1K82,1KFV,1R2Y,1PJI,1EE8


Conserved Protein Domain Family
EcFpg-like_N

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cd08966: EcFpg-like_N 
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N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases
This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. Escherichia coli Fpg mainly recognizes and excises damaged purines such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It is bifunctional, having both a DNA glycosylase (recognition activity) and a AP lyase activity. In addition to this EcFpg-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif, which also contribute residues to the active site.
Statistics
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PSSM-Id: 176800
View PSSM: cd08966
Aligned: 196 rows
Threshold Bit Score: 92.1744
Threshold Setting Gi: 87312113
Author:
Barrantes-Reynolds
Author Information
Name: Ramiro Barrantes-Reynolds
Address: Department of Microbiology and Molecular Genetics
University of Vermont
89 Beaumont Avenue
Burlington, VT 05405
USA
Created: 4-Jul-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site include 1 residue -Click on image for an interactive view with Cn3D
Feature 1:catalytic residue [active site]
Evidence:
  • Comment:catalytic proline
  • Comment: Site-directed mutagenesis of this residue resulted in a protein that could make the Schiff-base intermediate but was defective in catalysis.
  • Citation:PMID 9654091
  • Comment:1KFV_A , is a structure of a mutant Lactococcus Lactis Fpg which has a Gly in place of a Pro at this position.
  • Comment:This residue is almost perfectly conserved in FpgNei DNA glycolsylases. It acts as a nucleophile in catalysis.
  • Citation:PMID 9030608

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        #                                                                               
1K82_A         1 PELPEVETSRRGIEPh----LVGATILHAVVRNGrlrw---pvseEIYRLSDQPVLSVQRRAKYLLLELPe-GWIIIHLG 72  Escherichia coli
1R2Y_A         2 PQLPEVETIRRTLLPl----IVGKTIEDVRIFWPniirhprdseaFAARMIGQTVRGLERRGKFLKFLLDr-DALISHLR 76  Geobacillus ste...
YP_278569      2 PEYPEVTVVCQSLSKl----LLGKKINNCELLSEkfakn-ssvkdFEEFFNNKTFKKINNTGKFIEFIFDdkSRAIVHLR 76  Mycoplasma syno...
NP_072929      2 PELPEVTTVINELKEt----VLNKPLDQVQVNLRkvlkn-idpqlLNKQLKNQFFTDIKRKGKYIIFLLSngLYLVSHLR 76  Mycoplasma geni...
YP_003330610   2 PELPEVETVKNEIMPh----LLGKKITRIEALWAktlcp--peteFNKLVSGLQVTELSRRGKYIIISLSggLFISVHLK 75  Dehalococcoides...
NP_078249      2 PELPEVQTIVDYLNHhvldiFIKKTIVHLPKILKnkt-----pqeFEKLLINHKIVKIKRLGKYLLFFLSnnLVLSVHLR 76  Ureaplasma parv...
ZP_06610685    2 PEYPEVTVVSNSLNEl----VKFKKITKVEVNLEkiikn-tdvknFINSLENRVIFSIENIGKYIIFSFDndLKMISHLR 76  Mycoplasma alli...
NP_950926      2 PELPEVQIIVDFLKKk----LIGKKIVATKVFYEtvvk----ntkEFQKIEQTTILDIQRKGKFLLFFLTqeLVLIGHLR 73  Onion yellows p...
YP_002004111   2 PELPEVEVVVRSLKKn----LIDKKIINIKVLYEpivg----kldIFKKILNQKILNLTRKGKYLIFFFSneLVLVGHLR 73  Candidatus Phyt...
ADC31531       2 PELPEVQTVINYLKTk----IINQKINNVIVSALkvlkn-atpkeFKKFLVNEHFVDIKRIGKYIIFILSnnKVLVSHLR 76  Mycoplasma gall...
Feature 1                                                        
1K82_A        73 MSGSLRILpee---lppEKHDHVDLVMSNgKVLRYTDPRRFGAWLWTK 117 Escherichia coli
1R2Y_A        77 MEGRYAVAsal---eplEPHTHVVFCFTDgSELRYRDVRKFGTMHVYA 121 Geobacillus stearothermophilus
YP_278569     77 MEGKFFIRktsdlekyrFKHDHIYFHLGNdETLAYNDSRGFGSFETIS 124 Mycoplasma synoviae 53
NP_072929     77 MEGKYFFEergs--kfnQKHVLVEFHFDDgSQLNYHDTRQFGTFHLYE 122 Mycoplasma genitalium G37
YP_003330610  76 MSGGLTAVkaen--gqpPRFTRAVFHLENgEQVYFTDIRKFGRINLLT 121 Dehalococcoides sp. VS
NP_078249     77 MEGKFYYQakee--wfnLAHTHIIIEFNNgMQLRYNDTRQFGTFHIYE 122 Ureaplasma parvum serovar 3 str. ATCC 700970
ZP_06610685   77 MEGKFFYEnfls--drnKKHDLVIFTFEDnSKLIYNDTRRFGTMDLVQ 122 Mycoplasma alligatoris A21JP2
NP_950926     74 MEGKLFIKpcd---epkHKYEHFAIILEDkSSLRYYDFRKFGRFEVKN 118 Onion yellows phytoplasma OY-M
YP_002004111  74 MEGKLYFKpsd---eiiVKHEHFVLFLENnISLRFKDTRKFGRFIVYE 118 Candidatus Phytoplasma mali
ADC31531      77 MEGKYKISqfka--kydERHVLVRFILDD-FELHYHDTRRFGTFHIHS 121 Mycoplasma gallisepticum str. F

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