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P50465 (END8_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 132. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:nei
Ordered Locus Names:b0714, JW0704
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length263 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.7

Catalytic activity

Removes damaged bases from DNA, leaving an abasic site. HAMAP-Rule MF_01253

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. HAMAP-Rule MF_01253

Cofactor

Binds 1 zinc ion per subunit.

Sequence similarities

Belongs to the FPG family.

Contains 1 FPG-type zinc finger.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.1
Chain2 – 263262Endonuclease 8 HAMAP-Rule MF_01253
PRO_0000170893

Regions

Zinc finger229 – 26335FPG-type HAMAP-Rule MF_01253

Sites

Active site21Schiff-base intermediate with DNA
Active site31Proton donor Probable
Active site531Proton donor; for beta-elimination activity Probable
Active site2531Proton donor; for delta-elimination activity Probable
Binding site701DNA
Binding site1251DNA
Binding site1691DNA

Experimental info

Mutagenesis21P → T: Loss of glycosylase and AP lyase activity. Ref.6
Mutagenesis31E → A or Q: Loss of glycosylase activity. No effect on AP lyase activity. Ref.6 Ref.8
Mutagenesis31E → D: Much reduced glycosylase activity. No effect on AP lyase activity. Ref.6 Ref.8
Mutagenesis61E → Q: Reduced glycosylase activity. No effect on AP lyase activity. Ref.6
Mutagenesis531K → A: Loss of DNA cleavage at sites containing oxidized pyrimidine. No effect on AP lyase activity. Ref.8
Mutagenesis1291D → N: Reduced glycosylase activity. No effect on AP lyase activity. Ref.6
Mutagenesis1601D → N: No effect on glycosylase and AP lyase activity. Ref.6
Mutagenesis1741E → Q: Loss of glycosylase activity. No effect on AP lyase activity. Ref.6
Mutagenesis2131R → A: Slightly reduced activity. Ref.8
Mutagenesis2531R → A: Reduced DNA cleavage at sites containing oxidized pyrimidine. No effect on AP lyase activity. Ref.8

Secondary structure

...................................................... 263
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P50465 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 7D10B79F58ADDA24

FASTA26329,845
        10         20         30         40         50         60 
MPEGPEIRRA ADNLEAAIKG KPLTDVWFAF PQLKPYQSQL IGQHVTHVET RGKALLTHFS 

        70         80         90        100        110        120 
NDLTLYSHNQ LYGVWRVVDT GEEPQTTRVL RVKLQTADKT ILLYSASDIE MLTPEQLTTH 

       130        140        150        160        170        180 
PFLQRVGPDV LDPNLTPEVV KERLLSPRFR NRQFAGLLLD QAFLAGLGNY LRVEILWQVG 

       190        200        210        220        230        240 
LTGNHKAKDL NAAQLDALAH ALLEIPRFSY ATRGQVDENK HHGALFRFKV FHRDGEPCER 

       250        260 
CGSIIEKTTL SSRPFYWCPG CQH 

« Hide

References

« Hide 'large scale' references
[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]"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map."
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. expand/collapse author list , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T.
DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U38616 Genomic DNA. Translation: AAC45355.1.
D89754 Genomic DNA. Translation: BAA20414.1.
U00096 Genomic DNA. Translation: AAC73808.1.
AP009048 Genomic DNA. Translation: BAA35378.1.
PIRA64807.
RefSeqNP_415242.1. NC_000913.3.
YP_488994.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
DisProtDP00375.
ProteinModelPortalP50465.
SMRP50465. Positions 2-263.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10327N.
IntActP50465. 13 interactions.
MINTMINT-1221359.
STRING511145.b0714.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73808; AAC73808; b0714.
BAA35378; BAA35378; BAA35378.
GeneID12930934.
945320.
KEGGecj:Y75_p0694.
eco:b0714.
PATRIC32116623. VBIEscCol129921_0744.

Organism-specific databases

EchoBASEEB3026.
EcoGeneEG13237. nei.

Phylogenomic databases

eggNOGCOG0266.
HOGENOMHOG000020882.
KOK05522.
OMAGPDVLDM.
OrthoDBEOG6QP131.
PhylomeDBP50465.

Enzyme and pathway databases

BioCycEcoCyc:G6383-MONOMER.
ECOL316407:JW0704-MONOMER.
BRENDA4.2.99.18. 2026.

Gene expression databases

GenevestigatorP50465.

Family and domain databases

HAMAPMF_01253. Endonuclease_8.
InterProIPR015886. 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]
PfamPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]
SMARTSM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view]
SUPFAMSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
PROSITEPS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP50465.
PROP50465.

Entry information

Entry nameEND8_ECOLI
AccessionPrimary (citable) accession number: P50465
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 132 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene