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P51173

- APEA_DICDI

UniProt

P51173 - APEA_DICDI

Protein

DNA-(apurinic or apyrimidinic site) lyase

Gene

apeA

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 96 (01 Oct 2014)
      Sequence version 2 (04 Dec 2007)
      Previous versions | rss
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    Functioni

    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.PROSITE-ProRule annotation

    Cofactori

    Magnesium. Can also utilize manganese. Probably binds two magnesium or manganese ions per subunit By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi139 – 1391Magnesium 1By similarity
    Active sitei211 – 2111By similarity
    Active sitei252 – 2521Proton donor/acceptorBy similarity
    Metal bindingi252 – 2521Magnesium 2By similarity
    Metal bindingi254 – 2541Magnesium 2By similarity
    Sitei254 – 2541Transition state stabilizerBy similarity
    Sitei324 – 3241Important for catalytic activityBy similarity
    Metal bindingi350 – 3501Magnesium 1By similarity
    Sitei351 – 3511Interaction with DNA substrateBy similarity

    GO - Molecular functioni

    1. DNA-(apurinic or apyrimidinic site) lyase activity Source: RefGenome
    2. DNA binding Source: InterPro
    3. double-stranded DNA 3'-5' exodeoxyribonuclease activity Source: RefGenome
    4. endodeoxyribonuclease activity, producing 3'-phosphomonoesters Source: dictyBase
    5. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. base-excision repair Source: dictyBase
    2. DNA catabolic process, endonucleolytic Source: GOC
    3. DNA catabolic process, exonucleolytic Source: GOC

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    DNA damage, DNA repair

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    ReactomeiREACT_202785. Displacement of DNA glycosylase by APE1.
    REACT_215768. Base-free sugar-phosphate removal via the single-nucleotide replacement pathway.
    REACT_223018. Removal of DNA patch containing abasic residue.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA-(apurinic or apyrimidinic site) lyase (EC:4.2.99.18)
    Alternative name(s):
    Class II apurinic/apyrimidinic(AP)-endonuclease
    Gene namesi
    Name:apeA
    ORF Names:DDB_G0277701
    OrganismiDictyostelium discoideum (Slime mold)
    Taxonomic identifieri44689 [NCBI]
    Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
    ProteomesiUP000002195: Chromosome 2, UP000002195: Unassembled WGS sequence

    Organism-specific databases

    dictyBaseiDDB_G0277701. apeA.

    Subcellular locationi

    Nucleus PROSITE-ProRule annotation

    GO - Cellular componenti

    1. nucleus Source: RefGenome

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 361361DNA-(apurinic or apyrimidinic site) lyasePRO_0000200016Add
    BLAST

    Expressioni

    Inductioni

    By DNA-damaging agents including UV, MNNG, gamma rays, bleomycin and streptozotocin.

    Interactioni

    Protein-protein interaction databases

    STRINGi44689.DDB_0185018.

    Structurei

    3D structure databases

    ProteinModelPortaliP51173.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi41 – 444Nuclear localization signalSequence Analysis

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi27 – 3913Poly-GluAdd
    BLAST
    Compositional biasi70 – 8011Poly-GluAdd
    BLAST

    Sequence similaritiesi

    Belongs to the DNA repair enzymes AP/ExoA family.Curated

    Phylogenomic databases

    eggNOGiCOG0708.
    KOiK10771.
    OMAiGWRIDYY.
    PhylomeDBiP51173.

