Reviewed,
UniProtKB/Swiss-Prot Q8U2D5 (AGOG_PYRFU)
Last modified
January 19, 2010.
Version 41.
History...
Clusters with 100%,
90%,
50% identity |
Documents (2) |
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 furiosus [Complete proteome] [HAMAP] | ||
| Taxonomic identifier | 2261 [NCBI] | ||
| Taxonomic lineage | Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus |
Protein attributes
| Sequence length | 242 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence at protein level. |
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. HAMAP MF_01168 |
| 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 | 3D-structure 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 – 242 | 242 | N-glycosylase/DNA lyase HAMAP MF_01168 | PRO_0000185114 | ||||||||||||||||||||||||||||||||
Regions | ||||||||||||||||||||||||||||||||||||
| Region | 120 – 184 | 65 | Helix-hairpin-helix HAMAP MF_01168 | |||||||||||||||||||||||||||||||||
Sites | ||||||||||||||||||||||||||||||||||||
| Active site | 144 | 1 | Schiff-base intermediate with DNA By similarity | |||||||||||||||||||||||||||||||||
| Active site | 176 | 1 | Potential | |||||||||||||||||||||||||||||||||
| Binding site | 26 | 1 | 8-oxoguanine By similarity | |||||||||||||||||||||||||||||||||
| Binding site | 53 | 1 | 8-oxoguanine; via carbonyl oxygen By similarity | |||||||||||||||||||||||||||||||||
| Binding site | 64 | 1 | 8-oxoguanine By similarity | |||||||||||||||||||||||||||||||||
| Binding site | 148 | 1 | 8-oxoguanine By similarity | |||||||||||||||||||||||||||||||||
| Binding site | 174 | 1 | 8-oxoguanine; via carbonyl oxygen By similarity | |||||||||||||||||||||||||||||||||
| Binding site | 210 | 1 | 8-oxoguanine By similarity | |||||||||||||||||||||||||||||||||
| Binding site | 214 | 1 | 8-oxoguanine By similarity | |||||||||||||||||||||||||||||||||
Secondary structure | ||||||||||||||||||||||||||||||||||||
Helix Strand Turn | ||||||||||||||||||||||||||||||||||||
| Helix | 2 – 22 | 21 | ||||||||||||||||||||||||||||||||||
| Helix | 25 – 34 | 10 | ||||||||||||||||||||||||||||||||||
| Helix | 39 – 51 | 13 | ||||||||||||||||||||||||||||||||||
| Helix | 60 – 71 | 12 | ||||||||||||||||||||||||||||||||||
| Helix | 79 – 86 | 8 | ||||||||||||||||||||||||||||||||||
| Turn | 87 – 89 | 3 | ||||||||||||||||||||||||||||||||||
| Helix | 97 – 112 | 16 | ||||||||||||||||||||||||||||||||||
| Helix | 116 – 124 | 9 | ||||||||||||||||||||||||||||||||||
| Helix | 126 – 137 | 12 | ||||||||||||||||||||||||||||||||||
| Helix | 144 – 160 | 17 | ||||||||||||||||||||||||||||||||||
| Helix | 177 – 184 | 8 | ||||||||||||||||||||||||||||||||||
| Helix | 191 – 202 | 12 | ||||||||||||||||||||||||||||||||||
| Helix | 206 – 217 | 12 | ||||||||||||||||||||||||||||||||||
| Helix | 227 – 239 | 13 | ||||||||||||||||||||||||||||||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "The complete sequence of the Pyrococcus furiosus genome." Weiss R.B., Dunn D.M., Robb F.T., Brown J.R. Submitted (FEB-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1. |
| [2] | "Conserved hypothetical protein Pfu-877259-001 from Pyrococcus furiosus." Chang J., Zhao M., Horanyi P., Xu H., Yang H., Liu Z.-J., Chen L., Zhou W., Habel J., Tempel W., Lee D., Lin D., Chang S.-H., Eneh J.C., Hopkins R.C., Jenney F.E., Lee H.-S., Li T. Rose J.P.Submitted (SEP-2004) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS). |
Cross-references
Sequence databases | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EMBL GenBank DDBJ | AE009950 Genomic DNA. Translation: AAL81028.1. | ||||||||||||
| RefSeq | NP_578633.2. | ||||||||||||
3D structure databases | |||||||||||||
| PDBe RCSB PDB PDBj |
| ||||||||||||
| ModBase | Search... | ||||||||||||
Genome annotation databases | |||||||||||||
| GeneID | 1468768. | ||||||||||||
| GenomeReviews | Gene locus PF0904 in contig AE009950_GR. | ||||||||||||
| KEGG | pfu:PF0904. | ||||||||||||
Organism-specific databases | |||||||||||||
| CMR | Search... | ||||||||||||
Phylogenomic databases | |||||||||||||
| HOGENOM | HBG539606. | ||||||||||||
| OMA | PLHIDSI. | ||||||||||||
Enzyme and pathway databases | |||||||||||||
| BRENDA | 4.2.99.18. 321. | ||||||||||||
Family and domain databases | |||||||||||||
| HAMAP | MF_01168. AGOG. [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_PYRFU | ||||||||
| Accession | Primary (citable) accession number: Q8U2D5 | ||||||||
| Entry history |
| ||||||||
| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) | ||||||||
Relevant documents
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with


