Reviewed, UniProtKB/Swiss-Prot Q83LZ7 (END8_SHIFL)

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:	SF0583, S0596

Organism

Shigella flexneri [Complete proteome] [HAMAP]

Taxonomic identifier

623 [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	Inferred from homology.

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. 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 By similarity. 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	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 VIII HAMAP MF_01253		PRO_0000170899
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)
	Q83LZ7-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: A8A12258DB4E6A2E	FASTA	263	29,842
	10 20 30 40 50 60 MPEGPEIRRA ADNLEAAIKG KPLTDVWFAF PQLKTYQSQL IGQHVTHVET RGKALLTHFP 70 80 90 100 110 120 NGLTLYSHNQ 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 ALLEIPRFSY ATRGQVDENK HHGALFRFKV FHRDGELCER 250 260 CGGIIEKTTL SSRPFYWCPG CQH

References

[1]

"Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157." Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y. , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J. Nucleic Acids Res. 30:4432-4441(2002) [PubMed: 12384590] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 301 / Serotype 2a.

[2]

"Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T." Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G., Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T., Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R. Infect. Immun. 71:2775-2786(2003) [PubMed: 12704152] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700930 / 2457T / Serotype 2a.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE005674 Genomic DNA. Translation: AAN42226.1. AE014073 Genomic DNA. Translation: AAP16099.1.
RefSeq	NP_706519.1. NP_836293.1.
3D structure databases
SMR	Q83LZ7. Positions 2-263.
ModBase	Search...
Genome annotation databases
GeneID	1023561. 1077029.
GenomeReviews	Gene locus SF0583 in contig AE005674_GR. Gene locus S0596 in contig AE014073_GR.
KEGG	sfl:SF0583. sfx:S0596.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG690070.
OMA	RRCGTRI.
Enzyme and pathway databases
BioCyc	SFLE198214:AAN42226.1-MONOMER.
BRENDA	4.2.99.18. 189495.
Family and domain databases
HAMAP	MF_01253. Endonuclease_8. [Tree]
InterPro	IPR015886. DNA_glyclase/AP_lyase_DNA-bd. IPR000214. DNA_glyclase/AP_lyase_Znf_dom. IPR010663. DNA_glyclase/IsotRNA_synth_Znf. IPR015887. DNA_glyclase_Znf_dom_DNA_BS. IPR012319. DNA_glycosylase/AP_lyase_cat. IPR010979. Ribosomal_S13-like_H2TH. [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]
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_SHIFL

Accession

Primary (citable) accession number: Q83LZ7
Secondary accession number(s): Q7C2P2

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 4, 2005
Last sequence update:	January 23, 2007
Last modified:	January 19, 2010
This is version 54 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)