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Q5E9N9

- APEX2_BOVIN

UniProt

Q5E9N9 - APEX2_BOVIN

Protein

DNA-(apurinic or apyrimidinic site) lyase 2

Gene

APEX2

Organism
Bos taurus (Bovine)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 64 (01 Oct 2014)
      Sequence version 1 (15 Mar 2005)
      Previous versions | rss
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    Functioni

    Function as a weak 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. Displays also double-stranded DNA 3'-5' exonuclease, 3'-phosphodiesterase activities. Shows robust 3'-5' exonuclease activity on 3'-recessed heteroduplex DNA and is able to remove mismatched nucleotides preferentially. Shows fairly strong 3'-phosphodiesterase activity involved in the removal of 3'-damaged termini formed in DNA by oxidative agents. In the nucleus functions in the PCNA-dependent BER pathway. Required for somatic hypermutation (SHM) and DNA cleavage step of class switch recombination (CSR) of immunoglobulin genes. Required for proper cell cycle progression during proliferation of peripheral lymphocytes By similarity.By similarity

    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

    Enzyme regulationi

    3'-5' exonuclease activity is activated by sodium and manganese. 3'-5' exonuclease and 3'-phosphodiesterase activities are stimulated in presence of PCNA By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi8 – 81Magnesium 1By similarity
    Metal bindingi48 – 481Magnesium 1By similarity
    Active sitei156 – 1561By similarity
    Active sitei197 – 1971Proton donor/acceptorBy similarity
    Metal bindingi197 – 1971Magnesium 2By similarity
    Metal bindingi199 – 1991Magnesium 2By similarity
    Sitei199 – 1991Transition state stabilizerBy similarity
    Sitei277 – 2771Important for catalytic activityBy similarity
    Metal bindingi303 – 3031Magnesium 1By similarity
    Sitei304 – 3041Interaction with DNA substrateBy similarity

    GO - Molecular functioni

    1. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB-EC
    2. DNA binding Source: UniProtKB-KW
    3. exonuclease activity Source: UniProtKB-KW
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. cell cycle Source: UniProtKB-KW
    2. DNA recombination Source: UniProtKB-KW
    3. DNA repair Source: UniProtKB-KW

    Keywords - Molecular functioni

    Endonuclease, Exonuclease, Hydrolase, Lyase, Nuclease

    Keywords - Biological processi

    Cell cycle, DNA damage, DNA recombination, DNA repair

    Keywords - Ligandi

    DNA-binding, Magnesium, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA-(apurinic or apyrimidinic site) lyase 2 (EC:3.1.-.-, EC:4.2.99.18)
    Alternative name(s):
    APEX nuclease 2
    Apurinic-apyrimidinic endonuclease 2
    Short name:
    AP endonuclease 2
    Gene namesi
    Name:APEX2
    OrganismiBos taurus (Bovine)
    Taxonomic identifieri9913 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
    ProteomesiUP000009136: Unplaced

    Subcellular locationi

    Nucleus PROSITE-ProRule annotation. Cytoplasm PROSITE-ProRule annotation. Mitochondrion By similarity
    Note: Together with PCNA, is redistributed in discrete nuclear foci in presence of oxidative DNA damaging agents.By similarity

    GO - Cellular componenti

    1. mitochondrion Source: UniProtKB-SubCell
    2. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Mitochondrion, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 514514DNA-(apurinic or apyrimidinic site) lyase 2PRO_0000200013Add
    BLAST

    Proteomic databases

    PRIDEiQ5E9N9.

    Interactioni

    Subunit structurei

    Interacts with PCNA; this interaction is triggered by reactive oxygen species and increased by misincorporation of uracil in nuclear DNA.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ5E9N9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni390 – 3978Required for the colocalization with PCNA in nuclear foci in presence of oxidative-induced DNA damaging agentsBy similarity

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0708.
    HOGENOMiHOG000231386.
    HOVERGENiHBG054715.
    InParanoidiQ5E9N9.
    KOiK10772.

