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: 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 147899700  309 WQKIAPQRVLSFDIECAGRKGv-------FPEPDKD-PVIQIANMVLr----QGEKDPFIRNVFTLGTCASIVGSQVLCF 376
gi 157435999  266 YAVNAPIRVLSFDIESVSLQGg-------FPDAASD-YIITICSSLYil-tqSTADAPHANVALVLKSCAPIVGADVFCF 336
gi 116503123  253 LPEIAPLRVLSFDVETMVFRPtppatrapFPHPTTS-EVLQISNIISrrygkDQSMELSSRVIFTLGKCAAISGAQVFWF 331
gi 232011     296 YQQIPKLRILSFDIECIKLDGk------gFPEAKND-PIIQISSILYf---qGEPIDNCTKFIFTLLECASIPGSNVIWF 365
gi 66475912   288 WATLPPIRILSFDIECITESGv------gFPEPHKD-SVIQISSVVTl----LDSPESICNVIFTLKECASVAEAFVFWF 356
gi 118400060  294 WADIAPLRIFSFDIECLAKSGg-------FPNASKDdPIIQIATVLKi----HDQQEDIVRTVFTMDTCSNIPGCIVKSF 362
gi 123496446  241 YMKIPPMRILSFDIEVGGSPEn-------FPTADND-PVIQICCYVAv----QGEEHSRFSAAFILNTCTPIVGSALFQF 308
gi 156086780  264 WQSIGPIRTLSFDIECVKFTGp------gFPNANND-PVIQIASVLHt---hGDSLDSAQKFVFTLDTCDNLHGAHVLSF 333
gi 145514650  153 KSEIAPLRILSFDIECAAEKG--------FPNEEHD-PIIQIACIVKv----HNRNEELIRVVFTLGDCEKIPGAWVKSF 219
gi 85014201   187 YVVLPPLKVLSIDIECVSAGNg-------FPSSKCD-PIIQIGNTLMl----FGDNSYASQDIFCLKETTGIPGVNVHWY 254
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                 ##  ###                                                 
gi 147899700  377 EREDALLKAWAEFVRIIDPDIITGYNIQNFDMPYLINRAQTLKvs---------tFPFLGRIRSLKsvi----------- 436
gi 157435999  337 ETEQELLLAFNYLIQLFDPDLFTGYNIDGFDFSYIFKRAEVSQvlvqslpgsmgtDQLLSRMVRKGssayastlpralss 416
gi 116503123  332 DTEEELLLSWHQFVKSIDPDVITGYNMGRFDLPFLLARAKILGiq--------dtFGRLGRLEGGMlll----------- 392
gi 232011     366 NDEKTLLEAWNEFIIRIDPDFLTGYNIINFDLPYILNRGTALNlk---------kLKFLGRIKNVAstv----------- 425
gi 66475912   357 ESEKDMLLAWKDFLLALDPDVITGYNCINFDMNYLLERAKLFQln---------dFFFFTRLAKTKits----------- 416
gi 118400060  363 KTETELLLEWEKFLQNVDPDIFLGYNITNFDFPYILERGKQLKinn-------gkYGFMGRIKNTItri----------- 424
gi 123496446  309 ENEKDLLINFQRFIQWVDPEIITGYNICGFDIPYLVERSIAIKan---------eFCELGRYVKEFstc----------- 368
gi 156086780  334 ANEAALLMAWKQFFIAVDPDFLTGYNIINFDIPYLINRANALKlp---------eFTQLPRITRSKssv----------- 393
gi 145514650  220 QKEEDLLNEFQVFFQGLDPDIIIGYNIQNFDIPYILNRAQNLKlk---------nYGKFGRIPTDQsti----------- 279
gi 85014201   255 ETEKELLESWKKYFMELDPDVIVGYNVKGFDIPYILSRGEILGie---------sFSVLGRSRKKArtr----------- 314
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                          ##             
gi 147899700  437 ----rdsSFQSKQMGRREn----------------KVINTE-GRVQFDLLQVLLRDYK---LRSYTLNAVSFHFLQEQKE 492
gi 157435999  417 pmtiavsHLQSKQLGKRDt----------------YEIECP-GRISMDILPNIIHDYK---LRSYTLNSVCARFLNEQKD 476
gi 116503123  393 ----saeSWSFMRVCVPDpclhfspwdanapqnewKDMPIVpGRITFDASNYIARNKFalgLASARLGDVALQLLGEAKL 468
gi 232011     426 ----kdsSFSSKQFGTHEt----------------KEINIF-GRIQFDVYDLIKRDYK---LKSYTLNYVSFEFLKEQKE 481
gi 66475912   417 ----kdtRFSSRAFGTHEs----------------KLINIE-GRILWDILETIRREHK---LKSYSLNYVSTNFLKEQKE 472
gi 118400060  425 ----kdgKYLSKAMGMRDt----------------KEMNFE-GRIQLDMMMHMHRETK---LSSYSLNSVSYHFLNEQKE 480
gi 123496446  369 ----ketTKGTKQLGYREt----------------KDVDIN-GRIQYDMMIAIKNDFK---LRSYSLNAVSAQFIGDQKE 424
gi 156086780  394 ----rdiISSNNTMGTFEn----------------KEINIE-GRILFDVYDLVRRDHK---LKSYTLNYVSFEFLKQQKE 449
gi 145514650  280 ----kngKFLSKAMGMREt----------------KDINIE-GRIQLDMMIHMMKEHK---LSSFSLNNVSFQFLKQQKE 335
gi 85014201   315 -----dtTMSSNMFGSITt----------------TEVEID-GRLIIDMMVVIRRDFK---LRSYSLNSVSIHFLKEQKE 369
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
Feature 1                                #   #                  
gi 147899700  493 DVQHSIITDLQNGNEqtRRRLAVYCLKDAYLPLRLLEKLMCVINYM 538
gi 157435999  477 DVHYSMITPLFMQDEygRRRITLYCIKDCKLPLKLMEKLMILVNTI 522
gi 116503123  469 DLCFELVQDYQEGGPetRRRMALYCLKDAYLVQRLLDVHSCLRNDL 514
gi 232011     482 DVHYSIMNDLQNESPesRKRIATYCIKDGVLPLRLIDKLLFIYNYV 527
gi 66475912   473 DVHYSMIRGLQDGNPetRKRIAIYCLKDSILPLRLMKHLKLFPNII 518
gi 118400060  481 DVHHTQISGLQKGDAetRKRLAVYCLKDAQLPLKLMQKLMCIYNYT 526
gi 123496446  425 DVHYSMISKLQNGSDtdRHRLAIYCVKDAYLPLQLMNKLLSVLTTI 470
gi 156086780  450 DVHHSTMSKLQLGSAadRRRIASYCLKDSVLPLLLIDKLLLLFNYV 495
gi 145514650  336 DVHYSIIYTLQNKNPetRKRIAVYCLKDAELPILLMDKLCCLYNYA 381
gi 85014201   370 DVPYSSIGELQSKNKdtRRRIASYCLRDTVLPLRLFNTLNVLINYT 415

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