Reviewed, UniProtKB/Swiss-Prot P50465 (END8_ECOLI)

Names and origin

Protein names

Recommended name:
    Endonuclease VIII
Alternative name(s):
    DNA glycosylase/AP lyase Nei
    EC=3.2.2.-
    EC=4.2.99.18
    DNA-(apurinic or apyrimidinic site) lyase Nei

Gene names

Name:	nei
Ordered Locus Names:	b0714, JW0704

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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. 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. HAMAP MF_01253
Catalytic activity	Removes damaged bases from DNA, leaving an abasic site. HAMAP 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 MF_01253
Cofactor	Binds 1 zinc ion per subunit. HAMAP MF_01253
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
Gene Ontology (GO)
Biological process	base-excision repair Inferred from electronic annotation. Source: InterPro nucleotide-excision repair Inferred from electronic annotation. Source: InterPro
Molecular function	damaged DNA binding Inferred from electronic annotation. Source: InterPro oxidized pyrimidine base lesion DNA N-glycosylase activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
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 VIII HAMAP MF_01253

PRO_0000170893

Regions

Zinc finger

229 – 263

35

FPG-type HAMAP MF_01253

Sites

Active site

2

1

Schiff-base intermediate with DNA HAMAP MF_01253

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 HAMAP MF_01253

Binding site

125

1

DNA HAMAP MF_01253

Binding site

169

1

DNA HAMAP MF_01253

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.7

Mutagenesis

3

1

E → D: Much reduced glycosylase activity. No effect on AP lyase activity. Ref.6 Ref.7

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.7

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.7

Mutagenesis

253

1

R → A: Reduced DNA cleavage at sites containing oxidized pyrimidine. No effect on AP lyase activity. Ref.7

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 – 178

10

Helix

187 – 189

3

Helix

192 – 212

21

Turn

239 – 241

3

Beta strand

246 – 250

5

Beta strand

253 – 257

5

Turn

259 – 261

3

Sequences

	Sequence		Length	Mass (Da)
	P50465-1 [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: 9171429] [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: 9171430] [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: 8905232] [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: 9278503] [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: 16738553] [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: 11711552] [Abstract] Cited for: MUTAGENESIS OF PRO-2; GLU-3; GLU-6; ASP-129; ASP-160 AND GLU-174.
[7]	"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: 11847126] [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

EMBLGenBankDDBJ

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

AP_001352.1.
NP_415242.1.

3D structure databases

PDBPDBe

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	[»]
2OPF	X-ray	1.85	A	2-263	[»]
2OQ4	X-ray	2.60	A/B	4-263	[»]

DisProt

DP00375.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:10327N.

STRING

P50465.

Genome annotation databases

GeneID

945320.

GenomeReviews

Gene locus JW0704 in contig AP009048_GR.
Gene locus b0714 in contig U00096_GR.

KEGG

ecj:JW0704.
eco:b0714.

Organism-specific databases

EchoBASE

EB3026.

EcoGene

EG13237. nei.

CMR

Search...

Phylogenomic databases

HOGENOM

P50465.

OMA

RSDFRVP.

Enzyme and pathway databases

BioCyc

EcoCyc:G6383-MON.

Gene expression databases

Genevestigator

P50465.

Family and domain databases

HAMAP

MF_01253.
[Tree]

InterPro

IPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR000214. DNA_glyclase/AP_lyase_Znf_dom.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR012319. DNA_glycosylase/AP_lyase_cat.
[Graphical view]

Pfam

PF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
[Graphical view]

ProDom

PD003680. Fapy_DNA_glyco. 1 hit.
[Graphical view] [Entries sharing at least one domain]

PROSITE

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

ProtoNet

Search...

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:	November 3, 2009
This is version 92 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)