2GUI,1J53,2IDO


Conserved Protein Domain Family
DNA_pol_III_epsilon_Ecoli_like

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cd06131: DNA_pol_III_epsilon_Ecoli_like 
Click on image for an interactive view with Cn3D
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: 2-Oct-2020
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:
Feature 1            #### ##                                              ##  ##                 
2GUI_A        11 QIVLDTETTGMNqig-ahyEGHKIIEIGAVEVVNRRl---TGNNFHVYLKPDRlvDPEAFGVHGIADEFLLDKPTFAEVA 86  Escherichia coli
YP_001209798   5 SVIFDTETTGMNfesdnkaEGHRIIEIGCVELIDRVp---TEHYFHCYLNPEQpvDPQAFKVHGISDEFLADKPFFKDVL 81  Dichelobacter n...
ZP_01115649    3 QVVLDTETTGLNp-----tKGDRIVEVGCVEMVDRKl---TGRHFHYYINPERdiPDEVVAVHGIDNDKVKDSPKFRDIA 74  Reinekea sp. ME...
Q89AN3         7 KIVLDIETTGMNpag-cfyKNHKIIEIGAVEMINNVf---TGNNFHSYIQPNRliDKQSFKIHGITDNFLLDKPKFHEIS 82  Buchnera aphidi...
P57337         6 TIILDTETTGINqts-lphINHRIIEIGAVEIIDRCf---TGNNFHVYIQPGRsiESGALKVHGITNKFLLDKPIFKDIA 81  Buchnera aphidi...
ZP_01915745    3 YVVLDTETTGLEv-----rQGHRIIEIGCIEVNGRQv---TDHHFHQYINPERevDEGAFQVHGISDEMLADKPKFKQIA 74  Limnobacter sp....
ZP_01452496   55 LIMLDTETTGLSp-----lNGDRMVEIGAIEVLNRKvlsgDKHVFHRYINPERniPDEVVRIHGIDNAKVKDQPTFREIA 129 Mariprofundus f...
ZP_01642946    4 IVALDTETTGISh-----rLGHRVIEIGAVELIDGQl---TGRQFHTYLQPQRkvDWGAQRVHGISDAMLVGKPLFSSKA 75  Stenotrophomona...
YP_802722      8 QVFLDIETTGMNkyg-ciyLNHKIIEIGIIETINRKy---TGRYIHYYLYPQRsiESSAYKIHGISESFLSNKPTFKDIY 83  Buchnera aphidi...
YP_802484      4 IIFLDVETTGLFv-----eHGDRIIEIGCVEVINGHl---TGRVFHSYFNPEVkiTQGAFNVHGIKDDFLLLKPMFYEKI 75  Candidatus Cars...
Feature 1                       ## ###                                            ##             
2GUI_A        87 DEFMDYIRG-AELVIHNAAFDIGFMDYEFsll----krdIPKTNTFCKVTDSLAVARKMFPgKRNSLDALCARYEIDNsK 161 Escherichia coli
YP_001209798  82 PEFEAYLASaDELVAHNIAFDRQFIDRELqla-----gcDYRLGDKFTLVDSLKIAREKFAgARNNLDALCKRFGVDNtG 156 Dichelobacter n...
ZP_01115649   75 VELWTWLEG-AELVIHNAAFDMGFLNAEFerfaqeqrepFEKLETVCGVLDTLKVARDKHPgSKVSLDALCKRYGIDNsH 153 Reinekea sp. ME...
Q89AN3        83 VKFLEYITN-SDLIIHNAKFDVGFINYELnmi----nsdKRKISDYCNVVDTLPLARQLFPgKKNSLDALCNRYKINVsH 157 Buchnera aphidi...
P57337        82 DSFLNYIKN-SILVIHNASFDVGFINQELeil-----nkKIKINTFCSIIDTLKIARELFPgKKNTLDALCTRYKINKsH 155 Buchnera aphidi...
ZP_01915745   75 KDFLDFVQG-STLIIHNASFDIGFLDGELerl-----glGKMADYVDGVIDSLGMAREMFPgKRNNLDALCDRLGVNNaH 148 Limnobacter sp....
ZP_01452496  130 QEFLDFIEG-ATLVIHNAPFDLGFIMNELri-------nNFPEIGHMQVIDTLVFAREKHPhQRNNLDALCDRYNIERgH 201 Mariprofundus f...
ZP_01642946   76 AELLDFLRG-SEMVAHNATFDVGFLDNELrla-----giPGTLAQHCRITCSLKLARGRWPgQGNKLDDVLQRLRIPG-N 148 Stenotrophomona...
YP_802722     84 KEIFNFIKN-SEIIVHNSNFDISFLDYEFfll----nigINKIKTFSTITDTLFIARKLFPgKKNNLDALCARYKITNiN 158 Buchnera aphidi...
YP_802484     76 NEFIGFINN-STIIAHNAKFDINFINKEIylt----nfkIKKIQNYANILDSLLLFRKLYPrKKNNLNDLCLKFNLIKnK 150 Candidatus Cars...
Feature 1        #  #    #            
2GUI_A       162 RTLHGALLDAQILAEVYLAMT 182 Escherichia coli
YP_001209798 157 RELHGALLDAQLLAEVYLKLT 177 Dichelobacter nodosus VCS1703A
ZP_01115649  154 RTLHGALLDSEILADVYLMLT 174 Reinekea sp. MED297
Q89AN3       158 RDFHSALIDAKLLAKVYTFMT 178 Buchnera aphidicola (Baizongia pistaciae)
P57337       156 RNLHSAIVDSYLLGKLYLLMT 176 Buchnera aphidicola (Acyrthosiphon pisum)
ZP_01915745  149 RQLHGALLDSQILAEVYLAMT 169 Limnobacter sp. MED105
ZP_01452496  202 RELHGALLDSELLAEVYLGMT 222 Mariprofundus ferrooxydans PV-1
ZP_01642946  149 RGLHGALKDAHLLAQVIPHLR 169 Stenotrophomonas maltophilia R551-3
YP_802722    159 RNFHSALLDAKILMKLYMYMT 179 Buchnera aphidicola str. Cc (Cinara cedri)
YP_802484    151 KRIHGALNDAFLLAVLIIKTG 171 Candidatus Carsonella ruddii PV

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