Conserved Protein Domain Family

cd08773: FpgNei_N 
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N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes 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 glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In addition to this FpgNei_N domain, FpgNei proteins have a helix-two-turn-helix (H2TH) domain and a zinc (or zincless)-finger motif which also contribute residues to the active site. FpgNei DNA glycosylases have a broad substrate specificity. They are bifunctional, in addition to the glycosylase (recognition) activity, they have a lyase (cleaving) activity on the phosphodiester backbone of the DNA at the AP site. This superfamily includes eukaryotic, bacterial, and viral proteins.
PSSM-Id: 176798
View PSSM: cd08773
Aligned: 27 rows
Threshold Bit Score: 69.3139
Threshold Setting Gi: 157822593
Author Information
Name: Ramiro Barrantes-Reynolds
Address: Department of Microbiology and Molecular Genetics
University of Vermont
89 Beaumont Avenue
Burlington, VT 05405
Created: 18-Nov-2009
Updated: 2-Oct-2020
Aligned Rows:
Conserved site include 1 residue -Click on image for an interactive view with Cn3D
Feature 1:catalytic residue [active site]
  • Comment:This catalytic proline is almost perfectly conserved in FpgNei DNA glycolsylases. It acts as a nucleophile in catalysis.
  • Citation:PMID 9030608
  • Comment:Site-directed mutagenesis of this residue renders Fpg proteins defective in catalysis but still able to make the Schiff-base intermediate.
  • Citation:PMID 9654091
  • Comment:Site-directed mutagensis of this residue renders Escherichia coli Nei inactive but still able to make the Schiff-base intermediate.
  • Comment:1KFV_A , is a structure of a mutant Lactococcus Lactis Fpg which has a Gly in place of a Pro at this position.

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
Feature 1              #                                                                               
1EE8_A               1 PELPEVETTRRRLRPl-------VLGQTLrQVVHrdpary---------------------------rntalaEGRRIlE 46  Thermus t...
NP_001100740         2 PEGPSVRKFHHLVSP--------FVGQKVvKTGGsskkl-----------------------------hpatfQSLWLqD 44  Norway rat
1K3W_A               1 PEGPEIRRAADNLEAa-------IKGKPLtDVWFafpqlk---------------------------tyqsqlIGQHVtH 46  Escherich...
NP_060718            2 VEGPGCTLNGEKIRAr------vLPGQAVtGVRGsalrslqgralrlaastvvvspqaaalnndssqnvlslfNGYVYsG 75  human
ZP_01252849          2 PELPEVQGYKTYIDSt-------SLHQRItEVDCrdtkllkkp----------------------kadfdaylYNQELiE 52  Psychrofl...
YP_001972308         2 PEGPSIVLLREAASH--------FKGHVVrAVSGnsrvd------------------------------lsplQGRRVkA 43  Stenotrop...
ZP_04031420          2 PEGDTVWLAARRLHRa-------LAGWALtVCDVrvpry-----------------------------attdlRGQRVrE 45  Thermomon...
REF_jgi:Lferr_0623   2 AELPEIELLRQKLRRn-------ILHKRVgVMQMqnakgealpd--------------------gagikdaalKGRAItD 54  Acidithio...
Q5UNW7               2 VEAPRIRITYEKIRHtknhrivsISGPSYkRMNVd-------------------------------------lIDYIIrK 44  Acanthamo...
2OQ4_A               1 PQGPEIRRAADNLEAa-------IKGKPLtDVWFafpqlk---------------------------tyqsqlIGQHVtH 46  Escherich...
Feature 1                                                                                              
1EE8_A              47 VDRRGKFLLFALeg------------------------------------------------------------------ 60  Thermus t...
NP_001100740        45 AQVHGKKLFLQFdpdeemeplsrspqpvqgmwqkeagnpepalgpsaqetsvgpcgsgepgpstsdgpydlrgkkplaea 124 Norway rat
1K3W_A              47 VETRGKALLTHFsn------------------------------------------------------------------ 60  Escherich...
NP_060718           76 VETLGKELFMYFg------------------------------------------------------------------- 88  human
ZP_01252849         53 TQRIGKYLFLKTtg------------------------------------------------------------------ 66  Psychrofl...
YP_001972308        44 VRSWGKHFLLEFs------------------------------------------------------------------- 56  Stenotrop...
ZP_04031420         46 AVSRGKHLLIRVdg------------------------------------------------------------------ 59  Thermomon...
REF_jgi:Lferr_0623  55 LHRYGQYLFLELd------------------------------------------------------------------- 67  Acidithio...
Q5UNW7              45 WWFAGKYIYLMLissn--------------------------------------------------------------kp 62  Acanthamo...
2OQ4_A              47 VETRGKALLTHFsn------------------------------------------------------------------ 60  Escherich...
Feature 1                                                                                   
1EE8_A              61 gVELVAHLGMTGGFRLEp-----------TPHTRAALVLe----------gRTLYFHDpr--rFGRLFG 106 Thermus thermophilus
NP_001100740       125 qRWLEVRFGLFGSIWVNdfs------rakKANKRGDWIDpv--------prLVLHFSGggflaFYNCQM 179 Norway rat
1K3W_A              61 dLTLYSHNQLYGVWRVVdtge----epqtTRVLRVKLQTa----------dKTILLYS-----ASDIEM 110 Escherichia coli
NP_060718           89 pKALRIHFGMKGFIMINpley----kyknGASPVLEVQLt----------kDLICFFDss--vELRNSM 141 human
ZP_01252849         67 kKILVMHFGMTGRPHYYkne------edrPKFGHLELSFen---------gFHFAFENkr--kFGWWDL 118 Psychroflexus torqui...
YP_001972308        57 rHTLRIHLMMFGSWRIDe-----------RKPTPPRVSL------------RFDNGELn----FYACSV 98  Stenotrophomonas mal...
ZP_04031420         60 gLSVHVHLKMDGRWLIRpag-------pvPRDHRIRLALgn--------erHLALGYR-----LGVVEV 108 Thermomonospora curv...
REF_jgi:Lferr_0623  68 -RKDILALQLGGELSGElergpvhgeggeEPRAALEIQIng---------qQRLRFQGt---qLGNRLR 123 Acidithiobacillus fe...
Q5UNW7              63 tYVIRTHMMMHGRILVGnq---------dSPTKRAFMIIqldndivlrwyrSQITLLDpn--cLAEIKT 120 Acanthamoeba polypha...
2OQ4_A              61 dLTLYSHNQLYGVWRVVdtge----epqtTRVLRVKLQTa----------dKTILLYS-----ASDIEM 110 Escherichia coli

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