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Q8ZVK6

- AGOG_PYRAE

UniProt

Q8ZVK6 - AGOG_PYRAE

Protein

N-glycosylase/DNA lyase

Gene

PAE2237

Organism
Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 62 (01 Oct 2014)
      Sequence version 1 (01 Mar 2002)
      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.1 Publication

    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.1 Publication

    Temperature dependencei

    Highly thermostable. No decrease in activity was observed after heating 15 minutes at 80 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei31 – 3118-oxoguanine
    Binding sitei58 – 5818-oxoguanine; via carbonyl oxygen
    Binding sitei69 – 6918-oxoguanine
    Active sitei140 – 1401Schiff-base intermediate with DNA
    Binding sitei144 – 14418-oxoguanineSequence Analysis
    Binding sitei170 – 17018-oxoguanine; via carbonyl oxygen
    Active sitei172 – 1721Sequence Analysis
    Binding sitei218 – 21818-oxoguanine
    Binding sitei222 – 22218-oxoguanine

    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

    BioCyciPAER178306:GCEO-1610-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    N-glycosylase/DNA lyase
    Alternative name(s):
    8-oxoguanine DNA glycosylase (EC:3.2.2.-)
    AGOG
    DNA-(apurinic or apyrimidinic site) lyase (EC:4.2.99.18)
    Short name:
    AP lyase
    Pa-AGOG
    Gene namesi
    Ordered Locus Names:PAE2237
    OrganismiPyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
    Taxonomic identifieri178306 [NCBI]
    Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiThermoprotealesThermoproteaceaePyrobaculum
    ProteomesiUP000002439: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi140 – 1401K → Q: Loss of activity. 1 Publication
    Mutagenesisi147 – 1471K → Q: Great decrease in activity and thermostability. 1 Publication
    Mutagenesisi166 – 1661D → N: No effect. 1 Publication
    Mutagenesisi172 – 1721D → N: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 256256N-glycosylase/DNA lyasePRO_0000185112Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi178306.PAE2237.

    Structurei

    Secondary structure

    1
    256
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1412
    Helixi19 – 268
    Helixi30 – 4213
    Helixi44 – 5613
    Helixi65 – 7713
    Helixi84 – 9411
    Helixi102 – 11211
    Helixi122 – 13312
    Helixi140 – 15718
    Helixi173 – 1819
    Helixi189 – 1946
    Helixi196 – 21015
    Helixi214 – 22815
    Beta strandi235 – 2373
    Helixi239 – 2446

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1XQOX-ray1.03A1-256[»]
    1XQPX-ray1.69A1-256[»]
    ProteinModelPortaliQ8ZVK6.
    SMRiQ8ZVK6. Positions 2-254.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8ZVK6.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni125 – 18460Helix-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).1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG4047.
    HOGENOMiHOG000222574.
    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.

    Q8ZVK6-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAAESQLKRV IETLRRLGIE EVLKLERRDP QYRAVCNVVK RHGETVGSRL    50
    AMLNALISYR LTGKGEEHWE YFGKYFSQLE VIDLCRDFLK YIETSPFLKI 100
    GVEARKKRAL KACDYVPNLE DLGLTLRQLS HIVGARREQK TLVFTIKILN 150
    YAYMCSRGVN RVLPFDIPIP VDYRVARLTW CAGLIDFPPE EALRRYEAVQ 200
    KIWDAVARET GIPPLHLDTL LWLAGRAVLY GENLHGVPKE VIALFQWRGG 250
    CRPPSE 256
    Length:256
    Mass (Da):29,467
    Last modified:March 1, 2002 - v1
    Checksum:iE188433A957C9A16
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009441 Genomic DNA. Translation: AAL64050.1.
    RefSeqiNP_559868.1. NC_003364.1.
    WP_011008518.1. NC_003364.1.

    Genome annotation databases

    EnsemblBacteriaiAAL64050; AAL64050; PAE2237.
    GeneIDi1464384.
    KEGGipai:PAE2237.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009441 Genomic DNA. Translation: AAL64050.1 .
    RefSeqi NP_559868.1. NC_003364.1.
    WP_011008518.1. NC_003364.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1XQO X-ray 1.03 A 1-256 [» ]
    1XQP X-ray 1.69 A 1-256 [» ]
    ProteinModelPortali Q8ZVK6.
    SMRi Q8ZVK6. Positions 2-254.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 178306.PAE2237.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL64050 ; AAL64050 ; PAE2237 .
    GeneIDi 1464384.
    KEGGi pai:PAE2237.

    Phylogenomic databases

    eggNOGi COG4047.
    HOGENOMi HOG000222574.
    KOi K01741.
    OMAi VKMFGYA.

    Enzyme and pathway databases

    BioCyci PAER178306:GCEO-1610-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q8ZVK6.

    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. "Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum."
      Fitz-Gibbon S.T., Ladner H., Kim U.-J., Stetter K.O., Simon M.I., Miller J.H.
      Proc. Natl. Acad. Sci. U.S.A. 99:984-989(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827.
    2. "Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases."
      Sartori A.A., Lingaraju G.M., Hunziker P., Winkler F.K., Jiricny J.
      Nucleic Acids Res. 32:6531-6539(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF LYS-140; LYS-147; ASP-166 AND ASP-172.
    3. "A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure."
      Lingaraju G.M., Sartori A.A., Kostrewa D., Prota A.E., Jiricny J., Winkler F.K.
      Structure 13:87-98(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.0 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH 8-OXOGUANOSINE, DOMAIN.

    Entry informationi

    Entry nameiAGOG_PYRAE
    AccessioniPrimary (citable) accession number: Q8ZVK6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 10, 2006
    Last sequence update: March 1, 2002
    Last modified: October 1, 2014
    This is version 62 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3