Conserved Protein Domain Family
BaFpgNei_N_2

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cd08974: BaFpgNei_N_2 
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_2 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain. Most also contain a zinc-finger motif.
Statistics
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PSSM-Id: 176808
View PSSM: cd08974
Aligned: 12 rows
Threshold Bit Score: 160.183
Threshold Setting Gi: 255535130
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: 22-Apr-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         #                                                                              
YP_001972308   1 MPEGPSIVLLREAASH--FKGHVVRAVSGNSRVDLSPL-QGRRVKAVRSWGKHFLLEFS-RHTLRIHLMMFGSWRIDE-- 74  Stenotrophomona...
ZP_03852428    1 MPEGPSIILMKENLQP--FAGQQVTEVSGNAKFEKDSF-IGQTLREIRTFGKQTYLIFE-KAAVRIHLLMFGSYGIDEqt 76  Chryseobacteriu...
YP_001195697   1 MPEGPSILILKEEVQQ--FAGKRIIEVSGNASIDLERL-QDKTILSFKTWGKHFLICFD-DFTIRIHLMMFGTYRINE-- 74  Flavobacterium ...
YP_970206      1 MPEGPSLVLLKEAARPl-AEGRRIERASGNTTAIDTAAlPGRRVVSVRTWGKHFLLELDsGCTVRVHFLLFGSFRIDD-- 77  Acidovorax aven...
YP_001171397  38 MPEGPSIVILREEVAA--FTGQRIERAEGSAKVDMARL-TGQVVREFRSWGKHLLIELE-DVSVRIHLLLFGSYRINE-- 111 Pseudomonas stu...
NP_638873      1 MPEGPSLVILREEAAA--FVGRKILRVQGNSKQDIARL-QQQKVLALRSWGKHLLIECA-QFSVRIHFLLFGSYRINEd- 75  Xanthomonas cam...
YP_003096595   1 MPEGPTILNLTSKISR--FKGKTVTDATGYAEMDKTGI-AGQKLMAIDAYGKNFIFVFK-DFFVTVHLGLFGSMLINK-- 74  Flavobacteriace...
YP_003084570   1 MPEGPSIVILREAIEAlhLKGETVRLAEGRAKIDMDRL-INQKVTDFRSWGKHFLICFK-GFTVRIHFLLFGSYYIDD-- 76  Dyadobacter fer...
YP_003092879   1 MPEGPSIVILRELIEEldLEGQEVIALSGNTKIEKDRM-LHHKVKAFKSWGKHFLICFE-NFSLRIHFMMFGTYRINE-- 76  Pedobacter hepa...
ZP_03682947    1 MPEGPTIVILKEEVAA--FEGRTVVRVAGNSTQDIQRM-RGREILAIRSWGKHFLLEFS-DFSLRVHLMLYGSYRINE-- 74  Catenibacterium...
ZP_04763716    1 MPEGPSLIIPRGQAAA--SAGQAIVRVEGNTSIGRQRL-AGQRIVALRTWGKHFLVELP-TFTLRVHFLLFGSYRINE-- 74  Acidovorax dela...
YP_003095501   1 MPEGPSILILKEATQK--FIGEKVISATGNAKIAMEKL-PDLTFEEYRIFGKQSYLVFG-EAVIRVHLLLFGSYSVDEqi 76  Flavobacteriace...
Feature 1                                 
YP_001972308  75 RKPTPPRVSLRFDNGEL-NFYACSV 98  Stenotrophomonas maltophilia K279a
ZP_03852428   77 KPDKSLRLALFFPTGSI-YFYTCSV 100 Chryseobacterium gleum ATCC 35910
YP_001195697  75 KKETAPRLHLGFSNGEI-NFYTCSI 98  Flavobacterium johnsoniae UW101
YP_970206     78 PKDAPARLSLGFEGGHAiDFYACSV 102 Acidovorax avenae subsp. citrulli AAC00-1
YP_001171397 112 RKDATARLSLGFANGEL-NFYACSV 135 Pseudomonas stutzeri A1501
NP_638873     76 KPNAVPRLRLEFSKGETlNFYACSV 100 Xanthomonas campestris pv. campestris str. ATCC 33913
YP_003096595  75 RKKSNASFALHFDDKEI-NFYIANT 98  Flavobacteriaceae bacterium 3519-10
YP_003084570  77 RKKAPPHLSLLFDKHEL-NFYTTSI 100 Dyadobacter fermentans DSM 18053
YP_003092879  77 RKQTPARLSLSFENAEL-NFYTCSL 100 Pedobacter heparinus DSM 2366
ZP_03682947   75 RREAAPRLSLQFAGGDElNFYACSV 99  Catenibacterium mitsuokai DSM 15897
ZP_04763716   75 RKDTPPRLAQQCEQGEL-NFYTCSL 98  Acidovorax delafieldii 2AN
YP_003095501  77 KPDRQLRLQLKFPNGDL-YFNSCSV 100 Flavobacteriaceae bacterium 3519-10

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