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Protein

Endonuclease 8

Gene

nei

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. Acts on DNA bubble and 3'-fork structures, suggesting a role in replication-associated DNA repair. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.1 Publication

Catalytic activityi

Removes damaged bases from DNA, leaving an abasic site.
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.

Cofactori

Zn2+Note: Binds 1 zinc ion per subunit.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei2Schiff-base intermediate with DNA1
Active sitei3Proton donorCurated1
Active sitei53Proton donor; for beta-elimination activityCurated1
Binding sitei70DNA1 Publication1
Binding sitei125DNA1 Publication1
Binding sitei169DNA1 Publication1
Active sitei253Proton donor; for delta-elimination activityCurated1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri229 – 263FPG-typeAdd BLAST35

GO - Molecular functioni

  • damaged DNA binding Source: EcoliWiki
  • DNA-(apurinic or apyrimidinic site) lyase activity Source: EcoliWiki
  • oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity Source: UniProtKB-HAMAP
  • zinc ion binding Source: EcoliWiki

GO - Biological processi

  • base-excision repair Source: EcoliWiki
  • nucleotide-excision repair Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase, Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:G6383-MONOMER.
ECOL316407:JW0704-MONOMER.
BRENDAi3.2.2.23. 2026.
4.2.99.18. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Endonuclease 8
Alternative name(s):
DNA glycosylase/AP lyase Nei (EC:3.2.2.-, EC:4.2.99.18)
DNA-(apurinic or apyrimidinic site) lyase Nei
Endonuclease VIII
Gene namesi
Name:nei
Ordered Locus Names:b0714, JW0704
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13237. nei.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi2P → T: Loss of glycosylase and AP lyase activity. 1 Publication1
Mutagenesisi3E → A or Q: Loss of glycosylase activity. No effect on AP lyase activity. 2 Publications1
Mutagenesisi3E → D: Much reduced glycosylase activity. No effect on AP lyase activity. 2 Publications1
Mutagenesisi6E → Q: Reduced glycosylase activity. No effect on AP lyase activity. 1 Publication1
Mutagenesisi53K → A: Loss of DNA cleavage at sites containing oxidized pyrimidine. No effect on AP lyase activity. 1 Publication1
Mutagenesisi129D → N: Reduced glycosylase activity. No effect on AP lyase activity. 1 Publication1
Mutagenesisi160D → N: No effect on glycosylase and AP lyase activity. 1 Publication1
Mutagenesisi174E → Q: Loss of glycosylase activity. No effect on AP lyase activity. 1 Publication1
Mutagenesisi213R → A: Slightly reduced activity. 1 Publication1
Mutagenesisi253R → A: Reduced DNA cleavage at sites containing oxidized pyrimidine. No effect on AP lyase activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001708932 – 263Endonuclease 8Add BLAST262

Proteomic databases

PaxDbiP50465.
PRIDEiP50465.

Interactioni

Protein-protein interaction databases

BioGridi4259928. 110 interactors.
DIPiDIP-10327N.
IntActiP50465. 13 interactors.
MINTiMINT-1221359.
STRINGi511145.b0714.

Structurei

Secondary structure

1263
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 18Combined sources15
Beta strandi24 – 30Combined sources7
Helixi31 – 35Combined sources5
Helixi36 – 40Combined sources5
Beta strandi45 – 51Combined sources7
Beta strandi54 – 59Combined sources6
Beta strandi64 – 68Combined sources5
Turni70 – 72Combined sources3
Beta strandi74 – 79Combined sources6
Beta strandi90 – 95Combined sources6
Beta strandi97 – 105Combined sources9
Beta strandi108 – 112Combined sources5
Helixi116 – 119Combined sources4
Helixi121 – 125Combined sources5
Helixi137 – 145Combined sources9
Turni147 – 151Combined sources5
Helixi154 – 157Combined sources4
Turni161 – 163Combined sources3
Helixi169 – 179Combined sources11
Helixi187 – 189Combined sources3
Helixi192 – 212Combined sources21
Turni213 – 215Combined sources3
Helixi218 – 220Combined sources3
Beta strandi229 – 232Combined sources4
Turni239 – 241Combined sources3
Beta strandi246 – 250Combined sources5
Beta strandi253 – 257Combined sources5
Turni259 – 261Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K3WX-ray1.42A2-263[»]
1K3XX-ray1.25A2-263[»]
1Q39X-ray2.80A2-263[»]
1Q3BX-ray2.05A2-263[»]
1Q3CX-ray2.30A2-263[»]
2EA0X-ray1.40A2-263[»]
2OPFX-ray1.85A2-263[»]
2OQ4X-ray2.60A/B2-263[»]
DisProtiDP00375.
ProteinModelPortaliP50465.
SMRiP50465.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50465.

