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: 17-Jan-2013
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:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                   ####  #                                                               
2KFZ_A         22 KLEKAPVFAFDTETDSLDn-----------iSANLVGLSFAIe-----------PGVAAYIPVahdylda---------- 69
gi 116059733  192 TAKRPLYHACDTEVAYIDvsdq-----tpvgHGQVTCFSVFCgpdvnfapegesKRSLLWVDTlr--------------- 251
gi 145510849   68 NKYKKQPHAWDTETIDIDvkse-----tpinRGRLICASAFAgpev-----nfgNGPRLFIDNfa--------------- 122
gi 42565057   262 NQYRNLVHACDTEVSRIDvkte-----tpvdHGEMICFSIYCgsea----dfgdGKSCIWVDVlge-------------- 318
gi 168060384   33 SEYKNVVHACDTEVAGIDvkke-----spvgHGQITCFSIYCgpga----dfgyGKNRLWVDVld--------------- 88
gi 167630919   15 YLDKAGLIAFDFETAPREkyrrdekaaldahKADIAGVSFSVs-----------EGTAVYVPLkhkt------------- 70
gi 167462371  124 FLGVKSMTAGDFEGTGVDs-----------yIDLSIGFSIWLp----------lLGEGYYLPYghvdmrgvegfeflndt 182
gi 147678493  132 DLRHEPAFAFDTETTGVDv-----------yQDVIVGVSLTLp----------rAGYHVYIPVahnnag----------- 179
gi 66828405   649 MKQKDRFHACDTEVIDIDlkkf-----spigHGKMICFSIYCgpqv----kfhdGNSRVWVDVmdd-------------- 705
gi 75759443   123 YLNTFKVLAVDTETTGLDitfks----rtgeHDECVGLIITGk-----------EGESFYFPFkhtqfdn---------- 177
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                              ##   ###                                   
2KFZ_A         70 ------pdqisrERALELLKPLLEDek-----alKVGQNL--KYDRGILANYGIe-lRGIAFDTMLESYILNSva----- 130
gi 116059733  252 ----------ggEGVWEVFKEYFENpn-----vkKVWHNY--SFDRHVVENHHGiklAGFAADTMHMARLWNSnrgldgg 314
gi 145510849  123 ----------qnSDLIMLFKEYFEDek-----ilKIWHNY--GFDKHIFGNNGIn-vRGFFGDTMHMARLLDPskqpqey 184
gi 42565057   319 ----------ngRDILAEFKPFFEDss-----ikKVWHNY--SFDNHIIRNYGIk-lSGFHGDTMHMARLWDSsrrisgg 380
gi 168060384   89 ----------ggDDVLRVFKRYFEDps-----iqKVWHNY--SFDKHILSRHGIh-pQGFYADTMHLARLNDSarrgskg 150
gi 167630919   71 ---------gknAGSPDKIMQWLSEnvfanrkvvKIAHNL--SFEAMFLYALGVv-lQPPCYDTIAAALMTLKsntaf-- 136
gi 167462371  183 faykdsgpqltrSKVLDAIRPYLAQpt-----hgKTFHMGsaRYDLHVARNDGYe-iRGCVWDTLDAMHLLNEheek--- 253
gi 147678493  180 -------pqlrrSYVLNGLKRYLTDpt-----vgKVLHNA--KFDIHMLLRHGMr-mRGLAHDTMIAMKILNEneps--- 241
gi 66828405   706 ---------iegDEILQVFKEYFEDes-----ilKVWHNY--AFDRHIFYNHGIn-vKGFGGDTLHMARLWNAsrm---- 764
gi 75759443   178 -----lcggddwYFMETYMKPLLEKk-------dIIVHNA--SFDWKVIYIYGIv-lNVVIDTFAVFSLTLNAkyq---- 238
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                         ##                           ##                 
2KFZ_A        131 -----------------------------grHDMDSLAERWLKhk-------------tITFEEIAGk------------ 156
gi 116059733  315 yslealsssaevmsdcaemlgagaemmrakrGMKKIFGKPKLKkd-------------gTPGKTIILpp----------- 370
gi 145510849  185 slakls------------layeeeiklvktkRMECLLAKPNLTdeersslqlfgehlldINLKTSMKqifgqnkelk--n 250
gi 42565057   381 ysleal-------------tsdpkvlggtetKEEAELFGKISMkkifgk----gklkkdGSEGKLVIip----------- 432
gi 168060384  151 gy---------------------alevlsadRKVMDYCSKNFTeedgs------vfvgkKSMKELFGkaklkkdgt---- 199
gi 167630919  137 --------------------------rtladSGLKTLTQELFGvd-------------lPSFETVTAg------------ 165
gi 167462371  254 ----------------------------yglKKIVEKYGKYFDipg-----------piYTFEDMFGn------------ 282
gi 147678493  242 ----------------------------valKNLATRYGKFFGfdg-----------esHTFEDLFGk------------ 270
gi 66828405   765 ----------------------------nsgGYSLEALSKELLnk------------pkVPIKDLFGtrkikadgeegks 804
gi 75759443   239 -----------------------------tpVGLKHLISLLLKrd-------------sLELDDLCKngdf--------- 267
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                    #   #                                                
2KFZ_A        157 --------gKNQLTFNQIal--eeAGRYAAEDADVTLQLHLKMWPdlqk----------------------hkgpLNVFE 204
gi 116059733  371 -------veEIQEDVEQRd----kWIEYSALDAQATWFLRESLEAklrgmsceacpil-----askpgyrkcvtlWDFYT 434
gi 145510849  251 gqvsklkvyPKILQMHCLpqyinqWVEYSTLDSEITYFLCLTLKDllnktkifynlkptdsdyqtkqnefginslGDIYS 330
gi 42565057   433 --------pVKELQMEDRe----aWISYSALDSISTLKLYESMKKqlqakkwfld-----------gkliskknmFDFYQ 489
gi 168060384  200 pgkikvvppVDELQRDEElr--daWIHYSTLDAVCTWRLFVSLQHklsntpwsv------------aelrhkgsmYDFYE 265
gi 167630919  166 ---------RYFDELDPQde---eTVRYACADSDYTLRLYHLFNNwfnry---------------------lpkhRFIVE 212
gi 167462371  283 ---------RSPAPFSVEl-----VGIYAIKDVLYGWKLFEWQVEmmrks---------------------pgclLDCYA 327
gi 147678493  271 ---------ACFADVPLDm-----ALIYAAKDTHLTWELYKWQMEhltk----------------------redlLKLYR 314
gi 66828405   805 ivippleriQRDSKFILN------WIEYSSLDSELTWLLRENIHIklrdmew-----------------nqgttmWDFYY 861
gi 75759443   268 -----gsidQNFADLPKEl-----VRLYACADADNTLALYHYMLEtnml----------------------enwgATKVV 315
                         330
                  ....*....|..
Feature 1                     
2KFZ_A        205 NIEMPLVPVLSR 216
gi 116059733  435 FYLAEFGNLLTQ 446
gi 145510849  331 KYWNSLGEILTE 342
gi 42565057   490 EYWQPFGELLAK 501
gi 168060384  266 KYWRPFGEVLVQ 277
gi 167630919  213 KLESPAAVYCGL 224
gi 167462371  328 KIDSKLPEVDVF 339
gi 147678493  315 ELENPLVDICVE 326
gi 66828405   862 LMWRPFGHLLTE 873
gi 75759443   316 QFESIFACAIGY 327

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