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A0MTA1

- APEX1_DANRE

UniProt

A0MTA1 - APEX1_DANRE

Protein

DNA-(apurinic or apyrimidinic site) lyase

Gene

apex1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 59 (01 Oct 2014)
      Sequence version 1 (12 Dec 2006)
      Previous versions | rss
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    Functioni

    Function as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. Required for passage through the midblastula transition MBT. May also acts as a endoribonuclease involved in the control of single-stranded RNA metabolism. Has no redox activity. Binds DNA and RNA.2 Publications

    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 bindingi63 – 631Magnesium 1By similarity
    Metal bindingi89 – 891Magnesium 1By similarity
    Active sitei164 – 1641By similarity
    Active sitei203 – 2031Proton donor/acceptorBy similarity
    Metal bindingi203 – 2031Magnesium 2By similarity
    Metal bindingi205 – 2051Magnesium 2By similarity
    Sitei205 – 2051Transition state stabilizerBy similarity
    Sitei275 – 2751Important for catalytic activityBy similarity
    Metal bindingi300 – 3001Magnesium 1By similarity
    Sitei301 – 3011Interaction with DNA substrateBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

    1. base-excision repair Source: RefGenome
    2. DNA catabolic process, endonucleolytic Source: GOC
    3. DNA catabolic process, exonucleolytic Source: GOC
    4. DNA demethylation Source: UniProtKB
    5. heart contraction Source: ZFIN
    6. heart looping Source: ZFIN
    7. negative regulation of apoptotic process Source: ZFIN
    8. positive regulation of gene expression Source: ZFIN

    Keywords - Molecular functioni

    Endonuclease, Hydrolase, Lyase, Nuclease

    Keywords - Biological processi

    DNA damage, DNA repair

    Keywords - Ligandi

    DNA-binding, Magnesium, Metal-binding, RNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA-(apurinic or apyrimidinic site) lyase (EC:3.1.-.-, EC:4.2.99.18)
    Alternative name(s):
    APEX nuclease
    Short name:
    APEN
    Apurinic-apyrimidinic endonuclease 1
    Short name:
    AP endonuclease 1
    Short name:
    zAP1
    Gene namesi
    Name:apex1
    Synonyms:apex1a, apex1b
    ORF Names:si:ch211-214j24.12, zgc:66204
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Unplaced

    Organism-specific databases

    ZFINiZDB-GENE-040426-2761. apex1.

    Subcellular locationi

    Nucleus PROSITE-ProRule annotation. Nucleusnucleolus By similarity. Nucleus speckle PROSITE-ProRule annotation. Endoplasmic reticulum By similarity. Cytoplasm PROSITE-ProRule annotation. Mitochondrion By similarity

    GO - Cellular componenti

    1. endoplasmic reticulum Source: UniProtKB-SubCell
    2. mitochondrion Source: UniProtKB-SubCell
    3. nuclear speck Source: UniProtKB-SubCell
    4. nucleolus Source: UniProtKB-SubCell
    5. nucleus Source: RefGenome

    Keywords - Cellular componenti

    Cytoplasm, Endoplasmic reticulum, Mitochondrion, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi58 – 581T → C: Confers redox activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 310310DNA-(apurinic or apyrimidinic site) lyasePRO_0000402575Add
    BLAST

    Proteomic databases

    PRIDEiA0MTA1.

    Expressioni

    Developmental stagei

    Expressed in unfertilized eggs and embryos at two stages (at protein level). Expressed throughout embryogenesis.1 Publication

    Gene expression databases

    BgeeiA0MTA1.

    Interactioni

    Protein-protein interaction databases

    STRINGi7955.ENSDARP00000067373.

    Structurei

    Secondary structure

    1
    310
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi55 – 617
    Helixi65 – 706
    Helixi73 – 808
    Beta strandi83 – 886
    Helixi94 – 963
    Helixi99 – 1024
    Beta strandi108 – 1136
    Beta strandi124 – 1307
    Beta strandi133 – 1386
    Turni142 – 1465
    Beta strandi150 – 1545
    Beta strandi159 – 1646
    Helixi170 – 1723
    Helixi175 – 19521
    Beta strandi198 – 2036
    Helixi210 – 2123
    Helixi216 – 2194
    Helixi227 – 23812
    Beta strandi241 – 2433
    Helixi244 – 2485
    Helixi262 – 2643
    Helixi265 – 2684
    Beta strandi275 – 2806
    Helixi281 – 2866
    Beta strandi287 – 2926
    Beta strandi298 – 3014
    Beta strandi304 – 3085

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2O3CX-ray2.30A/B/C33-310[»]
    ProteinModelPortaliA0MTA1.
    SMRiA0MTA1. Positions 33-310.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiA0MTA1.

    Family & Domainsi

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0708.
    HOGENOMiHOG000034586.
    HOVERGENiHBG050531.
    InParanoidiQ7SXL6.
    KOiK10771.
    PhylomeDBiA0MTA1.
    TreeFamiTF315048.