Family & Domainsi

Sequence similaritiesi

Belongs to the FPG family.Curated
Contains 1 FPG-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri229 – 263FPG-typeAdd BLAST35

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG4108S0J. Bacteria.
COG0266. LUCA.
HOGENOMiHOG000020882.
InParanoidiP50465.
KOiK05522.
OMAiQRIGPDV.
PhylomeDBiP50465.

Family and domain databases

HAMAPiMF_01253. Endonuclease_8. 1 hit.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR023713. Endonuclease-VIII.
IPR012319. FPG_cat.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
IPR010663. Znf_FPG/IleRS.
[Graphical view]
PANTHERiPTHR22993:SF14. PTHR22993:SF14. 1 hit.
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
SM01232. H2TH. 1 hit.
[Graphical view]
SUPFAMiSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
PROSITEiPS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P50465-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEGPEIRRA ADNLEAAIKG KPLTDVWFAF PQLKPYQSQL IGQHVTHVET
60 70 80 90 100
RGKALLTHFS NDLTLYSHNQ LYGVWRVVDT GEEPQTTRVL RVKLQTADKT
110 120 130 140 150
ILLYSASDIE MLTPEQLTTH PFLQRVGPDV LDPNLTPEVV KERLLSPRFR
160 170 180 190 200
NRQFAGLLLD QAFLAGLGNY LRVEILWQVG LTGNHKAKDL NAAQLDALAH
210 220 230 240 250
ALLEIPRFSY ATRGQVDENK HHGALFRFKV FHRDGEPCER CGSIIEKTTL
260
SSRPFYWCPG CQH
Length:263
Mass (Da):29,845
Last modified:January 23, 2007 - v3
Checksum:i7D10B79F58ADDA24
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38616 Genomic DNA. Translation: AAC45355.1.
D89754 Genomic DNA. Translation: BAA20414.1.
U00096 Genomic DNA. Translation: AAC73808.1.
AP009048 Genomic DNA. Translation: BAA35378.1.
PIRiA64807.
RefSeqiNP_415242.1. NC_000913.3.
WP_001113989.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73808; AAC73808; b0714.
BAA35378; BAA35378; BAA35378.
GeneIDi945320.
KEGGiecj:JW0704.
eco:b0714.
PATRICi32116623. VBIEscCol129921_0744.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38616 Genomic DNA. Translation: AAC45355.1.
D89754 Genomic DNA. Translation: BAA20414.1.
U00096 Genomic DNA. Translation: AAC73808.1.
AP009048 Genomic DNA. Translation: BAA35378.1.
PIRiA64807.
RefSeqiNP_415242.1. NC_000913.3.
WP_001113989.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K3WX-ray1.42A2-263[»]
1K3XX-ray1.25A2-263[»]
1Q39X-ray2.80A2-263[»]
1Q3BX-ray2.05A2-263[»]
1Q3CX-ray2.30A2-263[»]
2EA0X-ray1.40A2-263[»]
2OPFX-ray1.85A2-263[»]
2OQ4X-ray2.60A/B2-263[»]
DisProtiDP00375.
ProteinModelPortaliP50465.
SMRiP50465.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259928. 110 interactors.
DIPiDIP-10327N.
IntActiP50465. 13 interactors.
MINTiMINT-1221359.
STRINGi511145.b0714.

Proteomic databases

PaxDbiP50465.
PRIDEiP50465.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73808; AAC73808; b0714.
BAA35378; BAA35378; BAA35378.
GeneIDi945320.
KEGGiecj:JW0704.
eco:b0714.
PATRICi32116623. VBIEscCol129921_0744.

Organism-specific databases

EchoBASEiEB3026.
EcoGeneiEG13237. nei.

Phylogenomic databases

eggNOGiENOG4108S0J. Bacteria.
COG0266. LUCA.
HOGENOMiHOG000020882.
InParanoidiP50465.
KOiK05522.
OMAiQRIGPDV.
PhylomeDBiP50465.

Enzyme and pathway databases

BioCyciEcoCyc:G6383-MONOMER.
ECOL316407:JW0704-MONOMER.
BRENDAi3.2.2.23. 2026.
4.2.99.18. 2026.

Miscellaneous databases

EvolutionaryTraceiP50465.
PROiP50465.

Family and domain databases

HAMAPiMF_01253. Endonuclease_8. 1 hit.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR023713. Endonuclease-VIII.
IPR012319. FPG_cat.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
IPR010663. Znf_FPG/IleRS.
[Graphical view]
PANTHERiPTHR22993:SF14. PTHR22993:SF14. 1 hit.
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
SM01232. H2TH. 1 hit.
[Graphical view]
SUPFAMiSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
PROSITEiPS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiEND8_ECOLI
AccessioniPrimary (citable) accession number: P50465
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 152 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.