P50465 (END8_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	nei
Ordered Locus Names:	b0714, JW0704

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	263 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Domain	Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Glycosidase Hydrolase Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	base-excision repair Inferred from direct assay PubMed 17002303. Source: EcoliWiki nucleotide-excision repair Inferred from electronic annotation. Source: InterPro
Molecular_function	DNA-(apurinic or apyrimidinic site) lyase activity Inferred from direct assay PubMed 10862773PubMed 17002303. Source: EcoliWiki damaged DNA binding Inferred from direct assay PubMed 10862773PubMed 17002303. Source: EcoliWiki endonuclease activity Inferred from electronic annotation. Source: InterPro oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from direct assay PubMed 16145054. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1

Chain

2 – 263

262

Endonuclease 8 HAMAP-Rule MF_01253

PRO_0000170893

Regions

Zinc finger

229 – 263

35

FPG-type HAMAP-Rule MF_01253

Sites

Active site

2

1

Schiff-base intermediate with DNA

Active site

3

1

Proton donor Probable

Active site

53

1

Proton donor; for beta-elimination activity Probable

Active site

253

1

Proton donor; for delta-elimination activity Probable

Binding site

70

1

DNA

Binding site

125

1

DNA

Binding site

169

1

DNA

Experimental info

Mutagenesis

2

1

P → T: Loss of glycosylase and AP lyase activity. Ref.6

Mutagenesis

3

1

E → A or Q: Loss of glycosylase activity. No effect on AP lyase activity. Ref.6 Ref.8

Mutagenesis

3

1

E → D: Much reduced glycosylase activity. No effect on AP lyase activity. Ref.6 Ref.8

Mutagenesis

6

1

E → Q: Reduced glycosylase activity. No effect on AP lyase activity. Ref.6

Mutagenesis

53

1

K → A: Loss of DNA cleavage at sites containing oxidized pyrimidine. No effect on AP lyase activity. Ref.8

Mutagenesis

129

1

D → N: Reduced glycosylase activity. No effect on AP lyase activity. Ref.6

Mutagenesis

160

1

D → N: No effect on glycosylase and AP lyase activity. Ref.6

Mutagenesis

174

1

E → Q: Loss of glycosylase activity. No effect on AP lyase activity. Ref.6

Mutagenesis

213

1

R → A: Slightly reduced activity. Ref.8

Mutagenesis

253

1

R → A: Reduced DNA cleavage at sites containing oxidized pyrimidine. No effect on AP lyase activity. Ref.8

Secondary structure

1

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263

Helix Strand Turn

Details...

Helix

4 – 18

15

Beta strand

24 – 30

7

Helix

31 – 35

5

Helix

36 – 40

5

Beta strand

45 – 51

7

Beta strand

54 – 59

6

Beta strand

64 – 68

5

Turn

70 – 72

3

Beta strand

74 – 79

6

Beta strand

90 – 95

6

Beta strand

97 – 105

9

Beta strand

108 – 112

5

Helix

116 – 119

4

Helix

121 – 125

5

Helix

137 – 145

9

Turn

147 – 151

5

Helix

154 – 157

4

Turn

161 – 163

3

Helix

169 – 179

11

Helix

187 – 189

3

Helix

192 – 212

21

Turn

213 – 215

3

Helix

218 – 220

3

Beta strand

229 – 232

4

Turn

239 – 241

3

Beta strand

246 – 250

5

Beta strand

253 – 257

5

Turn

259 – 261

3

Sequences

	Sequence		Length	Mass (Da)
	P50465 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 7D10B79F58ADDA24	FASTA	263	29,845
	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

References

	« Hide 'large scale' referencesShow '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. , 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 277:1453-1474(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.

PIR

A64807.

RefSeq

NP_415242.1. NC_000913.2.
YP_488994.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	2-262	[»]
1Q3B	X-ray	2.05	A	2-262	[»]
1Q3C	X-ray	2.30	A	4-262	[»]
2EA0	X-ray	1.40	A	2-263	[»]
2OPF	X-ray	1.85	A	2-263	[»]
2OQ4	X-ray	2.60	A/B	4-263	[»]

DisProt

DP00375.

ProteinModelPortal

P50465.

SMR

P50465. Positions 2-263.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10327N.

IntAct

P50465. 13 interactions.

MINT

MINT-1221359.

STRING

511145.b0714.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001946; EBESCP00000001946; EBESCG00000001596.
EBESCT00000001947; EBESCP00000001947; EBESCG00000001596.
EBESCT00000015176; EBESCP00000014467; EBESCG00000014236.

GeneID

12930934.
945320.

KEGG

ecj:Y75_p0694.
eco:b0714.

PATRIC

32116623. VBIEscCol129921_0744.

Organism-specific databases

EchoBASE

EB3026.

EcoGene

EG13237. nei.

Phylogenomic databases

eggNOG

COG0266.

HOGENOM

HOG000020882.

KO

K05522.

OMA

WFAFPEL.

ProtClustDB

PRK10445.

Enzyme and pathway databases

BioCyc

EcoCyc:G6383-MONOMER.
ECOL316407:JW0704-MONOMER.

BRENDA

4.2.99.18. 2026.

Gene expression databases

Genevestigator

P50465.

Family and domain databases

HAMAP

MF_01253. Endonuclease_8.

InterPro

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]

Pfam

PF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]

SMART

SM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view]

SUPFAM

SSF81624. Form_DNAglyc_cat. 1 hit.
SSF46946. Ribosomal_H2TH. 1 hit.

PROSITE

PS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P50465.

Entry information

Entry name

END8_ECOLI

Accession

Primary (citable) accession number: P50465

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 123 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program