Reviewed, UniProtKB/Swiss-Prot Q3Z489 (END8_SHISS)

Names and origin

Protein names

Recommended name:
    Endonuclease 8
Alternative name(s):
    Endonuclease VIII
    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:	SSON_0665

Organism

Shigella sonnei (strain Ss046) [Complete proteome] [HAMAP]

Taxonomic identifier

300269 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Shigella

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 By similarity.
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 By similarity.
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 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 By similarity
	Chain	2 – 263	262	Endonuclease 8 HAMAP MF_01253		PRO_1000067212
Regions
	Zinc finger	229 – 263	35	FPG-type HAMAP MF_01253
Sites
	Active site	2	1	Schiff-base intermediate with DNA By similarity
	Active site	3	1	Proton donor By similarity
	Active site	53	1	Proton donor; for beta-elimination activity By similarity
	Active site	253	1	Proton donor; for delta-elimination activity By similarity
	Binding site	70	1	DNA By similarity
	Binding site	125	1	DNA By similarity
	Binding site	169	1	DNA By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q3Z489-1 [UniParc]. Last modified September 27, 2005. Version 1. Checksum: 928547D3BD363A8C	FASTA	263	29,875
	10 20 30 40 50 60 MPEGPEIRRA ADNLEAAIKG KPLTDVWFAF PQLKTYQSQL IGQHVTHVET RGKALLTHFS 70 80 90 100 110 120 NDLTLYSHNQ LYGVWRVVDT GEEPQTTRVL RVKLQTADKT ILLYSASDIE MLRPEQLTTH 130 140 150 160 170 180 PFLQRVGPDV LDPNLTPEVV KERLLSPRFR NRQFAGLLLD QAFLAGLGNY LRVEILWQVG 190 200 210 220 230 240 LTGNHKAKDL NAAQLDALAH ALLDIPRFSY ATRGLVDENK HHGALFRFKV FHRDGEPCER 250 260 CGSIIEKTTL SSRPFYWCPG CQH

References

[1]

"Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery." Yang F., Yang J., Zhang X., Chen L., Jiang Y., Yan Y., Tang X., Wang J., Xiong Z., Dong J., Xue Y., Zhu Y., Xu X., Sun L., Chen S., Nie H., Peng J., Xu J. , Wang Y., Yuan Z., Wen Y., Yao Z., Shen Y., Qiang B., Hou Y., Yu J., Jin Q. Nucleic Acids Res. 33:6445-6458(2005) [PubMed: 16275786] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases

EMBLGenBankDDBJ

CP000038 Genomic DNA. Translation: AAZ87423.1.

RefSeq

YP_309658.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2EA0	X-ray	1.40	A	2-263	[»]

SMR

Q3Z489. Positions 2-263.

ModBase

Search...

Genome annotation databases

GeneID

3669660.

GenomeReviews

Gene locus SSON_0665 in contig CP000038_GR.

KEGG

ssn:SSON_0665.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

Q3Z489.

OMA

Q3Z489. RSDFRVP.

Enzyme and pathway databases

BioCyc

SSON300269:SSO_0665-MON.

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_SHISS

Accession

Primary (citable) accession number: Q3Z489

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 5, 2008
Last sequence update:	September 27, 2005
Last modified:	June 16, 2009
This is version 35 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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