Conserved Protein Domain Family
DNA_polB_II_exo

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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
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PSSM-Id: 99827
View PSSM: cd05784
Aligned: 25 rows
Threshold Bit Score: 252.488
Threshold Setting Gi: 162453773
Created: 1-Oct-2007
Updated: 17-Jan-2013
Structure
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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
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                ####                                                                    
1Q8I_A       148 PPLKWVSIDIETTRHg-----ELYCIGLEG----------CGQRIVYMLGPENgdas------sldfELEYVASRPQLLE 206
gi 119475072 152 PALKTISLDIETAMDn----iTLYSIGLYGre------kgEDYRLVLMVSDHWia-----------dDVEFFADEKSLLL 210
gi 118053049 152 PALKVVSLDIETSQHq-----DLYSIALDG----------MAERMVFMLGQPSsepep-----ttgfALVYCSSRQEMIK 211
gi 83644404  172 PYFKVLSLDIETSMDg----aQLYSIGLAAtsygadvgagAMQHRVFMVGENAeds---------pdYLVYCADESEVFR 238
gi 88798884  142 PELRVLSLDIETDWYipgqlpALYSIALAF----------DDQQQVLVVNDGAdfit------ddgvDVRLFSTVRDCLA 205
gi 152996232 147 PDWNVWSLDIETSVSt----nTLLSIGITS----------RDQRVAFVVTDQEts----------spIIRRFSDEKSLLL 202
gi 87119943  149 PSWHVWSLDIETSVSr----nTILSIAVVS----------EALEMCFMVSKKPln----------dvRVTCFDDEKSLLL 204
gi 89094696  151 PQFRILSIDLETTMRa----dQILSAAFYA----------DDFQLVLMQGQGIdt-----------dTLDYCADETTLIH 205
gi 94500920  141 PNFSYISFDIETTMPtrkvseKLLSIAFVYed------ssERKEMVYMLGDPSss----------tqQLIFFKNIRSLLI 204
gi 88793327  158 TRFSSLSIDIECDEHe-----MLFSIALAG----------EGVNLVLLVCPPTfekrgveqrndkpyQLLVLNSEKELLH 222
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                        ##  ###                                                         
1Q8I_A       207 KLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNS----ELEWREhgfknGVFFAQAKGRLIIDGIEALK 282
gi 119475072 211 RFFDWLSDYDPDIIIGWNIVNFDMWFLERVCQKHHIPFRLGRGRRgreaAPHWRLldddgDRRAMSVPGRVVLDGIELLK 290
gi 118053049 212 QLNDWFARNDPDVIVGWNVIQFDLRVLQKTADDCGIPLLPGRERT----PIAWRThpgkqGYLFAPMPGRAVIDGIEALR 287
gi 83644404  239 RFVEWFDGFDPDILIGWNVINFDLRFLQKKADELNFPFHPGRGGA----AMDWRQsrsddQHFTLCIPGRVVLDGIDTLK 314
gi 88798884  206 EAIARIQAYDPDCIVGWNVIDFDLRILQEHCDQVGLAFEVGRQRA----VPLWREmggqpGRYALELEGRQVVDGPGAFR 281
gi 152996232 203 AFIRYVKKYSPDIFIGWNLIGFDLQFIDQRCQILGIRPAFGVNGE----NWNIRSsd-nqGKYFASIPGRVALDGITLLK 277
gi 87119943  205 AFMKFTKQASPDIIIGWNVIGFDLNFIDQRCQAFGLKPAFGINGA----SWNVRGrd-gsAKRFISIPGRAVLDGIDLLK 279
gi 89094696  206 KFIQVVQQYDPDIFIGWNVINFDFKVLKNRADQLNIPLLLGRDQQ----PLQLYQsg--qGKVFARMAGRVVLDGIDTLK 279
gi 94500920  205 ASNQLISEWDPDLLLGWNVVNFDVSVLHRLYREHGLEMLWGRQQS----SLNIRQgq--nGFNFVDIPGRCILDGIDSLK 278
gi 88793327  223 AFFHHVTSYDPDIILGWNVKQFDMAVLARRAKANRLKFTLGRHER----EASVRQw---eDQTLVDVPGRCVIDGIEALK 295
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
Feature 1                 ##                                         #   #         
1Q8I_A       283 SAFWNFSSFSLETVAQELLGEGKSIDNPwd----rMDEIDRRFAEDKPALATYNLKDCELVTQIFH 344
gi 119475072 291 AAFYQFESFSLNTVATELLGDGKLIHGSg-----rGETITDLFTSDKLALAEYNIQDCRLVLDIFD 351
gi 118053049 288 AAVWSFSSFSLENVSQELLGEGKEIGDEyd----kMAEIERRYQQDKPALASYNLRDCELVLRIFE 349
gi 83644404  315 SATYNFESFSLEYVAQHLLGRGKLIHDPdn----rGDEITHLFLHDKPRLAAYNLEDCQLVWEIFQ 376
gi 88798884  282 SAAWAFEDYSLETVSRSLLNRGKRIEHSdd----rVGEIERLYREDLQAFAHYNAEDAQLVLDLFD 343
gi 152996232 278 VGGYHFESYSLNNVSNEILDDGKLLHGSe-----rWQEIERLHKEDLDAFVAYNLQDCDLVMRIFE 338
gi 87119943  280 VAGYHFESYSLENVSREILADGKLLHGSq-----rWQEIERLYEQEPLAFVEYNLQDCWLVWRIFK 340
gi 89094696  280 GATYQFESFSLENVSREFLDRGKLIDHVdd----rGGEIQRLFREDKASLARYNLEDCKLVWDIFE 341
gi 94500920  279 NASYHFESFALDFVAHQLLDKGKIIEGFdgdmsdrGHAITELFHHNKAALAQYNINDCQLVIDVFK 344
gi 88793327  296 TMTYQFESFSLDNVSEALLGENKLIQETd-----kLAAIKRLYHEDPIALADYNYKDTELVNRIQE 356

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