    Family and domain databases

    Gene3Di3.60.10.10. 1 hit.
    InterProiIPR004808. AP_endonuc_1.
    IPR020847. AP_endonuclease_F1_BS.
    IPR005135. Endo/exonuclease/phosphatase.
    IPR010666. Znf_GRF.
    [Graphical view]
    PANTHERiPTHR22748. PTHR22748. 1 hit.
    PfamiPF03372. Exo_endo_phos. 1 hit.
    PF06839. zf-GRF. 1 hit.
    [Graphical view]
    SUPFAMiSSF56219. SSF56219. 1 hit.
    TIGRFAMsiTIGR00633. xth. 1 hit.
    PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
    PS51435. AP_NUCLEASE_F1_4. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q5E9N9-1 [UniParc]FASTAAdd to Basket

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    MLRLVSWNIN GIRSPLQGVR CEEPSSCSAM AMGRILDKLD ADIVCLQETK    50
    VTRDVLTEPL AIIEGYNSYF SFSRNRSGYS GVATFCKDSA TPVAAEEGLS 100
    GLLSTQNGDV GCYGNMDDFT QEELRALDSE GRALLTQHKI CTWEGKEKTL 150
    TLINVYCPHA DPGKPERLTF KMRFYRLLQI RAEALLAAGS HVIILGDLNT 200
    AHRPIDHWDA VNMECFEEDP GRKWMDGLLS NLGCESGSHM GPFIDSYRCF 250
    QPKQKGAFTC WSTVSGARHL NYGSRLDYVL GDRTLVIDTF QSSFLLPEVM 300
    GSDHCPVGAV LSVSSVPAKQ CPPLCTCFLP EFAGTQLKIL RFLVHFKQDP 350
    VFKQSALQPS NQTQVHMRKN KARVRSTRSR PSKTGSSRGQ KNLMSYFQPS 400
    SSGPQTSNLD LPSLGTLITP KTSEEDVMAN VVEGQTKASE AKDEKEIRTS 450
    FWKSLLGGPS PMPLCGGHRE PCVMRTVKKP GPNLGRHFYM CARPQGPPTD 500
    PSSRCNFFLW SRPS 514
    Length:514
    Mass (Da):56,938
    Last modified:March 15, 2005 - v1
    Checksum:iD22E64035623C993
    GO

    Sequence cautioni

    The sequence AAX46554.1 differs from that shown. Reason: Frameshift at position 392.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti369 – 3691K → Q in AAX46554. (PubMed:16305752)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BT020881 mRNA. Translation: AAX08898.1.
    BT021707 mRNA. Translation: AAX46554.1. Frameshift.
    RefSeqiNP_001015577.1. NM_001015577.1.
    UniGeneiBt.1184.

    Genome annotation databases

    GeneIDi511790.
    KEGGibta:511790.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BT020881 mRNA. Translation: AAX08898.1 .
    BT021707 mRNA. Translation: AAX46554.1 . Frameshift.
    RefSeqi NP_001015577.1. NM_001015577.1.
    UniGenei Bt.1184.

    3D structure databases

    ProteinModelPortali Q5E9N9.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi Q5E9N9.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 511790.
    KEGGi bta:511790.

    Organism-specific databases

    CTDi 27301.

    Phylogenomic databases

    eggNOGi COG0708.
    HOGENOMi HOG000231386.
    HOVERGENi HBG054715.
    InParanoidi Q5E9N9.
    KOi K10772.

    Miscellaneous databases

    NextBioi 20870098.

    Family and domain databases

    Gene3Di 3.60.10.10. 1 hit.
    InterProi IPR004808. AP_endonuc_1.
    IPR020847. AP_endonuclease_F1_BS.
    IPR005135. Endo/exonuclease/phosphatase.
    IPR010666. Znf_GRF.
    [Graphical view ]
    PANTHERi PTHR22748. PTHR22748. 1 hit.
    Pfami PF03372. Exo_endo_phos. 1 hit.
    PF06839. zf-GRF. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56219. SSF56219. 1 hit.
    TIGRFAMsi TIGR00633. xth. 1 hit.
    PROSITEi PS00726. AP_NUCLEASE_F1_1. 1 hit.
    PS51435. AP_NUCLEASE_F1_4. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

    Entry informationi

    Entry nameiAPEX2_BOVIN
    AccessioniPrimary (citable) accession number: Q5E9N9
    Secondary accession number(s): Q58D90
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 30, 2005
    Last sequence update: March 15, 2005
    Last modified: October 1, 2014
    This is version 64 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

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3