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Q5JI79 (AGOG_PYRKO) Reviewed, UniProtKB/Swiss-Prot

Last modified November 16, 2011. Version 42. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
N-glycosylase/DNA lyase
Alternative name(s):
8-oxoguanine DNA glycosylase
EC=3.2.2.-
AGOG
DNA-(apurinic or apyrimidinic site) lyase
Short name=AP lyase
EC=4.2.99.18
Gene names
Ordered Locus Names:TK0940
OrganismPyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Thermococcus kodakaraensis (strain KOD1))
Taxonomic identifier69014 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus

Protein attributes

Sequence length263 AA.
Sequence statusComplete.
Protein existenceInferred 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. 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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 263263N-glycosylase/DNA lyase HAMAP MF_01168
PRO_0000185116

Regions

Region139 – 20466Helix-hairpin-helix HAMAP MF_01168

Sites

Active site1641Schiff-base intermediate with DNA By similarity
Active site1961 Potential
Binding site4318-oxoguanine By similarity
Binding site7118-oxoguanine; via carbonyl oxygen By similarity
Binding site8218-oxoguanine By similarity
Binding site16818-oxoguanine By similarity
Binding site19418-oxoguanine; via carbonyl oxygen By similarity
Binding site23018-oxoguanine By similarity
Binding site23418-oxoguanine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q5JI79 [UniParc].

Last modified February 15, 2005. Version 1.
Checksum: DBBD7B55740CDBDB

FASTA26330,553
        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

« Hide

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: ATCC BAA-918 / JCM 12380 / KOD1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AP006878 Genomic DNA. Translation: BAD85129.1.
RefSeqYP_183353.1. NC_006624.1.

3D structure databases

ProteinModelPortalQ5JI79.
SMRQ5JI79. Positions 17-253.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaEBPYRT00000008321; EBPYRP00000008102; EBPYRG00000008320.
GeneID3234448.
GenomeReviewsGene locus TK0940 in contig AP006878_GR.
KEGGtko:TK0940.
NMPDRfig|69014.3.peg.527.

Phylogenomic databases

eggNOGarNOG07656.
GeneTreeEBGT00050000022472.
HOGENOMHBG539606.
OMALTWCAGL.
ProtClustDBPRK13280.

Enzyme and pathway databases

BioCycTKOD69014:TK0940-MONOMER.

Family and domain databases

HAMAPMF_01168. AGOG.
[Tree]
InterProIPR011257. DNA_glycosylase.
IPR023170. HTH_base_excis_C.
IPR015254. N-Glyclase/DNA_lyase-like_arc.
IPR016544. N-Glyclase/DNA_lyase_arc.
[Graphical view]
Gene3DG3DSA:1.10.340.30. DNA_glycosylase. 1 hit.
G3DSA:1.10.1670.10. HTH_base_excis_C. 1 hit.
KOK01741.
PfamPF09171. DUF1886. 1 hit.
[Graphical view]
PIRSFPIRSF008955. AGOG. 1 hit.
SUPFAMSSF48150. DNA_glycsylse. 1 hit.
ProtoNetSearch...

Entry information

Entry nameAGOG_PYRKO
AccessionPrimary (citable) accession number: Q5JI79
Entry history
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: February 15, 2005
Last modified: November 16, 2011
This is version 42 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

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