Conserved Protein Domain Family
AcNei1_N

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cd08970: AcNei1_N 
N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases
This family contains the N-terminal domain of the actinomycetal Nei1 and related 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. This family contains mostly actinomycetes and includes Mycobacterium tuberculosis Nei1 (MtuNei1). MtuNei1 recognizes oxidized pyrimidines such as thymine glycol (Tg) and 5,6-dihydrouracil on both double stranded and single stranded DNA, it has a strong preference for the 5R isomer of Tg. In addition to this 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: 176804
View PSSM: cd08970
Aligned: 26 rows
Threshold Bit Score: 127.757
Threshold Setting Gi: 84497372
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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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         #                                                                              
NP_216980      1 MPEGHTLHRLARLHQRrFAGAPVSVSSPQGRFADSAsaLNGRVLrRASAWGKHLFHHYvg-------------------- 60  Mycobacterium t...
NP_826604      1 MPEGHTIHRLADDYEArFGGAAARVTSPQGKFADAAalLDGTVLeTADAHGKHLFLGFrr-------------------- 60  Streptomyces av...
NP_870679     34 MPEGHKTHYLAREHNQrYAGERLDVSSPQGRFSDGAraVSGRVLeSVRAAGKHLFYEFeg-------------------- 93  Rhodopirellula ...
AAV31649      28 LPEGHTIHRAARDHNSlLANQKLTVLSPQGRFTEGAsrLTGRICiNIEAFGKHLIYHFdn-------------------- 87  uncultured alph...
ZP_00996075    7 MPEGHTLHALARDLDIaFRGTSPTVSSPQGKFGGGAalLSGHEVlEATSWGKHLFVEFag-------------------- 66  Janibacter sp. ...
YP_001363124   1 MPEAHSLHRHARDQRAaLAGQVLSVSSPQGRFDATP--FDGHRLvDVQAHGKHLLYSFeq-------------------- 58  Kineococcus rad...
ZP_02044874    1 MPEGDAVRRLAGTLDElFVGGIVSASSPQGRFASSAalLDGWVMqRVRVHGKHMFIGFvppiegetyeagvallegaaag 80  Actinomyces odo...
ZP_03922596   15 VPEGHAIHRLAAQFAQvMSGEVVAASSPQGRFTAGAavLNGQRLtDVQAYGKHLFLGFaprqvdtaq------------- 81  Mobiluncus curt...
ZP_06245757    1 MPEGHSVHRLARQFTDvFGGRRIRATSPQGRFAEGAalLDGQVLeRARAHGKHFFADVsg-------------------- 60  Micrococcus lut...
YP_003514889   1 MPEGHVIHRLADRYATaFTGGPLAVSSPQGRFADSAkrLDGLSMtGTEAHGKQLFLEFeg-------------------- 60  Stackebrandtia ...
Feature 1                                                                                        
NP_216980     61 -------------gPVVHVHLGLYGTFTEWArptd--------------------------------------------- 82  Mycobacterium t...
NP_826604     61 -------------aDWIHIHLGLFGKVGFGDap----------------------------------------------- 80  Streptomyces av...
NP_870679     94 -------------nRIVHVHLGRYGSYVEQTsp----------------------------------------------- 113 Rhodopirellula ...
AAV31649      88 -------------gEALHVHLGLFGKIRKQRlp----------------------------------------------- 107 uncultured alph...
ZP_00996075   67 -------------dRILWVHLGLIGTFTIDTtsy---------------------------------------------- 87  Janibacter sp. ...
YP_001363124  59 -------------aPDVHVHLGMKGIFLRTEdl----------------------------------------------- 78  Kineococcus rad...
ZP_02044874   81 sgepilgedapwpdRWVHIHLGLYGWWRFNGdetvvdeghgvahripnvpkgew-------------nghsetrwgegfg 147 Actinomyces odo...
ZP_03922596   82 -----ttpdsksppTWLHIHLGIYGSWRFYGdseftsrhvgtalnlpestqqtaeiveipvhthhddsafaphehfadrw 156 Mobiluncus curt...
ZP_06245757   61 -------------gHVLHVHLGMYGAWTFGGdqdfaaassigaprrigerev-----------------hddgapaaepc 110 Micrococcus lut...
YP_003514889  61 -------------qQWIRIHLGIYGKVAFGEpp----------------------------------------------- 80  Stackebrandtia ...
Feature 1                                              
NP_216980     83 ------gwlPEPAGQVRMRMvGAEFGTDLRGPTVCESI 114 Mycobacterium tuberculosis H37Rv
NP_826604     81 --------aPPPTDTVRLRLaNDTSYVDLRGPTTCALI 110 Streptomyces avermitilis MA-4680
NP_870679    114 --------pEPPQGQVRLRAiSPTHTLDLRGPSQCRLI 143 Rhodopirellula baltica SH 1
AAV31649     108 --------aAEPRGAVRVRLvGNTHLIDINGPNICEIL 137 uncultured alpha proteobacterium EBAC2C11
ZP_00996075   88 ------ageVPVVGQVRCRFaTSDHVADLRGPMVCDVV 119 Janibacter sp. HTCC2649
YP_001363124  79 --------sLPPRAGTRMRLaGETTAFSLIAPSRCEAL 108 Kineococcus radiotolerans SRS30216
ZP_02044874  148 eakagewepPEPVGAVRLRLfNDHAVADLVGPNRCDLI 185 Actinomyces odontolyticus ATCC 17982
ZP_03922596  157 fwtpapftaPPPYGTVRLRLvTAHGAADLSGPNTCELL 194 Mobiluncus curtisii ATCC 43063
ZP_06245757  111 rdadgwvqpPSPAATVRLRLrAEHGWADLIGASRCRAL 148 Micrococcus luteus NCTC 2665
YP_003514889  81 --------aPAVEGAVRLRLeGERAYSDLRGPAVCELI 110 Stackebrandtia nassauensis DSM 44728

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