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P50465

- END8_ECOLI

UniProt

P50465 - END8_ECOLI

Protein

Endonuclease 8

Gene

nei

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 133 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    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

    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 – 1815
    Beta strandi24 – 307
    Helixi31 – 355
    Helixi36 – 405
    Beta strandi45 – 517
    Beta strandi54 – 596
    Beta strandi64 – 685
    Turni70 – 723
    Beta strandi74 – 796
    Beta strandi90 – 956
    Beta strandi97 – 1059
    Beta strandi108 – 1125
    Helixi116 – 1194
    Helixi121 – 1255
    Helixi137 – 1459
    Turni147 – 1515
    Helixi154 – 1574
    Turni161 – 1633
    Helixi169 – 17911
    Helixi187 – 1893
    Helixi192 – 21221
    Turni213 – 2153
    Helixi218 – 2203
    Beta strandi229 – 2324
    Turni239 – 2413
    Beta strandi246 – 2505
    Beta strandi253 – 2575
    Turni259 – 2613

    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.
    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

    MPEGPEIRRA ADNLEAAIKG KPLTDVWFAF PQLKPYQSQL IGQHVTHVET    50
    RGKALLTHFS NDLTLYSHNQ LYGVWRVVDT GEEPQTTRVL RVKLQTADKT 100
    ILLYSASDIE MLTPEQLTTH PFLQRVGPDV LDPNLTPEVV KERLLSPRFR 150
    NRQFAGLLLD QAFLAGLGNY LRVEILWQVG LTGNHKAKDL NAAQLDALAH 200
    ALLEIPRFSY ATRGQVDENK HHGALFRFKV FHRDGEPCER CGSIIEKTTL 250
    SSRPFYWCPG CQH 263
    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.
    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

    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 1, 2014
    This is version 133 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