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P50465

- END8_ECOLI

UniProt

P50465 - END8_ECOLI

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Protein

Endonuclease 8

Gene

nei

Organism
Escherichia coli (strain K12)
Status
Reviewed - 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

Binds 1 zinc ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei2 – 21Schiff-base intermediate with DNA
Active sitei3 – 31Proton donorCurated
Active sitei53 – 531Proton donor; for beta-elimination activityCurated
Binding sitei70 – 701DNA1 Publication
Binding sitei125 – 1251DNA1 Publication
Binding sitei169 – 1691DNA1 Publication
Active sitei253 – 2531Proton donor; for delta-elimination activityCurated

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri229 – 26335FPG-typeAdd
BLAST

GO - Molecular functioni

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

GO - Biological processi

  1. base-excision repair Source: EcoliWiki
  2. DNA catabolic process, endonucleolytic Source: GOC
  3. 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.
BRENDAi4.2.99.18. 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG13237. nei.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi2 – 21P → T: Loss of glycosylase and AP lyase activity. 1 Publication
Mutagenesisi3 – 31E → A or Q: Loss of glycosylase activity. No effect on AP lyase activity. 2 Publications
Mutagenesisi3 – 31E → D: Much reduced glycosylase activity. No effect on AP lyase activity. 2 Publications
Mutagenesisi6 – 61E → Q: Reduced glycosylase activity. No effect on AP lyase activity. 1 Publication
Mutagenesisi53 – 531K → A: Loss of DNA cleavage at sites containing oxidized pyrimidine. No effect on AP lyase activity. 1 Publication
Mutagenesisi129 – 1291D → N: Reduced glycosylase activity. No effect on AP lyase activity. 1 Publication
Mutagenesisi160 – 1601D → N: No effect on glycosylase and AP lyase activity. 1 Publication
Mutagenesisi174 – 1741E → Q: Loss of glycosylase activity. No effect on AP lyase activity. 1 Publication
Mutagenesisi213 – 2131R → A: Slightly reduced activity. 1 Publication
Mutagenesisi253 – 2531R → A: Reduced DNA cleavage at sites containing oxidized pyrimidine. No effect on AP lyase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 263262Endonuclease 8PRO_0000170893Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriP50465.

Interactioni

Protein-protein interaction databases

DIPiDIP-10327N.
IntActiP50465. 13 interactions.
MINTiMINT-1221359.
STRINGi511145.b0714.

Structurei

Secondary structure

1
263
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1815Combined sources
Beta strandi24 – 307Combined sources
Helixi31 – 355Combined sources
Helixi36 – 405Combined sources
Beta strandi45 – 517Combined sources
Beta strandi54 – 596Combined sources
Beta strandi64 – 685Combined sources
Turni70 – 723Combined sources
Beta strandi74 – 796Combined sources
Beta strandi90 – 956Combined sources
Beta strandi97 – 1059Combined sources
Beta strandi108 – 1125Combined sources
Helixi116 – 1194Combined sources
Helixi121 – 1255Combined sources
Helixi137 – 1459Combined sources
Turni147 – 1515Combined sources
Helixi154 – 1574Combined sources
Turni161 – 1633Combined sources
Helixi169 – 17911Combined sources
Helixi187 – 1893Combined sources
Helixi192 – 21221Combined sources
Turni213 – 2153Combined sources
Helixi218 – 2203Combined sources
Beta strandi229 – 2324Combined sources
Turni239 – 2413Combined sources
Beta strandi246 – 2505Combined sources
Beta strandi253 – 2575Combined sources
Turni259 – 2613Combined sources

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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. Positions 2-263.
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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri229 – 26335FPG-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0266.
HOGENOMiHOG000020882.
InParanoidiP50465.
KOiK05522.
OMAiGPDVLDM.
OrthoDBiEOG6QP131.
PhylomeDBiP50465.

