Conserved Protein Domain Family
DNA_pol_III_epsilon_Ecoli_like

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cd06131: DNA_pol_III_epsilon_Ecoli_like 
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DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins
This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved 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 epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.
Statistics
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PSSM-Id: 99835
View PSSM: cd06131
Aligned: 40 rows
Threshold Bit Score: 233.578
Threshold Setting Gi: 116515093
Created: 3-Mar-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 20 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:2GUI_A; Escherichia coli DNA polymerase III epsilon subunit binds two UMP molecules and two Mn ions; defined at 3.5A contacts.
    View structure with Cn3D
  • Structure:1J53_A; Escherichia coli DNA polymerase III epsilon subunit binds two dTMP molecules and two Mn ions; defined at 3.5A contacts.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1            #### ##                                              ##  ##                 
2GUI_A        11 QIVLDTETTGMNqig-ahyEGHKIIEIGAVEVVNRRl---TGNNFHVYLKPDRlvDPEAFGVHGIADEFLLDKPTFAEVA 86
gi 146329568   5 SVIFDTETTGMNfesdnkaEGHRIIEIGCVELIDRVp---TEHYFHCYLNPEQpvDPQAFKVHGISDEFLADKPFFKDVL 81
gi 88800079    3 QVVLDTETTGLNp-----tKGDRIVEVGCVEMVDRKl---TGRHFHYYINPERdiPDEVVAVHGIDNDKVKDSPKFRDIA 74
gi 31340041    7 KIVLDIETTGMNpag-cfyKNHKIIEIGAVEMINNVf---TGNNFHSYIQPNRliDKQSFKIHGITDNFLLDKPKFHEIS 82
gi 11132278    6 TIILDTETTGINqts-lphINHRIIEIGAVEIIDRCf---TGNNFHVYIQPGRsiESGALKVHGITNKFLLDKPIFKDIA 81
gi 149927491   3 YVVLDTETTGLEv-----rQGHRIIEIGCIEVNGRQv---TDHHFHQYINPERevDEGAFQVHGISDEMLADKPKFKQIA 74
gi 114777499  55 LIMLDTETTGLSp-----lNGDRMVEIGAIEVLNRKvlsgDKHVFHRYINPERniPDEVVRIHGIDNAKVKDQPTFREIA 129
gi 119875887   4 IVALDTETTGISh-----rLGHRVIEIGAVELIDGQl---TGRQFHTYLQPQRkvDWGAQRVHGISDAMLVGKPLFSSKA 75
gi 116515093   8 QVFLDIETTGMNkyg-ciyLNHKIIEIGIIETINRKy---TGRYIHYYLYPQRsiESSAYKIHGISESFLSNKPTFKDIY 83
gi 116334989   4 IIFLDVETTGLFv-----eHGDRIIEIGCVEVINGHl---TGRVFHSYFNPEVkiTQGAFNVHGIKDDFLLLKPMFYEKI 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       ## ###                                            ##             
2GUI_A        87 DEFMDYIRG-AELVIHNAAFDIGFMDYEFsll----krdIPKTNTFCKVTDSLAVARKMFPgKRNSLDALCARYEIDNsK 161
gi 146329568  82 PEFEAYLASaDELVAHNIAFDRQFIDRELqla-----gcDYRLGDKFTLVDSLKIAREKFAgARNNLDALCKRFGVDNtG 156
gi 88800079   75 VELWTWLEG-AELVIHNAAFDMGFLNAEFerfaqeqrepFEKLETVCGVLDTLKVARDKHPgSKVSLDALCKRYGIDNsH 153
gi 31340041   83 VKFLEYITN-SDLIIHNAKFDVGFINYELnmi----nsdKRKISDYCNVVDTLPLARQLFPgKKNSLDALCNRYKINVsH 157
gi 11132278   82 DSFLNYIKN-SILVIHNASFDVGFINQELeil-----nkKIKINTFCSIIDTLKIARELFPgKKNTLDALCTRYKINKsH 155
gi 149927491  75 KDFLDFVQG-STLIIHNASFDIGFLDGELerl-----glGKMADYVDGVIDSLGMAREMFPgKRNNLDALCDRLGVNNaH 148
gi 114777499 130 QEFLDFIEG-ATLVIHNAPFDLGFIMNELri-------nNFPEIGHMQVIDTLVFAREKHPhQRNNLDALCDRYNIERgH 201
gi 119875887  76 AELLDFLRG-SEMVAHNATFDVGFLDNELrla-----giPGTLAQHCRITCSLKLARGRWPgQGNKLDDVLQRLRIPG-N 148
gi 116515093  84 KEIFNFIKN-SEIIVHNSNFDISFLDYEFfll----nigINKIKTFSTITDTLFIARKLFPgKKNNLDALCARYKITNiN 158
gi 116334989  76 NEFIGFINN-STIIAHNAKFDINFINKEIylt----nfkIKKIQNYANILDSLLLFRKLYPrKKNNLNDLCLKFNLIKnK 150
                        170       180
                 ....*....|....*....|.
Feature 1        #  #    #            
2GUI_A       162 RTLHGALLDAQILAEVYLAMT 182
gi 146329568 157 RELHGALLDAQLLAEVYLKLT 177
gi 88800079  154 RTLHGALLDSEILADVYLMLT 174
gi 31340041  158 RDFHSALIDAKLLAKVYTFMT 178
gi 11132278  156 RNLHSAIVDSYLLGKLYLLMT 176
gi 149927491 149 RQLHGALLDSQILAEVYLAMT 169
gi 114777499 202 RELHGALLDSELLAEVYLGMT 222
gi 119875887 149 RGLHGALKDAHLLAQVIPHLR 169
gi 116515093 159 RNFHSALLDAKILMKLYMYMT 179
gi 116334989 151 KRIHGALNDAFLLAVLIIKTG 171

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