVYDLIKRDYK---LKSYTLNYVSFEFLKEQKE 481  Plasmodium fa...
XP_627772     417 ----kdtRFSSRAFGTHEs----------------KLINIE-GRILWDILETIRREHK---LKSYSLNYVSTNFLKEQKE 472  Cryptosporidi...
XP_001032353  425 ----kdgKYLSKAMGMRDt----------------KEMNFE-GRIQLDMMMHMHRETK---LSSYSLNSVSYHFLNEQKE 480  Tetrahymena t...
XP_001326973  369 ----ketTKGTKQLGYREt----------------KDVDIN-GRIQYDMMIAIKNDFK---LRSYSLNAVSAQFIGDQKE 424  Trichomonas v...
XP_001610797  394 ----rdiISSNNTMGTFEn----------------KEINIE-GRILFDVYDLVRRDHK---LKSYTLNYVSFEFLKQQKE 449  Babesia bovis...
XP_001443230  280 ----kngKFLSKAMGMREt----------------KDINIE-GRIQLDMMIHMMKEHK---LSSFSLNNVSFQFLKQQKE 335  Paramecium te...
XP_955596     315 -----dtTMSSNMFGSITt----------------TEVEID-GRLIIDMMVVIRRDFK---LRSYSLNSVSIHFLKEQKE 369  Encephalitozo...
Feature 1                                #   #                  
NP_001087694  493 DVQHSIITDLQNGNEqtRRRLAVYCLKDAYLPLRLLEKLMCVINYM 538  African clawed frog
EDO80217      477 DVHYSMITPLFMQDEygRRRITLYCIKDCKLPLKLMEKLMILVNTI 522  Giardia lamblia ATCC 50803
EAU86018      469 DLCFELVQDYQEGGPetRRRMALYCLKDAYLVQRLLDVHSCLRNDL 514  Coprinopsis cinerea okayama7#130
P30315        482 DVHYSIMNDLQNESPesRKRIATYCIKDGVLPLRLIDKLLFIYNYV 527  Plasmodium falciparum K1/Thailand
XP_627772     473 DVHYSMIRGLQDGNPetRKRIAIYCLKDSILPLRLMKHLKLFPNII 518  Cryptosporidium parvum Iowa II
XP_001032353  481 DVHHTQISGLQKGDAetRKRLAVYCLKDAQLPLKLMQKLMCIYNYT 526  Tetrahymena thermophila SB210
XP_001326973  425 DVHYSMISKLQNGSDtdRHRLAIYCVKDAYLPLQLMNKLLSVLTTI 470  Trichomonas vaginalis G3
XP_001610797  450 DVHHSTMSKLQLGSAadRRRIASYCLKDSVLPLLLIDKLLLLFNYV 495  Babesia bovis T2Bo
XP_001443230  336 DVHYSIIYTLQNKNPetRKRIAVYCLKDAELPILLMDKLCCLYNYA 381  Paramecium tetraurelia strain d4-2
XP_955596     370 DVPYSSIGELQSKNKdtRRRIASYCLRDTVLPLRLFNTLNVLINYT 415  Encephalitozoon cuniculi GB-M1

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