Family and domain databases

HAMAPiMF_01253. Endonuclease_8.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR012319. DNA_glycosylase/AP_lyase_cat.
IPR023713. Endonuclease-VIII.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
[Graphical view]
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 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:
EMBL
GenBank
DDBJ
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.
YP_488994.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73808; AAC73808; b0714.
BAA35378; BAA35378; BAA35378.
GeneIDi12930934.
945320.
KEGGiecj:Y75_p0694.
eco:b0714.
PATRICi32116623. VBIEscCol129921_0744.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
PIRi A64807.
RefSeqi NP_415242.1. NC_000913.3.
YP_488994.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1K3W X-ray 1.42 A 2-263 [» ]
1K3X X-ray 1.25 A 2-263 [» ]
1Q39 X-ray 2.80 A 2-263 [» ]
1Q3B X-ray 2.05 A 2-263 [» ]
1Q3C X-ray 2.30 A 2-263 [» ]
2EA0 X-ray 1.40 A 2-263 [» ]
2OPF X-ray 1.85 A 2-263 [» ]
2OQ4 X-ray 2.60 A/B 2-263 [» ]
DisProti DP00375.
ProteinModelPortali P50465.
SMRi P50465. Positions 2-263.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-10327N.
IntActi P50465. 13 interactions.
MINTi MINT-1221359.
STRINGi 511145.b0714.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73808 ; AAC73808 ; b0714 .
BAA35378 ; BAA35378 ; BAA35378 .
GeneIDi 12930934.
945320.
KEGGi ecj:Y75_p0694.
eco:b0714.
PATRICi 32116623. VBIEscCol129921_0744.

Organism-specific databases

EchoBASEi EB3026.
EcoGenei EG13237. nei.

Phylogenomic databases

eggNOGi COG0266.
HOGENOMi HOG000020882.
InParanoidi P50465.
KOi K05522.
OMAi GPDVLDM.
OrthoDBi EOG6QP131.
PhylomeDBi P50465.

Enzyme and pathway databases

BioCyci EcoCyc:G6383-MONOMER.
ECOL316407:JW0704-MONOMER.
BRENDAi 4.2.99.18. 2026.

Miscellaneous databases

EvolutionaryTracei P50465.
PROi P50465.

Gene expression databases

Genevestigatori P50465.

Family and domain databases

HAMAPi MF_01253. Endonuclease_8.
InterProi IPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR012319. DNA_glycosylase/AP_lyase_cat.
IPR023713. Endonuclease-VIII.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
[Graphical view ]
Pfami PF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view ]
SMARTi SM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view ]
SUPFAMi SSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
PROSITEi PS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Escherichia coli endonuclease VIII: cloning, sequencing, and overexpression of the nei structural gene and characterization of nei and nei nth mutants."
    Jiang D., Hatahet Z., Blaisdell J.O., Melamede R.J., Wallace S.S.
    J. Bacteriol. 179:3773-3782(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-36; 189-206 AND 214-227.
  2. "Characterization of endonuclease III (nth) and endonuclease VIII (nei) mutants of Escherichia coli K-12."
    Saito Y., Uraki F., Nakajima S., Asaeda A., Ono K., Kubo K., Yamamoto K.
    J. Bacteriol. 179:3783-3785(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Determination of active site residues in Escherichia coli endonuclease VIII."
    Burgess S., Jaruga P., Dodson M.L., Dizdaroglu M., Lloyd R.S.
    J. Biol. Chem. 277:2938-2944(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF PRO-2; GLU-3; GLU-6; ASP-129; ASP-160 AND GLU-174.
  7. "The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts."
    Guo Y., Bandaru V., Jaruga P., Zhao X., Burrows C.J., Iwai S., Dizdaroglu M., Bond J.P., Wallace S.S.
    DNA Repair 9:177-190(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBSTRATES.
  8. "Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate."
    Zharkov D.O., Golan G., Gilboa R., Fernandes A.S., Gerchman S.E., Kycia J.H., Rieger R.A., Grollman A.P., Shoham G.
    EMBO J. 21:789-800(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.42 ANGSTROMS) IN COMPLEX WITH DNA, MUTAGENESIS OF GLU-3; LYS-53; ARG-213 AND ARG-253.

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: October 29, 2014
This is version 134 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

External Data

Dasty 3