Conserved Protein Domain Family
BaFpgNei_N_4

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cd08976: BaFpgNei_N_4 
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. This N-terminal proline is conserved in this family. 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_4 domain, most 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: 176810
View PSSM: cd08976
Aligned: 8 rows
Threshold Bit Score: 160.979
Threshold Setting Gi: 120437537
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: 19-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             #                                                                               
ZP_01252849         2 PELPEVQGYKTYIDStSLHQRItEVDCRDTKLlkkpka--dfdayLYNQELiETQRIGKYLFLKTtg-kKILVMHFGMTG 78  Psychrofle...
YP_003390356        2 PELPEVEIRRQYLETsSLYQPVsHIEVEDKKLlttdla--tlqqaLIGRQFtGTRRVGKNLFIFTdapdVIIHMHFGMTG 79  Spirosoma ...
ZP_01864982         2 PELPENEAQRLTLEReCLHRTIeAVELGEDVTyielpg-dnerarLVGRQFtETRRHGKNIFAGSkt-gPWMTVHLGMTG 79  Erythrobac...
YP_644557           2 PELPDVEVLKGRLERtSLGRRIsRVEVRDGRVvgevsa-rglreaLEGRSLrRVHRHGKNLFAGVeg-gGWVLMHFGMAG 79  Rubrobacte...
ADF50486            2 PELPEVAYQKKYADAtILHKKIvEIETGDKKIyqsaka--dfekiLTDNAFeSTSRIGKYLFLKLkk-nGVLVMHFGMTG 78  Zunongwang...
REF_tigr:SRU_0462   2 PELPDAVVYRRRLADaALDRPIaDATVVDPLIlgdglephrlgevLRGRTLtDTHRHGKHVFVRYgeetGWLALHFGMTG 81  Salinibact...
ZP_01690605         2 PELPEVERFKQYFEGtALHQKVvQVEIADAGVlactae--tlkevAEKHTFdKTDRIGKYLFIETsa-dKVLMIHFGMSG 78  Microscill...
YP_863223          35 PELPEVAYQKIYVDStSLHHKIvKVDMGADKIfqspks--efeatLLKNEFvSSTQIGKYLLLKLke-kGYLVVHFGMTG 111 Gramella f...
Feature 1                                                     
ZP_01252849        79 RPHYYkneedrPKFGHLELSFengFHFAFENkRKFGWWDL 118 Psychroflexus torquis ATCC 700755
YP_003390356       80 DLEYYhasldrPRFARIVFEFtsgFNLGFLCpRKFERVGL 119 Spirosoma linguale DSM 74
ZP_01864982        80 KLVPFdapddpPDHTKLLIRFegdRRLAFQCpRKLGHVRV 119 Erythrobacter sp. SD-21
YP_644557          80 GLSHLpgteeePPHVRLLLGFdggDRLAFTDrRALGRVHP 119 Rubrobacter xylanophilus DSM 9941
ADF50486           79 KLDYYqhd-dtPKYTQLKLIFedhSKLAFTCpRKFAKLYL 117 Zunongwangia profunda SM-A87
REF_tigr:SRU_0462  82 RVQVVpdg-tmPEYAYVQVHFedgGALAFECpRKFARVRL 120 Salinibacter ruber DSM 13855
ZP_01690605        79 SLKYYrd--dpPRFGRVVFHLangFHLAFDCpRKFGRIDV 116 Microscilla marina ATCC 23134
YP_863223         112 KMDYFqhd-eiQKHAQLTLTFedgGKLSFVCpRKFGKLFL 150 Gramella forsetii KT0803

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