1K3W,2OQ4


Conserved Protein Domain Family
EcNei-like_N

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cd08965: EcNei-like_N 
Click on image for an interactive view with Cn3D
N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases
This family contains the N-terminal domain of proteobacteria Nei and related DNA glycosylases. It includes Escherichia coli Nei, and 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. Escherichia coli Nei has been well studied, it is a DNA glycosylase/AP lyase that excises damaged pyrimidines, including 5-hydroxycytosine, 5-hydroxyuracil, and uracil glycol. In addition to this EcNei-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a canonical zinc-finger motif.
Statistics
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PSSM-Id: 176799
View PSSM: cd08965
Aligned: 11 rows
Threshold Bit Score: 205.67
Threshold Setting Gi: 124026034
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: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site include 1 residue -Click on image for an interactive view with Cn3D
Feature 1:catalytic residue [active site]
Evidence:
  • Comment:This proline residue is almost perfectly conserved in FpgNei DNA glycolsylases. It acts as a nucleophile in catalysis.
  • Citation:PMID 9030608
  • Comment:Site-directed mutagensis of this residue renders Escherichia coli Nei inactive but still able to make a Schiff-base intermediate.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        #                                                                               
1K3W_A         1 PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVtHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVdtg 80  Escherichia coli
2OQ4_A         1 PQGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVtHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVdtg 80  Escherichia coli
YP_002934271   2 PEGPEIRRVADELRAAVGGGTLTQVWFGVPSLQRHAAGLVGCRVtTIEARGKALLIHFSNGVSMYSHNQLYGIWRVAatg 81  Edwardsiella ic...
ZP_01627030    2 PEGPEIRRAADKIEAVLKDRVAEKVEFGLQPLKKYVKPLKGSNIlALETRGKALLTHFDSGFTIYSHNQLYGVWRVVkrd 81  marine gamma pr...
ZP_03227589    2 PEGPEIRRAADQVEKAIKGRTIEEMYFAFPHLEEFEELFRGATCiRVDTKGKAMLIRLDNGYTIYSHNQLYGRWYSRnvy 81  Bacillus coahui...
ZP_02170146    2 PEGPEIRLAADEVEHAVLNKPLLEVFFGLPPLKDYEDILTRATVnRVQTKGKALLTHFDNGYSVYSHNQLYGKWYIKpsy 81  Bacillus seleni...
ZP_04715414    2 PEGPEIRRAADKVEAVIKDIPLEKVEFGLAQLKPYAKQLEGEKVlRMETRGKALITHFSNGLSMYSHNQLYGVWHTCkrn 81  Alteromonas mac...
YP_001515012   2 PEGPEIRRAADRIASEIANQPLQEVWFAFSHLKIYEAQLGASQIqQVETRGKGLLMHFDCGLSIYSHNQLYGKWMIRkay 81  Acaryochloris m...
YP_001015150   2 PEGPEIKRAADRISKVLIGEEIIESNFYYERIKEKEEIVKNQNIkDITTRGKAMIIRFKNDWSMYSHNQLYGRWTVNlnt 81  Prochlorococcus...
ZP_05127773    2 PEGPEIRRAADRIADVLVDRTIEEVVFAFPELQRFGGLLTGQQVlDIETRGKALLTHFDNDYAIYSHNQLYGVWKIAkrg 81  gamma proteobac...
ZP_05038725    2 PEGPEIRIAADKIQRAIRPYPTTEVFFAFDHLKPFEADLSGCRVtEVETRGKAMLTHFDNGLSVYTHNQLYGKWMVRkah 81  Synechococcus s...
Feature 1                                           
1K3W_A        81 eEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQ 115 Escherichia coli
2OQ4_A        81 eEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQ 115 Escherichia coli
YP_002934271  82 qIPPTSRSLRVRLETAERAILLYSASDIQLAPRAQ 116 Edwardsiella ictaluri 93-146
ZP_01627030   82 kLPKTNRQLRLAIHTDNHSALLYSASDISVWKTQN 116 marine gamma proteobacterium HTCC2080
ZP_03227589   82 nYPKTNRVLRMAIHNEKKSALLYSASDIDVLRNEE 116 Bacillus coahuilensis m4-4
ZP_02170146   82 sYPKTNRQLRLALHTGDRSALLYSASDIAVLRTDE 116 Bacillus selenitireducens MLS10
ZP_04715414   82 rMPDTTRQLRVGLHTETHSAILYSASDISIWPTQT 116 Alteromonas macleodii ATCC 27126
YP_001515012  82 nYPQTKRQLRLALHCDRKSALLYSASDIDVLDAAG 116 Acaryochloris marina MBIC11017
YP_001015150  82 tKVKSRRALRVVFTTNKHAVRLWSATDIDLIPTNE 116 Prochlorococcus marinus str. NATL1A
ZP_05127773   82 kMPATNRSLRLALHTATHSALLYSASDISVWAREE 116 gamma proteobacterium NOR5-3
ZP_05038725   82 dFPETNRQLRFAIHNEKKSALLYSASDIQILSSQS 116 Synechococcus sp. PCC 7335

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