Reviewed,
UniProtKB/Swiss-Prot Q5JI79 (AGOG_PYRKO)
Last modified
November 3, 2009.
Version 25.
History...
Clusters with 100%,
90%,
50% identity |
Documents (1) |
Third-party data |
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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 |
| ||
| 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 activityInferred 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
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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 | |
|---|---|
| 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 |
| ||||||||
| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) | ||||||||

Clusters with


