Conserved Protein Domain Family
DNA_polB_epsilon_exo

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cd05779: DNA_polB_epsilon_exo 
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase
The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon 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 delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal 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. DNA polymerase epsilon also carries a unique large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is orthologous to the archaeal DNA polymerase B3 rather than to the eukaryotic alpha, delta, or zeta polymerases. 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
Statistics
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PSSM-Id: 99822
View PSSM: cd05779
Aligned: 24 rows
Threshold Bit Score: 366.585
Threshold Setting Gi: 19074730
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 116241339  268 DPVVLAFDIETTKLPLKFPD-AETDQIMMISYMIDGQGYLITNREIVSEDIEDFEFTPKPEYEGP--FCVFNEPDEAHLI 344
gi 19074730   207 DLRILAFDIETSKRPLKFPN-ADSDEVMMISVKTEGYGELIVNRGLVSKDIRGFEYSPKEDMQCT--FCAVNESSEEGVL 283
gi 66359706   275 DLRSLAWDIETTKDPLKFPN-VEKDQIMMISCMFEGQGYLITNREIVSADIYDFEYSPKKEYESF--FKCINYPDEKELI 351
gi 71029614   296 PLNVFAWDIECYKAPLKFPD-METDEIMLISVMFNGQGYLIVNRTIVSRDIEEFLYQPREDIVGNacFKIYNERTERDLL 374
gi 118354772  230 DLKYLAFDIETSKAELRFPD-AKTDCVMMISLMYEGDAYLIVNRDFCGQDVVGFDYAPTPEFECS--ITVYNEPNEKACI 306
gi 145490728  219 ELKYLAFDIETYKQPLKFPD-AKNDQIMMISITHSQNSILITNMQTLGQEVQNFDYAPKPEFATQ--AIIYNQPDEKSLL 295
gi 3387878     73 TPRILAFDIECSKQPLQFPN-TETDQIMMISYMLDGTGYLVINREWFSEEIEDFEYSPLPEYFCE--FHVTNYPNEREML 149
gi 158280174  298 EPRICAFDIETTKLPLQFPN-AEYDQVFMISYMLDRQGYLIVNREVVGADIADFEYTPKPEFEGP--FKVTNAANERELL 374
gi 159115199  259 VPKVLAYDIETTKKPLRFPNaEAGDQIMCISYMFDDQGYLLINRSIFSRDITDFEYTPKPEFPGK--FACFNLPTEKDLL 336
gi 162677598  280 EVRVCAFDIETTKLPLKFPD-ASYDSVMMISYMIDGQGYLIVNRECVGAEIEDLEYTPKPEFEGH--FKVTNTRTEKELL 356
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                          ##  ###                                                        
gi 116241339  345 QRWFEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQEIGFQKDs------------qGEYKAPQCIHMDCLRWVK 412
gi 19074730   284 IRFVETIQRHRPHLITTFNGALFDFPFLEKRMLRYGISLRETAGFVRRd-------------EYYISPFIVHLDCYKWVR 350
gi 66359706   352 WGFIKLIQTLRPHIIASYNGDNFDFPFLYERAKKYDIDVSKEWGIRMEidhssggglqssnkTIFSGTNIIHLDCFRWVE 431
gi 71029614   375 MRFFYLINYLKPHIFVTYNGDNFDFPYVNRRAEINGIHMNKVSGLHLSs-------------ELFQHASILNMDCYKWVE 441
gi 118354772  307 KKFFDIIVDYKAFIITSFNGDKFDWPFIHERCNQLGLSLEKEIGIHLEe------------gPEYFGRYLTHLDCLYWVI 374
gi 145490728  296 LKFFQVILDYKPNIISSFNGDRFDWPYIEERCLTHGFYLEQEIGIKKNee-----------nNEYYGRYIIHMDCFAWVE 364
gi 3387878    150 KGWFNHIREVKPHIFVTFNGDFFDWEFIQERARILNLSMYYEIGFHKFg-------------EEFVSNYAPHIDCFHWVQ 216
gi 158280174  375 QAFFSHMRSAQPAIYVTYNGDFFDFPFIEARCAVLGLDMHESIGFRCRggqgs----gpgaaKECLSRSAVHMDCMHWVD 450
gi 159115199  337 IFFFTHIRTARPNIFATFNGDFFDWPFVDVRAAAYGMDLLDEIGVLKSestsr----aglveKQYYARAVPHLDCFRWVR 412
gi 162677598  357 VSWFSHMREVKPSIYVTYNGDFFDWPFIQARALHHGMRMHDEIGFQHNet-----------lGECLSKFACHLDCFAWVK 425
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
Feature 1                   ##                                 #   #         
gi 116241339  413 RDSYLPVGSHNLKAAAKAKLGYDPVELDPEDMCRMATEQPQTLATYSVSDAVATYYLYM 471
gi 19074730   351 RDSYLPAGSQGLKAVTKAKLGYFPDEVDPEDMVGLAVSDPERMGSYSASDSVATYFLYI 409
gi 66359706   432 RDSYLPCGSRGLKSVTKAKLRYNPVELDPELMVPYAKTNPQGLAEYSVSDAVATYFLYK 490
gi 71029614   442 RDSYLPFGSRTLKQVCKLMLKYNPVEIDPEDMVHLARVTPQKLAVYSVSDAVATYHLYM 500
gi 118354772  375 RDAYLPQGSHGLKAVTRSKLGYEPIEVDPEEMVPLARNNTQELAEYSVSDAVATYFIYK 433
gi 145490728  365 RDAYLPQGSHGLKAVTKAKLGYQPIEVDPEKMVPMALQDSQQFAGYSISDSVATYWLYR 423
gi 3387878    217 RDSYLPAGSQGLKAVTKAKLNYNPLELDPEDICPLGMEDPQRLANYSASDAYATYYLYE 275
gi 158280174  451 RDSYLPQGSRGLKSVTKYKLGYDPVEVHPEDMVRLARETPQAMASYSVSDAVSTYYLYM 509
gi 159115199  413 RDSYLPQGSQGLKAVTRAKLKYHPDELSPELMVSYAQTDPQVLASYSVSDAVATYYLYR 471
gi 162677598  426 RDSYLPQGSQGLKAVTKAKLGFDPLEVNPEDMVRFAIEQPQTMASYSVSDAVSTYYLYM 484

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