Reviewed, UniProtKB/Swiss-Prot Q5JI79 (AGOG_PYRKO)

Names and origin

Protein names

Recommended name:
    N-glycosylase/DNA lyase
Alternative name(s):
    AGOG
    8-oxoguanine DNA glycosylase
    EC=3.2.2.-
    DNA-(apurinic or apyrimidinic site) lyase
      Short name=AP lyase
    EC=4.2.99.18

Gene names

Ordered Locus Names:

TK0940

Organism

Pyrococcus kodakaraensis (Thermococcus kodakaraensis) [Complete proteome] [HAMAP]

Taxonomic identifier

311400 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus

Protein attributes

Sequence length	263 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	DNA repair enzyme that is part of the base excision repair (BER) pathway; protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates By similarity.
Catalytic activity	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_01168
Domain	Contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. Contains a helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif). HAMAP MF_01168
Sequence similarities	Belongs to the archaeal N-glycosylase/DNA lyase (AGOG) family.

Ontologies

Keywords
Biological process	DNA damage DNA excision DNA repair
Molecular function	Hydrolase Lyase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	base-excision repair Inferred from electronic annotation. Source: HAMAP
Molecular function	DNA-(apurinic or apyrimidinic site) lyase activity Inferred from electronic annotation. Source: HAMAP oxidized base lesion DNA N-glycosylase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 263	263	N-glycosylase/DNA lyase HAMAP MF_01168		PRO_0000185116
Regions
	Region	139 – 204	66	Helix-hairpin-helix HAMAP MF_01168
Sites
	Active site	164	1	Schiff-base intermediate with DNA By similarity
	Active site	196	1	Potential
	Binding site	43	1	8-oxoguanine By similarity
	Binding site	71	1	8-oxoguanine; via carbonyl oxygen By similarity
	Binding site	82	1	8-oxoguanine By similarity
	Binding site	168	1	8-oxoguanine By similarity
	Binding site	194	1	8-oxoguanine; via carbonyl oxygen By similarity
	Binding site	230	1	8-oxoguanine By similarity
	Binding site	234	1	8-oxoguanine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q5JI79-1 [UniParc]. Last modified February 15, 2005. Version 1. Checksum: DBBD7B55740CDBDB	FASTA	263	30,553
	10 20 30 40 50 60 MSLERFVKIK YQTNEEKADK LVEGLKELGI ECARIIEEKV DLQFDALRHL RENLNDDETF 70 80 90 100 110 120 IKLVIANSIV SYQLSGKGED WWWEFSKYFS QNPPEKSIVE ACSKFLPSSR TNRRLVAGKI 130 140 150 160 170 180 KRLEKLEPFL NSLTLQELRR YYFENMMGLR NDIAEALGSP KTAKTVVFAV KMFGYAGRIA 190 200 210 220 230 240 FGEFVPYPME IDIPEDVRIK AYTERITNEP PVSFWRRVAE ETGIPPLHID SILWPVLGGK 250 260 REVMERLKKV CEKWELVLEL GSL

References

[1]

"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes." Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T. Genome Res. 15:352-363(2005) [PubMed: 15710748] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: KOD1.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AP006878 Genomic DNA. Translation: BAD85129.1.
RefSeq	YP_183353.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	Q5JI79.
Genome annotation databases
GeneID	3234448.
GenomeReviews	Gene locus TK0940 in contig AP006878_GR.
KEGG	tko:TK0940.
NMPDR	fig|69014.3.peg.527.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q5JI79.
OMA	PLHIDSI.
Enzyme and pathway databases
BioCyc	TKOD69014:TK0940-MON.
BRENDA	4.2.99.18. 192130.
Family and domain databases
HAMAP	MF_01168. [Tree]
InterPro	IPR015254. N-Glyclase/DNA_lyase-like_arc. IPR016544. N-Glyclase/DNA_lyase_arc. [Graphical view]
Pfam	PF09171. DUF1886. 1 hit. [Graphical view]
PIRSF	PIRSF008955. AGOG. 1 hit.
ProtoNet	Search...

Entry information

Entry name

AGOG_PYRKO

Accession

Primary (citable) accession number: Q5JI79

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 10, 2006
Last sequence update:	February 15, 2005
Last modified:	November 3, 2009
This is version 25 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)