    Family and domain databases

    Gene3Di3.60.10.10. 1 hit.
    InterProiIPR004808. AP_endonuc_1.
    IPR020847. AP_endonuclease_F1_BS.
    IPR020848. AP_endonuclease_F1_CS.
    IPR005135. Endo/exonuclease/phosphatase.
    [Graphical view]
    PANTHERiPTHR22748. PTHR22748. 1 hit.
    PfamiPF03372. Exo_endo_phos. 1 hit.
    [Graphical view]
    SUPFAMiSSF56219. SSF56219. 1 hit.
    TIGRFAMsiTIGR00633. xth. 1 hit.
    PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
    PS00727. AP_NUCLEASE_F1_2. 1 hit.
    PS00728. AP_NUCLEASE_F1_3. 1 hit.
    PS51435. AP_NUCLEASE_F1_4. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P51173-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTSRTKKLKM DEEEILKKED GSETTSEEEK EEVEEEEEED KKRKLVKKTP    50
    AKKAPAKKAA AKKKSKDEDE DEEEKEEEEE TNKTTASVSI AIDNLDEPKV 100
    EENQMKIISW NVAGFKSVLS KGFTEYVEKE NPDVLCLQET KINPSNIKKD 150
    QMPKGYEYHF IEADQKGHHG TGVLTKKKPN AITFGIGIAK HDNEGRVITL 200
    EYDQFYIVNT YIPNAGTRGL QRLDYRIKEW DVDFQAYLEK LNATKPIIWC 250
    GDLNVAHTEI DLKNPKTNKK SAGFTIEERT SFSNFLEKGY VDSYRHFNPG 300
    KEGSYTFWSY LGGGRSKNVG WRLDYFVVSK RLMDSIKISP FHRTSVMGSD 350
    HCPIGVVVDL N 361
    Length:361
    Mass (Da):41,327
    Last modified:December 4, 2007 - v2
    Checksum:iBBD46E1CE3B5135A
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti126 – 1261Y → C in AAC47024. (PubMed:8657579)Curated
    Sequence conflicti203 – 2031D → V in AAC47024. (PubMed:8657579)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U31631 Genomic DNA. Translation: AAC47024.1.
    AAFI02000021 Genomic DNA. Translation: EAL68586.1.
    PIRiS68268.
    RefSeqiXP_642518.1. XM_637426.1.

    Genome annotation databases

    EnsemblProtistsiDDB0185018; DDB0185018; DDB_G0277701.
    GeneIDi8621167.
    KEGGiddi:DDB_G0277701.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U31631 Genomic DNA. Translation: AAC47024.1 .
    AAFI02000021 Genomic DNA. Translation: EAL68586.1 .
    PIRi S68268.
    RefSeqi XP_642518.1. XM_637426.1.

    3D structure databases

    ProteinModelPortali P51173.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 44689.DDB_0185018.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblProtistsi DDB0185018 ; DDB0185018 ; DDB_G0277701 .
    GeneIDi 8621167.
    KEGGi ddi:DDB_G0277701.

    Organism-specific databases

    dictyBasei DDB_G0277701. apeA.

    Phylogenomic databases

    eggNOGi COG0708.
    KOi K10771.
    OMAi GWRIDYY.
    PhylomeDBi P51173.

    Enzyme and pathway databases

    Reactomei REACT_202785. Displacement of DNA glycosylase by APE1.
    REACT_215768. Base-free sugar-phosphate removal via the single-nucleotide replacement pathway.
    REACT_223018. Removal of DNA patch containing abasic residue.

    Miscellaneous databases

    PROi P51173.

    Family and domain databases

    Gene3Di 3.60.10.10. 1 hit.
    InterProi IPR004808. AP_endonuc_1.
    IPR020847. AP_endonuclease_F1_BS.
    IPR020848. AP_endonuclease_F1_CS.
    IPR005135. Endo/exonuclease/phosphatase.
    [Graphical view ]
    PANTHERi PTHR22748. PTHR22748. 1 hit.
    Pfami PF03372. Exo_endo_phos. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56219. SSF56219. 1 hit.
    TIGRFAMsi TIGR00633. xth. 1 hit.
    PROSITEi PS00726. AP_NUCLEASE_F1_1. 1 hit.
    PS00727. AP_NUCLEASE_F1_2. 1 hit.
    PS00728. AP_NUCLEASE_F1_3. 1 hit.
    PS51435. AP_NUCLEASE_F1_4. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Apurinic/apyrimidinic (AP) endonuclease from Dictyostelium discoideum: cloning, nucleotide sequence and induction by sublethal levels of DNA damaging agents."
      Freeland T.M., Guyer R.B., Ling A.Z., Deering R.A.
      Nucleic Acids Res. 24:1950-1953(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AX4.
    3. "The genome of the social amoeba Dictyostelium discoideum."
      Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
      , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
      Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AX4.

    Entry informationi

    Entry nameiAPEA_DICDI
    AccessioniPrimary (citable) accession number: P51173
    Secondary accession number(s): Q54Z97, Q75K06
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: December 4, 2007
    Last modified: October 1, 2014
    This is version 96 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Dictyostelium discoideum
      Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3