1Q8I


Conserved Protein Domain Family
DNA_polB_II_exo

?
cd05784: DNA_polB_II_exo 
Click on image for an interactive view with Cn3D
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases
The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This 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. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Pol II is also involved in lagging strand synthesis.
Statistics
?
PSSM-Id: 99827
View PSSM: cd05784
Aligned: 25 rows
Threshold Bit Score: 252.488
Threshold Setting Gi: 162453773
Created: 1-Oct-2007
Updated: 2-Oct-2020
Structure
?
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
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                ####                                                                    
1Q8I_A       148 PPLKWVSIDIETTRHg-----ELYCIGLEG----------CGQRIVYMLGPENgdas------sldfELEYVASRPQLLE 206 Escherichia coli
ZP_01615425  152 PALKTISLDIETAMDn----iTLYSIGLYGre------kgEDYRLVLMVSDHWia-----------dDVEFFADEKSLLL 210 marine gamma pr...
ZP_01521594  152 PALKVVSLDIETSQHq-----DLYSIALDG----------MAERMVFMLGQPSsepep-----ttgfALVYCSSRQEMIK 211 Comamonas testo...
YP_432839    172 PYFKVLSLDIETSMDg----aQLYSIGLAAtsygadvgagAMQHRVFMVGENAeds---------pdYLVYCADESEVFR 238 Hahella chejuen...
ZP_01114466  142 PELRVLSLDIETDWYipgqlpALYSIALAF----------DDQQQVLVVNDGAdfit------ddgvDVRLFSTVRDCLA 205 Reinekea sp. ME...
YP_001341067 147 PDWNVWSLDIETSVSt----nTLLSIGITS----------RDQRVAFVVTDQEts----------spIIRRFSDEKSLLL 202 Marinomonas sp....
ZP_01075839  149 PSWHVWSLDIETSVSr----nTILSIAVVS----------EALEMCFMVSKKPln----------dvRVTCFDDEKSLLL 204 Marinomonas sp....
ZP_01167632  151 PQFRILSIDLETTMRa----dQILSAAFYA----------DDFQLVLMQGQGIdt-----------dTLDYCADETTLIH 205 Neptuniibacter ...
ZP_01307445  141 PNFSYISFDIETTMPtrkvseKLLSIAFVYed------ssERKEMVYMLGDPSss----------tqQLIFFKNIRSLLI 204 Oceanobacter sp...
ZP_01109042  158 TRFSSLSIDIECDEHe-----MLFSIALAG----------EGVNLVLLVCPPTfekrgveqrndkpyQLLVLNSEKELLH 222 Alteromonas mac...
Feature 1                        ##  ###                                                         
1Q8I_A       207 KLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNS----ELEWREhgfknGVFFAQAKGRLIIDGIEALK 282 Escherichia coli
ZP_01615425  211 RFFDWLSDYDPDIIIGWNIVNFDMWFLERVCQKHHIPFRLGRGRRgreaAPHWRLldddgDRRAMSVPGRVVLDGIELLK 290 marine gamma pr...
ZP_01521594  212 QLNDWFARNDPDVIVGWNVIQFDLRVLQKTADDCGIPLLPGRERT----PIAWRThpgkqGYLFAPMPGRAVIDGIEALR 287 Comamonas testo...
YP_432839    239 RFVEWFDGFDPDILIGWNVINFDLRFLQKKADELNFPFHPGRGGA----AMDWRQsrsddQHFTLCIPGRVVLDGIDTLK 314 Hahella chejuen...
ZP_01114466  206 EAIARIQAYDPDCIVGWNVIDFDLRILQEHCDQVGLAFEVGRQRA----VPLWREmggqpGRYALELEGRQVVDGPGAFR 281 Reinekea sp. ME...
YP_001341067 203 AFIRYVKKYSPDIFIGWNLIGFDLQFIDQRCQILGIRPAFGVNGE----NWNIRSsd-nqGKYFASIPGRVALDGITLLK 277 Marinomonas sp....
ZP_01075839  205 AFMKFTKQASPDIIIGWNVIGFDLNFIDQRCQAFGLKPAFGINGA----SWNVRGrd-gsAKRFISIPGRAVLDGIDLLK 279 Marinomonas sp....
ZP_01167632  206 KFIQVVQQYDPDIFIGWNVINFDFKVLKNRADQLNIPLLLGRDQQ----PLQLYQsg--qGKVFARMAGRVVLDGIDTLK 279 Neptuniibacter ...
ZP_01307445  205 ASNQLISEWDPDLLLGWNVVNFDVSVLHRLYREHGLEMLWGRQQS----SLNIRQgq--nGFNFVDIPGRCILDGIDSLK 278 Oceanobacter sp...
ZP_01109042  223 AFFHHVTSYDPDIILGWNVKQFDMAVLARRAKANRLKFTLGRHER----EASVRQw---eDQTLVDVPGRCVIDGIEALK 295 Alteromonas mac...
Feature 1                 ##                                         #   #         
1Q8I_A       283 SAFWNFSSFSLETVAQELLGEGKSIDNPwd----rMDEIDRRFAEDKPALATYNLKDCELVTQIFH 344 Escherichia coli
ZP_01615425  291 AAFYQFESFSLNTVATELLGDGKLIHGSg-----rGETITDLFTSDKLALAEYNIQDCRLVLDIFD 351 marine gamma proteobacterium ...
ZP_01521594  288 AAVWSFSSFSLENVSQELLGEGKEIGDEyd----kMAEIERRYQQDKPALASYNLRDCELVLRIFE 349 Comamonas testosteroni KF-1
YP_432839    315 SATYNFESFSLEYVAQHLLGRGKLIHDPdn----rGDEITHLFLHDKPRLAAYNLEDCQLVWEIFQ 376 Hahella chejuensis KCTC 2396
ZP_01114466  282 SAAWAFEDYSLETVSRSLLNRGKRIEHSdd----rVGEIERLYREDLQAFAHYNAEDAQLVLDLFD 343 Reinekea sp. MED297
YP_001341067 278 VGGYHFESYSLNNVSNEILDDGKLLHGSe-----rWQEIERLHKEDLDAFVAYNLQDCDLVMRIFE 338 Marinomonas sp. MWYL1
ZP_01075839  280 VAGYHFESYSLENVSREILADGKLLHGSq-----rWQEIERLYEQEPLAFVEYNLQDCWLVWRIFK 340 Marinomonas sp. MED121
ZP_01167632  280 GATYQFESFSLENVSREFLDRGKLIDHVdd----rGGEIQRLFREDKASLARYNLEDCKLVWDIFE 341 Neptuniibacter caesariensis
ZP_01307445  279 NASYHFESFALDFVAHQLLDKGKIIEGFdgdmsdrGHAITELFHHNKAALAQYNINDCQLVIDVFK 344 Oceanobacter sp. RED65
ZP_01109042  296 TMTYQFESFSLDNVSEALLGENKLIQETd-----kLAAIKRLYHEDPIALADYNYKDTELVNRIQE 356 Alteromonas macleodii 'Deep e...

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