Conserved Protein Domain Family
BaFpgNei_N_3

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cd08975: BaFpgNei_N_3 
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases
This family is an uncharacterized bacterial subgroup of the FpgNei_N 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. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In this family the N-terminal proline is replaced by an isoleucine or valine. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_3 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.
Statistics
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PSSM-Id: 176809
View PSSM: cd08975
Aligned: 11 rows
Threshold Bit Score: 175.976
Threshold Setting Gi: 237733045
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: 14-May-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
Feature 1:catalytic residue [active site]
Evidence:
  • 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
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Format: Row Display: Color Bits: Type Selection:
Feature 1              #                                                                               
REF_wustl:BD1965     2 IEIPESATIGKQASEtLKGKRIaHVIEsnsPHRFTFYNGDPa-eYSNRLVGRTVlGAQGYGAFVDIFMdadTHLLIGDGT 80  Parabacte...
YP_003307893         2 LEIPESFNLAKQLNQtVKNKVIkNVKAaqsPHKFAFYFNDDpdnYNALLSGKKIeKIEPIGGQVEITAe-nIRILFGDGV 80  Sebaldell...
REF_mbpwusl:BT4488   2 IEAPEARYLCEQLTEtVVGKRIsDVFIqfsPHKFAWFNGNSd-eFAEWLVDKRInSAQSQGGMVEITIe-dKVLVLTDGV 79  Bacteroid...
REF_mbpwusl:BT2359   2 KELPENQTLSKQINEtLKDRVItEVFNatkFHKNTFYFGDPl-tYSELLIGRRInSSMSFGMYVDIILd--KETKISFGD 78  Bacteroid...
ZP_02072966          2 LELPEVITLSKQVNNaLSGKTItQVFNatkPHKFTFYNGNPs-eYGKLLVGKTIlSSEGYGMFVNFNLs--DNVIMNIGD 78  Bacteroid...
ZP_04803649          2 LEIPESSVLSTQISEvLRNKKIiGVISnhsPHKFAWFHGDPn-eYNKILVDKTIhKATPYGGMIEIKVe-sSILLFADGV 79  Clostridi...
REF_jgi:Cphy_3389    2 LEIPESIVLSKEINEsLVGKVIrYVKAnqsPHSFAWYHGNPe-nYDELLSGKTIvKARPCGGMLEIKAd-dCKIVFTDGT 79  Clostridi...
ZP_02418319          2 IELPEALARADELKSeLKGKRAeKVWPpssPHKFCWFNGEAs-sYDDMLSGRKVvDAQGFGIFAEIIFegdLRVCFNDGV 80  Anaerosti...
YP_516986           70 LELPEVLTLVRQLNEsVKNRRIrKVWPptkAHKFCWYNGEPe-eYDKALSGSRIaGAEGFGTFAELIFdngRKLCVNDGV 148 Desulfito...
ZP_03758225         22 LEYPEIAVISRQLQKeTAGKMVtAVLPpmkPHKFCWFNGDPa-gYEAQLTGSRItAAEGFGIFVELVFdngRRLCFNDGV 100 Clostridi...
ZP_04563526          6 IELPEAYAIADDLKKeILGKTIiDLGGnytDHKFTFYEGNPn-sYKELLVGKKVtGIIKRNYYVEIVIe-nYRLTFRDGA 83  Mollicute...
Feature 1                                                        
REF_wustl:BD1965    81 NMRYYTSae--kaPKKYQLMIVFeddSFLAFTVs-MYGSIYA 119 Parabacteroides distasonis ATCC 8503
YP_003307893        81 NARYLPAge--kiPEKHQLLMEFd-dNSCIVCTvqMYGVLHA 119 Sebaldella termitidis ATCC 33386
REF_mbpwusl:BT4488  80 NLRYLTPgt--klPAKHQLLIAFedeSCLIASVr-MYGGLMC 118 Bacteroides thetaiotaomicron VPI-5482
REF_mbpwusl:BT2359  79 GTNLKYGtisnkmPNNYQLLLALdnnTYLTFTVg-MFGVIAA 119 Bacteroides thetaiotaomicron VPI-5482
ZP_02072966         79 GVSVRYYsagdeiPANYQLLLTFnddSFLVFTVa-MYGFINV 119 Bacteroides uniformis ATCC 8492
ZP_04803649         80 SLKYNAPne--klPPKHQLLLKFedsSSVTASVq-MYGGIWC 118 Clostridium cellulovorans 743B
REF_jgi:Cphy_3389   80 SIRYYADrn--kaPKKNQLYIEFeddSALVVTVm-MYGGIWA 118 Clostridium phytofermentans ISDg
ZP_02418319         81 NVRIFGEgd--niPGKYQLRIDFsdgTVLVFTVa-MYGSIAC 119 Anaerostipes caccae DSM 14662
YP_516986          149 NLRLMPAgk---vPGNYQLMMELddgQALVFTVa-MYGGIFE 186 Desulfitobacterium hafniense Y51
ZP_03758225        101 NVRLTGGek---pPAACQLLIRLddgTALAFTVa-MYGGIYL 138 Clostridium asparagiforme DSM 15981
ZP_04563526         84 NIRYYQKpt---kLKKSKLLITFadqSFINVTTs-MYCFIGL 121 Mollicutes bacterium D7

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