    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.
    PS00728. AP_NUCLEASE_F1_3. 1 hit.
    PS51435. AP_NUCLEASE_F1_4. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    A0MTA1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPKRAKKNEE GVDGEADNGT AAAKKEKKGK EPEAPILYED PPEKLTSKDG    50
    RAANMKITSW NVDGLRAWVK KNGLDWVRKE DPDILCLQET KCAEKALPAD 100
    ITGMPEYPHK YWAGSEDKEG YSGVAMLCKT EPLNVTYGIG KEEHDKEGRV 150
    ITAEFPDFFL VTAYVPNASR GLVRLDYRKT WDVDFRAYLC GLDARKPLVL 200
    CGDLNVAHQE IDLKNPKGNR KNAGFTPEER EGFTQLLEAG FTDSFRELYP 250
    DQAYAYTFWT YMMNARSKNV GWRLDYFVLS SALLPGLCDS KIRNTAMGSD 300
    HCPITLFLAV 310
    Length:310
    Mass (Da):34,881
    Last modified:December 12, 2006 - v1
    Checksum:iF57493D443106F4B
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti16 – 161A → S in CAI11781. (PubMed:23594743)Curated
    Sequence conflicti80 – 9314Missing in AAI64240. 1 PublicationCuratedAdd
    BLAST
    Sequence conflicti80 – 9314Missing in AAH97053. 1 PublicationCuratedAdd
    BLAST
    Sequence conflicti103 – 1031G → A in AAH55545. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    EF041101 mRNA. Translation: ABK35081.1.
    EF041102 mRNA. Translation: ABK35082.1.
    EF041103 Genomic DNA. Translation: ABK35083.1.
    EF041104 Genomic DNA. Translation: ABK35084.1.
    BX323558 Genomic DNA. Translation: CAI11781.1.
    BC055545 mRNA. Translation: AAH55545.1.
    BC097053 mRNA. Translation: AAH97053.1.
    BC164240 mRNA. Translation: AAI64240.1.
    RefSeqiNP_998586.1. NM_213421.1.
    UniGeneiDr.20170.

    Genome annotation databases

    GeneIDi406730.
    KEGGidre:406730.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    EF041101 mRNA. Translation: ABK35081.1 .
    EF041102 mRNA. Translation: ABK35082.1 .
    EF041103 Genomic DNA. Translation: ABK35083.1 .
    EF041104 Genomic DNA. Translation: ABK35084.1 .
    BX323558 Genomic DNA. Translation: CAI11781.1 .
    BC055545 mRNA. Translation: AAH55545.1 .
    BC097053 mRNA. Translation: AAH97053.1 .
    BC164240 mRNA. Translation: AAI64240.1 .
    RefSeqi NP_998586.1. NM_213421.1.
    UniGenei Dr.20170.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2O3C X-ray 2.30 A/B/C 33-310 [» ]
    ProteinModelPortali A0MTA1.
    SMRi A0MTA1. Positions 33-310.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 7955.ENSDARP00000067373.

    Proteomic databases

    PRIDEi A0MTA1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 406730.
    KEGGi dre:406730.

    Organism-specific databases

    CTDi 328.
    ZFINi ZDB-GENE-040426-2761. apex1.

    Phylogenomic databases

    eggNOGi COG0708.
    HOGENOMi HOG000034586.
    HOVERGENi HBG050531.
    InParanoidi Q7SXL6.
    KOi K10771.
    PhylomeDBi A0MTA1.
    TreeFami TF315048.

    Miscellaneous databases

    EvolutionaryTracei A0MTA1.
    NextBioi 20818249.
    PROi A0MTA1.

    Gene expression databases

    Bgeei A0MTA1.

    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.
    PS00728. AP_NUCLEASE_F1_3. 1 hit.
    PS51435. AP_NUCLEASE_F1_4. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "DNA repair protein involved in heart and blood development."
      Wang Y., Shupenko C.C., Melo L.F., Strauss P.R.
      Mol. Cell. Biol. 26:9083-9093(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, DEVELOPMENTAL STAGE.
      Tissue: Embryo.
    2. "The zebrafish reference genome sequence and its relationship to the human genome."
      Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
      , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
      Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Tuebingen.
    3. NIH - Zebrafish Gene Collection (ZGC) project
      Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Olfactory epithelium.
    4. "Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease."
      Georgiadis M.M., Luo M., Gaur R.K., Delaplane S., Li X., Kelley M.R.
      Mutat. Res. 643:54-63(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 33-310, FUNCTION, MUTAGENESIS OF THR-58.

    Entry informationi

    Entry nameiAPEX1_DANRE
    AccessioniPrimary (citable) accession number: A0MTA1
    Secondary accession number(s): Q4V955, Q5RHZ7, Q7SXL6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 11, 2011
    Last sequence update: December 12, 2006
    Last modified: October 1, 2014
    This is version 59 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata 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