Conserved Protein Domain Family
DNA_polB_epsilon_exo

?
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
?
PSSM-Id: 99822
View PSSM: cd05779
Aligned: 24 rows
Threshold Bit Score: 366.585
Threshold Setting Gi: 19074730
Created: 1-Oct-2007
Updated: 2-Oct-2020
Structure
?
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
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                ####                                                                     
Q07864        268 DPVVLAFDIETTKLPLKFPD-AETDQIMMISYMIDGQGYLITNREIVSEDIEDFEFTPKPEYEGP--FCVFNEPDEAHLI 344  human
NP_586236     207 DLRILAFDIETSKRPLKFPN-ADSDEVMMISVKTEGYGELIVNRGLVSKDIRGFEYSPKEDMQCT--FCAVNESSEEGVL 283  Encephalitozo...
XP_627031     275 DLRSLAWDIETTKDPLKFPN-VEKDQIMMISCMFEGQGYLITNREIVSADIYDFEYSPKKEYESF--FKCINYPDEKELI 351  Cryptosporidi...
XP_764450     296 PLNVFAWDIECYKAPLKFPD-METDEIMLISVMFNGQGYLIVNRTIVSRDIEEFLYQPREDIVGNacFKIYNERTERDLL 374  Theileria par...
XP_001010647  230 DLKYLAFDIETSKAELRFPD-AKTDCVMMISLMYEGDAYLIVNRDFCGQDVVGFDYAPTPEFECS--ITVYNEPNEKACI 306  Tetrahymena t...
XP_001431364  219 ELKYLAFDIETYKQPLKFPD-AKNDQIMMISITHSQNSILITNMQTLGQEVQNFDYAPKPEFATQ--AIIYNQPDEKSLL 295  Paramecium te...
AAC72340       73 TPRILAFDIECSKQPLQFPN-TETDQIMMISYMLDGTGYLVINREWFSEEIEDFEYSPLPEYFCE--FHVTNYPNEREML 149  Trichomonas v...
EDP05932      298 EPRICAFDIETTKLPLQFPN-AEYDQVFMISYMLDRQGYLIVNREVVGADIADFEYTPKPEFEGP--FKVTNAANERELL 374  Chlamydomonas...
XP_001707823  259 VPKVLAYDIETTKKPLRFPNaEAGDQIMCISYMFDDQGYLLINRSIFSRDITDFEYTPKPEFPGK--FACFNLPTEKDLL 336  Giardia lambl...
EDQ64066      280 EVRVCAFDIETTKLPLKFPD-ASYDSVMMISYMIDGQGYLIVNRECVGAEIEDLEYTPKPEFEGH--FKVTNTRTEKELL 356  Physcomitrell...
Feature 1                          ##  ###                                                        
Q07864        345 QRWFEHVQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQEIGFQKDs------------qGEYKAPQCIHMDCLRWVK 412  human
NP_586236     284 IRFVETIQRHRPHLITTFNGALFDFPFLEKRMLRYGISLRETAGFVRRd-------------EYYISPFIVHLDCYKWVR 350  Encephalitozo...
XP_627031     352 WGFIKLIQTLRPHIIASYNGDNFDFPFLYERAKKYDIDVSKEWGIRMEidhssggglqssnkTIFSGTNIIHLDCFRWVE 431  Cryptosporidi...
XP_764450     375 MRFFYLINYLKPHIFVTYNGDNFDFPYVNRRAEINGIHMNKVSGLHLSs-------------ELFQHASILNMDCYKWVE 441  Theileria par...
XP_001010647  307 KKFFDIIVDYKAFIITSFNGDKFDWPFIHERCNQLGLSLEKEIGIHLEe------------gPEYFGRYLTHLDCLYWVI 374  Tetrahymena t...
XP_001431364  296 LKFFQVILDYKPNIISSFNGDRFDWPYIEERCLTHGFYLEQEIGIKKNee-----------nNEYYGRYIIHMDCFAWVE 364  Paramecium te...
AAC72340      150 KGWFNHIREVKPHIFVTFNGDFFDWEFIQERARILNLSMYYEIGFHKFg-------------EEFVSNYAPHIDCFHWVQ 216  Trichomonas v...
EDP05932      375 QAFFSHMRSAQPAIYVTYNGDFFDFPFIEARCAVLGLDMHESIGFRCRggqgs----gpgaaKECLSRSAVHMDCMHWVD 450  Chlamydomonas...
XP_001707823  337 IFFFTHIRTARPNIFATFNGDFFDWPFVDVRAAAYGMDLLDEIGVLKSestsr----aglveKQYYARAVPHLDCFRWVR 412  Giardia lambl...
EDQ64066      357 VSWFSHMREVKPSIYVTYNGDFFDWPFIQARALHHGMRMHDEIGFQHNet-----------lGECLSKFACHLDCFAWVK 425  Physcomitrell...
Feature 1                   ##                                 #   #         
Q07864        413 RDSYLPVGSHNLKAAAKAKLGYDPVELDPEDMCRMATEQPQTLATYSVSDAVATYYLYM 471  human
NP_586236     351 RDSYLPAGSQGLKAVTKAKLGYFPDEVDPEDMVGLAVSDPERMGSYSASDSVATYFLYI 409  Encephalitozoon cuniculi GB-M1
XP_627031     432 RDSYLPCGSRGLKSVTKAKLRYNPVELDPELMVPYAKTNPQGLAEYSVSDAVATYFLYK 490  Cryptosporidium parvum Iowa II
XP_764450     442 RDSYLPFGSRTLKQVCKLMLKYNPVEIDPEDMVHLARVTPQKLAVYSVSDAVATYHLYM 500  Theileria parva strain Muguga
XP_001010647  375 RDAYLPQGSHGLKAVTRSKLGYEPIEVDPEEMVPLARNNTQELAEYSVSDAVATYFIYK 433  Tetrahymena thermophila SB210
XP_001431364  365 RDAYLPQGSHGLKAVTKAKLGYQPIEVDPEKMVPMALQDSQQFAGYSISDSVATYWLYR 423  Paramecium tetraurelia strain d4-2
AAC72340      217 RDSYLPAGSQGLKAVTKAKLNYNPLELDPEDICPLGMEDPQRLANYSASDAYATYYLYE 275  Trichomonas vaginalis
EDP05932      451 RDSYLPQGSRGLKSVTKYKLGYDPVEVHPEDMVRLARETPQAMASYSVSDAVSTYYLYM 509  Chlamydomonas reinhardtii
XP_001707823  413 RDSYLPQGSQGLKAVTRAKLKYHPDELSPELMVSYAQTDPQVLASYSVSDAVATYYLYR 471  Giardia lamblia ATCC 50803
EDQ64066      426 RDSYLPQGSQGLKAVTKAKLGFDPLEVNPEDMVRFAIEQPQTMASYSVSDAVSTYYLYM 484  Physcomitrella patens subsp. patens

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap