2KFZ,1KFS,1KLN


Conserved Protein Domain Family
DNA_polA_I_Ecoli_like_exo

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cd06139: DNA_polA_I_Ecoli_like_exo 
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DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases
Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved 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 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Statistics
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PSSM-Id: 176651
View PSSM: cd06139
Aligned: 121 rows
Threshold Bit Score: 130.333
Threshold Setting Gi: 145510849
Created: 17-Mar-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 16 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:2KFZ_A; Escherichia coli Klenow Fragment exonuclease domain binds two zinc metal ions and ssDNA; defined at 3.5A contacts.
    View structure with Cn3D
  • Citation:PMID 9888810
  • Structure:1KFS_A; Escherichia coli Klenow Fragment exonuclease domain binds Mg and Zn ions and ssDNA; defined at 3.5A contacts.
    View structure with Cn3D
  • Citation:PMID 1989886

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                   ####  #                                                               
2KFZ_A         22 KLEKAPVFAFDTETDSLDn-----------iSANLVGLSFAIe-----------PGVAAYIPVahdylda---------- 69   Escherichia coli
CAL55440      192 TAKRPLYHACDTEVAYIDvsdq-----tpvgHGQVTCFSVFCgpdvnfapegesKRSLLWVDTlr--------------- 251  Ostreococcus ...
XP_001441352   68 NKYKKQPHAWDTETIDIDvkse-----tpinRGRLICASAFAgpev-----nfgNGPRLFIDNfa--------------- 122  Paramecium te...
NP_188690     262 NQYRNLVHACDTEVSRIDvkte-----tpvdHGEMICFSIYCgsea----dfgdGKSCIWVDVlge-------------- 318  thale cress
XP_001782176   33 SEYKNVVHACDTEVAGIDvkke-----spvgHGQITCFSIYCgpga----dfgyGKNRLWVDVld--------------- 88   Physcomitrell...
YP_001681418   15 YLDKAGLIAFDFETAPREkyrrdekaaldahKADIAGVSFSVs-----------EGTAVYVPLkhkt------------- 70   Heliobacteriu...
ZP_02327460   124 FLGVKSMTAGDFEGTGVDs-----------yIDLSIGFSIWLp----------lLGEGYYLPYghvdmrgvegfeflndt 182  Paenibacillus...
YP_001212708  132 DLRHEPAFAFDTETTGVDv-----------yQDVIVGVSLTLp----------rAGYHVYIPVahnnag----------- 179  Pelotomaculum...
XP_647557     649 MKQKDRFHACDTEVIDIDlkkf-----spigHGKMICFSIYCgpqv----kfhdGNSRVWVDVmdd-------------- 705  Dictyostelium...
ZP_00739536   123 YLNTFKVLAVDTETTGLDitfks----rtgeHDECVGLIITGk-----------EGESFYFPFkhtqfdn---------- 177  Bacillus thur...
Feature 1                                              ##   ###                                   
2KFZ_A         70 ------pdqisrERALELLKPLLEDek-----alKVGQNL--KYDRGILANYGIe-lRGIAFDTMLESYILNSva----- 130  Escherichia coli
CAL55440      252 ----------ggEGVWEVFKEYFENpn-----vkKVWHNY--SFDRHVVENHHGiklAGFAADTMHMARLWNSnrgldgg 314  Ostreococcus ...
XP_001441352  123 ----------qnSDLIMLFKEYFEDek-----ilKIWHNY--GFDKHIFGNNGIn-vRGFFGDTMHMARLLDPskqpqey 184  Paramecium te...
NP_188690     319 ----------ngRDILAEFKPFFEDss-----ikKVWHNY--SFDNHIIRNYGIk-lSGFHGDTMHMARLWDSsrrisgg 380  thale cress
XP_001782176   89 ----------ggDDVLRVFKRYFEDps-----iqKVWHNY--SFDKHILSRHGIh-pQGFYADTMHLARLNDSarrgskg 150  Physcomitrell...
YP_001681418   71 ---------gknAGSPDKIMQWLSEnvfanrkvvKIAHNL--SFEAMFLYALGVv-lQPPCYDTIAAALMTLKsntaf-- 136  Heliobacteriu...
ZP_02327460   183 faykdsgpqltrSKVLDAIRPYLAQpt-----hgKTFHMGsaRYDLHVARNDGYe-iRGCVWDTLDAMHLLNEheek--- 253  Paenibacillus...
YP_001212708  180 -------pqlrrSYVLNGLKRYLTDpt-----vgKVLHNA--KFDIHMLLRHGMr-mRGLAHDTMIAMKILNEneps--- 241  Pelotomaculum...
XP_647557     706 ---------iegDEILQVFKEYFEDes-----ilKVWHNY--AFDRHIFYNHGIn-vKGFGGDTLHMARLWNAsrm---- 764  Dictyostelium...
ZP_00739536   178 -----lcggddwYFMETYMKPLLEKk-------dIIVHNA--SFDWKVIYIYGIv-lNVVIDTFAVFSLTLNAkyq---- 238  Bacillus thur...
Feature 1                                         ##                           ##                 
2KFZ_A        131 -----------------------------grHDMDSLAERWLKhk-------------tITFEEIAGk------------ 156  Escherichia coli
CAL55440      315 yslealsssaevmsdcaemlgagaemmrakrGMKKIFGKPKLKkd-------------gTPGKTIILpp----------- 370  Ostreococcus ...
XP_001441352  185 slakls------------layeeeiklvktkRMECLLAKPNLTdeersslqlfgehlldINLKTSMKqifgqnkelk--n 250  Paramecium te...
NP_188690     381 ysleal-------------tsdpkvlggtetKEEAELFGKISMkkifgk----gklkkdGSEGKLVIip----------- 432  thale cress
XP_001782176  151 gy---------------------alevlsadRKVMDYCSKNFTeedgs------vfvgkKSMKELFGkaklkkdgt---- 199  Physcomitrell...
YP_001681418  137 --------------------------rtladSGLKTLTQELFGvd-------------lPSFETVTAg------------ 165  Heliobacteriu...
ZP_02327460   254 ----------------------------yglKKIVEKYGKYFDipg-----------piYTFEDMFGn------------ 282  Paenibacillus...
YP_001212708  242 ----------------------------valKNLATRYGKFFGfdg-----------esHTFEDLFGk------------ 270  Pelotomaculum...
XP_647557     765 ----------------------------nsgGYSLEALSKELLnk------------pkVPIKDLFGtrkikadgeegks 804  Dictyostelium...
ZP_00739536   239 -----------------------------tpVGLKHLISLLLKrd-------------sLELDDLCKngdf--------- 267  Bacillus thur...
Feature 1                                    #   #                                                
2KFZ_A        157 --------gKNQLTFNQIal--eeAGRYAAEDADVTLQLHLKMWPdlqk----------------------hkgpLNVFE 204  Escherichia coli
CAL55440      371 -------veEIQEDVEQRd----kWIEYSALDAQATWFLRESLEAklrgmsceacpil-----askpgyrkcvtlWDFYT 434  Ostreococcus ...
XP_001441352  251 gqvsklkvyPKILQMHCLpqyinqWVEYSTLDSEITYFLCLTLKDllnktkifynlkptdsdyqtkqnefginslGDIYS 330  Paramecium te...
NP_188690     433 --------pVKELQMEDRe----aWISYSALDSISTLKLYESMKKqlqakkwfld-----------gkliskknmFDFYQ 489  thale cress
XP_001782176  200 pgkikvvppVDELQRDEElr--daWIHYSTLDAVCTWRLFVSLQHklsntpwsv------------aelrhkgsmYDFYE 265  Physcomitrell...
YP_001681418  166 ---------RYFDELDPQde---eTVRYACADSDYTLRLYHLFNNwfnry---------------------lpkhRFIVE 212  Heliobacteriu...
ZP_02327460   283 ---------RSPAPFSVEl-----VGIYAIKDVLYGWKLFEWQVEmmrks---------------------pgclLDCYA 327  Paenibacillus...
YP_001212708  271 ---------ACFADVPLDm-----ALIYAAKDTHLTWELYKWQMEhltk----------------------redlLKLYR 314  Pelotomaculum...
XP_647557     805 ivippleriQRDSKFILN------WIEYSSLDSELTWLLRENIHIklrdmew-----------------nqgttmWDFYY 861  Dictyostelium...
ZP_00739536   268 -----gsidQNFADLPKEl-----VRLYACADADNTLALYHYMLEtnml----------------------enwgATKVV 315  Bacillus thur...
Feature 1                     
2KFZ_A        205 NIEMPLVPVLSR 216  Escherichia coli
CAL55440      435 FYLAEFGNLLTQ 446  Ostreococcus tauri
XP_001441352  331 KYWNSLGEILTE 342  Paramecium tetraurelia strain d4-2
NP_188690     490 EYWQPFGELLAK 501  thale cress
XP_001782176  266 KYWRPFGEVLVQ 277  Physcomitrella patens subsp. patens
YP_001681418  213 KLESPAAVYCGL 224  Heliobacterium modesticaldum Ice1
ZP_02327460   328 KIDSKLPEVDVF 339  Paenibacillus larvae subsp. larvae BRL-230010
YP_001212708  315 ELENPLVDICVE 326  Pelotomaculum thermopropionicum SI
XP_647557     862 LMWRPFGHLLTE 873  Dictyostelium discoideum AX4
ZP_00739536   316 QFESIFACAIGY 327  Bacillus thuringiensis serovar israelensis ATCC 35646

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