Conserved Protein Domain Family
MeNeil2_N

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cd08968: MeNeil2_N 
N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2)
This family contains the N-terminal domain of the metazoan protein Neil2. 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. NEIL2 repairs 5-hydroxyuracil (5-OHU) and other oxidized derivatives of cytosine, but it shows preference for DNA bubble structures. In addition to this MeNeil2_N domain, NEIL2 contains a helix-two turn-helix (H2TH) domain and a characteristic CHCC zinc finger motif. Neil2 is one of three homologs found in eukaryotes.
Statistics
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PSSM-Id: 176802
View PSSM: cd08968
Aligned: 6 rows
Threshold Bit Score: 208.46
Threshold Setting Gi: 126303985
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: 3-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_001100740   1 MPEGPSVRKFHHLVSPFVGQKVVKTGGSSKKLHPAtFQSLWLQDAQVHGKKLFLQFDPDEEMEplsrspqpvqgmwqkea 80  Norway rat
XP_001381635   1 MPEGPSLRKFHQLVAPFVGQLVVTVGGNSKKINPNmLEMLRLQDSQVHGKNLYLNFGLTEDLGlpesfllpkhlqkkvrl 80  gray short-tail...
NP_001107382   1 MPEGPTVRRFCSLVSPFVGQNVVKVGGSTKKIALQdLQGKQFHYCQVHGKNLYLEFTTKAVGNilsgtedakehidqagg 80  western clawed ...
XP_420042      1 MPEGPSVRKFQLLTSRFVGQVVAKVGGSSKKINVNdLNALRLQDSQVHGKNLFLAFVAASSPLgpnveetvlqeeaatga 80  chicken
NP_659480      1 MPEGPLVRKFHHLVSPFVGQQVVKTGGSSKKLQPAsLQSLWLQDTQVHGKKLFLRFDLDEEMGppgssptpeppqkevqk 80  human
XP_798656    174 MPEGPSVRRWGDTARQFIHKRIKVVRGVSKVMERErWRGACINAVVVYGKQLFLHLLQNSPSGndtsgnsepdtsar--- 250 purple urchin
Feature 1                                                                                        
NP_001100740  81 gnpepalgpsa-------qetsvgpcgsgepgpstsdgpydlrgkkPLAEAQRWLEVRFGLFGSIWVNDFSRA----KKA 149 Norway rat
XP_001381635  81 pkeksdhklettsrldgqevpgsslaikalelgeeeketvmpwwlnTSQNSGLWLCFHFGLFGSVRASELSRA----TKA 156 gray short-tail...
NP_001107382  81 sqkd----------------------ysiiqptseehseslqdadySEIHMSRWLRFHFGLYGSVRSNEFARA----KQA 134 western clawed ...
XP_420042     81 sslvqgkqeq----------vcapltppqeeelqdlqnsrpgapsaPTEGPGSWLRFHFGLFGSIRANEFSRA----SRA 146 chicken
NP_659480     81 egaadpkqvgeps----gqktldgssrsaelvpqgeddseylerdaPAGDAGRWLRVSFGLFGSVWVNDFSRA----KKA 152 human
XP_798656    251 --------------------------------kktmkacdlkeeniDDRDDSIWYRYHFLMWGSLRANEYKEPskrsKRA 298 purple urchin
Feature 1                                         
NP_001100740 150 NKRGDWIDPVPRLVLHFSGGGFlAFYNCQMSWS 182 Norway rat
XP_001381635 157 NKRGDWKDPIPRLVLHFAKGFL-AFYNCRIYWC 188 gray short-tailed opossum
NP_001107382 135 NKRGDWRDPTPRLILNFESGGFlVFYNCRMAWC 167 western clawed frog
XP_420042    147 NKRGDWKDPAPRLVLYFESGGFlVFYNCRMHWC 179 chicken
NP_659480    153 NKRGDWRDPSPRLVLHFGGGGFlAFYNCQLSWS 185 human
XP_798656    299 KKSEAPKAPNPMVEFYFEDKTFlVFYGGSIRIV 331 purple urchin

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