1S5J,1Q8I,1QHT,1CLQ


Conserved Protein Domain Family
DEDDy_DNA_polB_exo

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cd05160: DEDDy_DNA_polB_exo 
Click on image for an interactive view with Cn3D
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases
The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. 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 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 that serve as ligands for the two metal ions required for 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. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Statistics
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PSSM-Id: 176646
View PSSM: cd05160
Aligned: 20 rows
Threshold Bit Score: 161.754
Threshold Setting Gi: 68553042
Created: 26-Apr-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.
  • Structure:1CLQ_A; Enterobacteria phage RB69 family-B DNA polymerase exonuclease domain binds two calcium ions and the 3 'end of primer DNA; defined at 3.5A contacts.
    View structure with Cn3D
  • 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             ####                                                                        
1S5J_A        192 RVAIDIEVYtpvkgrip----dsqkaefPIISIALAGs-------------DGLKKVLVLnrndvnegsv---------- 244
1QHT_A        137 MLAFAIATLyhege---------efgtgPILMISYAD--------------GSEARVITWkkidlp-------------- 179
1CLQ_A        110 VANFDIEVTspdgfpe------psqakhPIDAITHYDs------------iDDRFYVFDLlnspygnveewsieiaaklq 171
gi 114320509    3 VLVFDIETVpdvvggrrllgldpslsdqEVAEAMMALrr----------qsAGTDFQRLHlhrivaisiaadld------ 66
gi 544185     543 VMSFSMKTMqnvq-----------nhqhEIIAMAALVhh----------sfALDKAPPEPpfqthfcvvskpkdcifp-- 599
gi 147899700  317 VLSFDIECAgrkgvf-------pepdkdPVIQIANMVl------------rQGEKDPFIRnvftlgtcas---------- 367
gi 68553042   179 RMQLDIETYfkpesgks---skveigkdQVIIVSLSDn-------------RGWEKVIHAh------------------- 223
gi 116241339  271 VLAFDIETTklplkf-------pdaetdQIMMISYMId------------gQGYLITNREivsediedfeftp------- 324
gi 143811385 2307 RTRRDLEPDpe---------------fdPICALFYCIssdtplpdtektelTGVIVIDKDktvfsqdiryqtpl------ 2365
gi 20089769   194 YLAFDIECLpldggm-------pspdvsPIIMISFSFep----------eyKGHKTLILLakpaagm------------- 243
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                     ##  ###                             
1S5J_A        245 ----------kldgisverfNTEYELLGRFFDILLE--YPIVLTFNGdDFDLPYIYFRALKLGyfp------------ee 300
1QHT_A        180 ---------------yvdvvSTEKEMIKRFLRVVREkdPDVLITYNGdNFDFAYLKKRCEELGikftl--------grdg 236
1CLQ_A        172 eqggdevpseiidkiiympfDNEKELLMEYLNFWQQktPVILTGWNVeSFDIPYVYNRIKNIFgestak------rlsph 245
gi 114320509   67 -------rhgfrvwslgdpeDDEAELIRRFFDGVERy-APRLVSWNGgGFDLPVLHYRALLHGita-------------r 125
gi 544185     600 ---cdfkeviskknmkveiaATERTLIGFFLAKVHKidPDILVGHNIcSFELEVLLQRINECKvpyws---------kig 667
gi 147899700  368 -----------ivgsqvlcfEREDALLKAWAEFVRIidPDIITGYNIqNFDMPYLINRAQTLKvst------------fp 424
gi 68553042   224 -------------------gRTEKELLIELIAIIREkdPDVIEGHNIfRFDLPYLHRRCEINGief-------------r 271
gi 116241339  325 -------kpeyegpfcvfnePDEAHLIQRWFEHVQEtkPTIMVTYNGdFFDWPFVEARAAVHGls--------------- 382
gi 143811385 2366 ------lirsgitglevtyaADEKALFHEIANIIKRydPDILLGYEIqMHSWGYLLQRAAALSidlc-----------rm 2428
gi 20089769   244 -------------dgdvlscMDETEMLNKFFEIICEydPDIVAGYNHqDFDIPYITERVKALVakgetinsvvgrdgspi 310
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                      ##                 
1S5J_A        301 iPIDVAg-------------------kDEAKYLAGLHIDLYKFFfnkavrnyafegkyneyNLDAVAKALLgt--sKVKV 359
1QHT_A        237 sEPKIQrmg----------------drFAVEVKGRIHFDLYPVIrrtin--------lptyTLEAVYEAVFgk--pKEKV 290
1CLQ_A        246 rKTRVKvienm------------ygsrEIITLFGISVLDYIDLYkkfsft------nqpsySLDYISEFELnv--gKLKY 305
gi 114320509  126 rYWDSGqedrdf---------rfnnylNRFHDRHTDLMDVLAGYqar-----------anaPLDEIATLLGyp--gKMGM 183
gi 544185     668 rLRRSNmpklgs----------rsgfgERNATCGRMICDVEISAkelih--------cksyHLSELVQQILk---tERIV 726
gi 147899700  425 fLGRIRslksvirdssfqskqmgrrenKVINTEGRVQFDLLQVLlrdyk--------lrsyTLNAVSFHFLqe--qKEDV 494
gi 68553042   272 iGRDQSiprnypasi---rfaersidyTFYDIAGRHVIDTWFLVqsfdvsk----rampgyGLKAAAKFFGvarenRVYV 344
gi 116241339  383 mQQEIGfqk---------------dsqGEYKAPQCIHMDCLRWVkrdsyl------pvgshNLKAAAKAKLgy--dPVEL 439
gi 143811385 2429 iSRVPDdkienrfaae--rdeygsytmSEINIVGRITLNLWRIMrneva--------ltnyTFENVSFHVLhq--rFPLF 2496
gi 20089769   311 gYRKFGl-------------------iTRTEMKGRVVVDALPLVrrafs--------lkqyTLRAVSKELLsr--eKLDV 361
                         250       260       270
                  ....*....|....*....|....*....|....*.
Feature 1                               #   #         
1S5J_A        360 DTlis--------fldVEKLIEYNFRDAEITLQLTT 387
1QHT_A        291 YAeeiaqa--wesgegLERVARYSMEDAKVTYELGR 324
1CLQ_A        306 DGpiskl-----resnHQRYISYNIIDVYRVLQIDA 336
gi 114320509  184 SGgkvwea---vqageLGAVRDYCETDVLNTYLVWL 216
gi 544185     727 IPtenirnm-ysessyLLYLLEHIWKDARFILQIMC 761
gi 147899700  495 QHsiitdlq-ngneqtRRRLAVYCLKDAYLPLRLLE 529
gi 68553042   345 DYadmad----lwennPEKLLEYALDDVRETREIAS 376
gi 116241339  440 DPedmcr----mateqPQTLATYSVSDAVATYYLYM 471
gi 143811385 2497 TFrvlsdwfdnktdlyRWKMVDHYVSRVRGNLQMLE 2532
gi 20089769   362 PPlemeehw-ndsgdkFRKFVDYARRDSELALELVL 396

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