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Q5JI79

- AGOG_THEKO

UniProt

Q5JI79 - AGOG_THEKO

Protein

N-glycosylase/DNA lyase

Gene

TK0940

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 57 (01 Oct 2014)
      Sequence version 1 (15 Feb 2005)
      Previous versions | rss
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    Functioni

    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.UniRule annotation

    Catalytic activityi

    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.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei43 – 4318-oxoguanineUniRule annotation
    Binding sitei71 – 7118-oxoguanine; via carbonyl oxygenUniRule annotation
    Binding sitei82 – 8218-oxoguanineUniRule annotation
    Active sitei164 – 1641Schiff-base intermediate with DNAUniRule annotation
    Binding sitei168 – 16818-oxoguanineUniRule annotation
    Binding sitei194 – 19418-oxoguanine; via carbonyl oxygenUniRule annotation
    Active sitei196 – 1961UniRule annotation
    Binding sitei230 – 23018-oxoguanineUniRule annotation
    Binding sitei234 – 23418-oxoguanineUniRule annotation

    GO - Molecular functioni

    1. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB-HAMAP
    2. oxidized base lesion DNA N-glycosylase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. base-excision repair Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Hydrolase, Lyase

    Keywords - Biological processi

    DNA damage, DNA excision, DNA repair

    Enzyme and pathway databases

    BioCyciTKOD69014:GH72-953-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    N-glycosylase/DNA lyaseUniRule annotation
    Alternative name(s):
    8-oxoguanine DNA glycosylaseUniRule annotation (EC:3.2.2.-UniRule annotation)
    AGOGUniRule annotation
    DNA-(apurinic or apyrimidinic site) lyaseUniRule annotation (EC:4.2.99.18UniRule annotation)
    Short name:
    AP lyaseUniRule annotation
    Gene namesi
    Ordered Locus Names:TK0940
    OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    ProteomesiUP000000536: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 263263N-glycosylase/DNA lyasePRO_0000185116Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi69014.TK0940.

    Structurei

    3D structure databases

    ProteinModelPortaliQ5JI79.
    SMRiQ5JI79. Positions 17-253.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni139 – 20466Helix-hairpin-helixAdd
    BLAST

    Domaini

    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).

    Sequence similaritiesi

    Belongs to the archaeal N-glycosylase/DNA lyase (AGOG) family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG4047.
    HOGENOMiHOG000254352.
    KOiK01741.
    OMAiVKMFGYA.

    Family and domain databases

    Gene3Di1.10.1670.10. 1 hit.
    1.10.340.30. 1 hit.
    HAMAPiMF_01168. AGOG.
    InterProiIPR011257. DNA_glycosylase.
    IPR023170. HTH_base_excis_C.
    IPR015254. N-Glyclase/DNA_lyase-like_arc.
    IPR016544. N-Glyclase/DNA_lyase_arc.
    [Graphical view]
    PfamiPF09171. DUF1886. 1 hit.
    [Graphical view]
    PIRSFiPIRSF008955. AGOG. 1 hit.
    SUPFAMiSSF48150. SSF48150. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q5JI79-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSLERFVKIK YQTNEEKADK LVEGLKELGI ECARIIEEKV DLQFDALRHL    50
    RENLNDDETF IKLVIANSIV SYQLSGKGED WWWEFSKYFS QNPPEKSIVE 100
    ACSKFLPSSR TNRRLVAGKI KRLEKLEPFL NSLTLQELRR YYFENMMGLR 150
    NDIAEALGSP KTAKTVVFAV KMFGYAGRIA FGEFVPYPME IDIPEDVRIK 200
    AYTERITNEP PVSFWRRVAE ETGIPPLHID SILWPVLGGK REVMERLKKV 250
    CEKWELVLEL GSL 263
    Length:263
    Mass (Da):30,553
    Last modified:February 15, 2005 - v1
    Checksum:iDBBD7B55740CDBDB
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP006878 Genomic DNA. Translation: BAD85129.1.
    RefSeqiYP_183353.1. NC_006624.1.

    Genome annotation databases

    EnsemblBacteriaiBAD85129; BAD85129; TK0940.
    GeneIDi3234448.
    KEGGitko:TK0940.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP006878 Genomic DNA. Translation: BAD85129.1 .
    RefSeqi YP_183353.1. NC_006624.1.

    3D structure databases

    ProteinModelPortali Q5JI79.
    SMRi Q5JI79. Positions 17-253.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 69014.TK0940.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD85129 ; BAD85129 ; TK0940 .
    GeneIDi 3234448.
    KEGGi tko:TK0940.

    Phylogenomic databases

    eggNOGi COG4047.
    HOGENOMi HOG000254352.
    KOi K01741.
    OMAi VKMFGYA.

    Enzyme and pathway databases

    BioCyci TKOD69014:GH72-953-MONOMER.

    Family and domain databases

    Gene3Di 1.10.1670.10. 1 hit.
    1.10.340.30. 1 hit.
    HAMAPi MF_01168. AGOG.
    InterProi IPR011257. DNA_glycosylase.
    IPR023170. HTH_base_excis_C.
    IPR015254. N-Glyclase/DNA_lyase-like_arc.
    IPR016544. N-Glyclase/DNA_lyase_arc.
    [Graphical view ]
    Pfami PF09171. DUF1886. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF008955. AGOG. 1 hit.
    SUPFAMi SSF48150. SSF48150. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.

    Entry informationi

    Entry nameiAGOG_THEKO
    AccessioniPrimary (citable) accession number: Q5JI79
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 10, 2006
    Last sequence update: February 15, 2005
    Last modified: October 1, 2014
    This is version 57 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3