Conserved Protein Domain Family
PF_Nei_N

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cd08972: PF_Nei_N 
N-terminal domain of the plant and fungal Nei and related proteins
This family contains the N-terminal domain of plant and Fungi Nei and related proteins. 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. The plant and fungal FpgNei glycosylases prefer the oxidized pyrimidines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh) over 8-oxoguanine in double stranded oligonucleotides and also show weak activity on single stranded DNA. In addition to this domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a characteristic zincless finger motif. They share a common ancestor not shared with other eukaryotic members of the FpgNei family.
Statistics
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PSSM-Id: 176806
View PSSM: cd08972
Aligned: 14 rows
Threshold Bit Score: 156.313
Threshold Setting Gi: 147828418
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         #                                                                              
XP_958637      1 MPEIAEIARAVHFLRLHFVGKVIkHAEAId----DGNVFgkvgtdg------pkmaagLIGKKMVSAGTQGKYFWMELSk 70  Neurospora cras...
XP_001777468   1 MPELPEVEAAKRLLDSHCLGATIvKAVVDn----DTKVIdgvtpa--------alqesLTGKKILSTHRKGKHLWLKLDs 68  Physcomitrella ...
ACO64895       1 MPELPEVESARCLVEAHCIGAKVtKVEFNedgsfDEKIFkdverk--------afvsaLLNKTLTAAHRRGKHMWWDMSg 72  Micromonas sp. ...
CAP97795       1 MPELAEIHRIVHFIREHLVGKTLsKVQAQh----DDIIFgkvgtsg------aefqkaMQGKKIVGAGQQGKYFWMTMSs 70  Penicillium chr...
NP_564608      1 MPELPEVEAARRAIEENCLGKKIkRVIIAd----DNKVIhgisps--------dfqtsILGKTIISARRKGKNLWLELDs 68  thale cress
CAA21931       1 MPEVAEVSHVCALLKRNILGFRItKVNLLh----DPLLFpvlkdtnnaekelnkmrkaLTNAVVTSVGRHGKYFWIRLNn 76  Candida albicans
XP_001906155   1 MPEIAEVARIVHFLRLHLVGKTIrTASAVd----DQIVFgkagttg------davsaaLTGRKVISSGSQGKLFWLVLDk 70  Podospora anser...
XP_001828971   1 MPELPEVQRAVNTLKHVAKGKRItKVVTYp----DPIVFnattne--------efgkeLENRTVSDAKRYGKVFYLDLDg 68  Coprinopsis cin...
CAN77708       1 MPELPEVEAARRAVEEHCVGKKItKAVIAn----DSKVIdgvsps--------dfeasLLGKTIVSAHRKGKNMWLQLDs 68  wine grape
YP_003201779   1 MPELPEVESARRVLADGALHRRIaDVDDH-----DDYVTrpltpg--------alrsaLIGRTFTAAHRRGKSMWLTVSg 67  Nakamurella mul...
Feature 1                                                                                        
XP_958637     71 -------------aPHLVMHFGMTGWIHIKgertaytny----------------------------------------- 96  Neurospora cras...
XP_001777468  69 -------------pPWPSFQFGMSGAVIIKgvkgpqyr------------------------------------------ 93  Physcomitrella ...
ACO64895      73 g------------aDSPLFHFGMTGAFSIRgkgamky------------------------------------------- 97  Micromonas sp. ...
CAP97795      71 -------------pPHAVMHFGMAGWLKIKdadtyyy------------------------------------------- 94  Penicillium chr...
NP_564608     69 -------------pPFPSFQFGMAGAIYIKgvavtkyk------------------------------------------ 93  thale cress
CAA21931      77 hn----------ttNVLLMHFGMTGMVKLRnvhshlafmenggdkkale------------------------------- 115 Candida albicans
XP_001906155  71 -------------aPHVVMHFGMTGWLQIRgvqtsyssl----------------------------------------- 96  Podospora anser...
XP_001828971  69 k------------gKKPVLHFGMTGMLHVKgvkpmhyk------------------------------------------ 94  Coprinopsis cin...
CAN77708      69 ppf-------psfqFVCVQVLGKESLISLNevfsiiraeegrrsvvldtlrkerleeisnfsxxtxarkpstswpraffr 141 wine grape
YP_003201779  68 drddptdpdaspgdPDLGIHLGMSGIVVVTgpsapeasgtdl-------------------------------------- 109 Nakamurella mul...
Feature 1                                                                               
XP_958637     97 ----------------ykkmkpdelDKWPPKYWKFKIETEDg---------DEMAFTDP---RRFGRVRVV 139 Neurospora crassa OR74A
XP_001777468  94 -----------------sskvgdeeEAFPTTYSKVHLVLSTg---------VELAFTDK---RRFARVRLL 135 Physcomitrella patens su...
ACO64895      98 ------------------kafvvdtSNWPPRFAKLVVTFDNg---------IALAYTDP---RRFGRIRLV 138 Micromonas sp. RCC299
CAP97795      95 ------------------rsdkpadQEWPPKYWKFLLETNDes-------kTEAAFVDA---RRLGRIRLV 137 Penicillium chrysogenum ...
NP_564608     94 ------------------rsavkdsEEWPSKYSKFFVELDDg---------LELSFTDK---RRFAKVRLL 134 thale cress
CAA21931     116 ------klerfrykdsrikpdvevkQEWPPRFTKFDMELENnd------kkLEFAFSDP---RRLARVRLL 171 Candida albicans
XP_001906155  97 -----------------yrdtdtrvETWPPKYTKFHLTTTCnp-------aVEVAFTDY---RRLARVRLV 140 Podospora anserina DSM 980
XP_001828971  95 -----------------eaprkdseDTWPPRFCKFILHLQNptgssngepeTEVAFIDAq--NWLFGHRWN 146 Coprinopsis cinerea okay...
CAN77708     142 paiashaparexlsgdalpppgspdADQPPFLPVSXIRALHalrsv-fpasSGYFFSTPipaRALGSVLLP 211 wine grape
YP_003201779 110 --------------vggdyrrdreqFVDRGAYQRFAVTFADg---------GRMRLLDP---RRLSRVRLD 154 Nakamurella multipartita...

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