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Q9D842

- APLF_MOUSE

UniProt

Q9D842 - APLF_MOUSE

Protein

Aprataxin and PNK-like factor

Gene

Aplf

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 99 (01 Oct 2014)
      Sequence version 2 (16 Aug 2005)
      Previous versions | rss
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    Functioni

    Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage 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.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei371 – 3711Poly-ADP-riboseBy similarity
    Binding sitei376 – 3761Poly-ADP-riboseBy similarity
    Binding sitei381 – 3811Poly-ADP-riboseBy similarity
    Binding sitei382 – 3821Poly-ADP-riboseBy similarity
    Binding sitei418 – 4181Poly-ADP-riboseBy similarity
    Binding sitei423 – 4231Poly-ADP-riboseBy similarity
    Binding sitei424 – 4241Poly-ADP-riboseBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri372 – 39322PBZ-type 1Add
    BLAST
    Zinc fingeri414 – 43522PBZ-type 2Add
    BLAST

    GO - Molecular functioni

    1. 3'-5' exonuclease activity Source: UniProtKB
    2. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB
    3. endodeoxyribonuclease activity Source: UniProtKB
    4. metal ion binding Source: UniProtKB-KW
    5. nucleotide binding Source: UniProtKB

    GO - Biological processi

    1. cellular response to DNA damage stimulus Source: UniProtKB
    2. DNA catabolic process, endonucleolytic Source: GOC
    3. double-strand break repair Source: UniProtKB
    4. nucleic acid phosphodiester bond hydrolysis Source: GOC
    5. regulation of isotype switching Source: MGI
    6. single strand break repair Source: UniProtKB

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    DNA damage, DNA repair

    Keywords - Ligandi

    Metal-binding, Nucleotide-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Aprataxin and PNK-like factor (EC:4.2.99.18)
    Alternative name(s):
    Apurinic-apyrimidinic endonuclease APLF
    Gene namesi
    Name:Aplf
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 6

    Organism-specific databases

    MGIiMGI:1919353. Aplf.

    Subcellular locationi

    Nucleus. Cytoplasmcytosol
    Note: Localizes to DNA damage sites. Accumulates at single-strand breaks and double-strand breaks via the PBZ-type zinc fingers By similarity.By similarity

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 499499Aprataxin and PNK-like factorPRO_0000089343Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei116 – 1161Phosphoserine; by ATMBy similarity

    Post-translational modificationi

    Poly-ADP-ribosylated. In addition to binding non covalently poly(ADP-ribose) via its PBZ-type zinc fingers, the protein is also covalently poly-ADP-ribosylated by PARP1 By similarity.By similarity
    Phosphorylated in an ATM-dependent manner upon double-strand DNA break.By similarity

    Keywords - PTMi

    ADP-ribosylation, Phosphoprotein

    Proteomic databases

    PRIDEiQ9D842.

    PTM databases

    PhosphoSiteiQ9D842.

    Expressioni

    Gene expression databases

    BgeeiQ9D842.
    GenevestigatoriQ9D842.

    Interactioni

    Subunit structurei

    Interacts with LIG4, PARP1, XRCC1, XRCC4 and XRCC5.By similarity

    Protein-protein interaction databases

    BioGridi215153. 1 interaction.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9D842.
    SMRiQ9D842. Positions 354-441.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 108108FHA-likeAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni401 – 41111Flexible linkerBy similarityAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi274 – 2774Poly-Ser
    Compositional biasi445 – 48541Asp-richAdd
    BLAST

    Domaini

    The PBZ-type zinc fingers (also named CYR) mediate non-covalent poly(ADP-ribose)-binding. Poly(ADP-ribose)-binding is dependent on the presence of zinc and promotes its recruitment to DNA damage sites By similarity.By similarity
    The FHA-like domain mediates interaction with XRCC1 and XRCC4.By similarity

    Sequence similaritiesi

    Belongs to the APLF family.Curated
    Contains 1 FHA-like domain.Curated
    Contains 2 PBZ-type zinc fingers.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri372 – 39322PBZ-type 1Add
    BLAST
    Zinc fingeri414 – 43522PBZ-type 2Add
    BLAST

    Keywords - Domaini

    Coiled coil, Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiNOG85452.
    GeneTreeiENSGT00390000010591.
    HOGENOMiHOG000033995.
    HOVERGENiHBG095728.
    InParanoidiQ9D842.
    KOiK13295.
    OMAiKRILPAW.
    OrthoDBiEOG73805W.
    PhylomeDBiQ9D842.
    TreeFamiTF326160.

    Family and domain databases

    Gene3Di2.60.200.20. 1 hit.
    InterProiIPR000253. FHA_dom.
    IPR008984. SMAD_FHA_domain.
    IPR019406. Znf_C2H2_APLF-like.
    [Graphical view]
    PfamiPF10283. zf-CCHH. 2 hits.
    [Graphical view]
    SUPFAMiSSF49879. SSF49879. 1 hit.

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9D842-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MPSDFFLQPL DGGPRVPVGP GQTVIGRGPL LGITDKRVSR RHAILEVVDS    50
    QLRIKPIHRN PCFYQSSEKS QHSPMETQVW SQLHPGDSFS LLLDKYAFRV 100
    FSAESEVEME CTLRNSQMLD EDDILSEMQK SPVVNLPDKT TGASQLQGSP 150
    EITKTKCPTI DPMSSSGECR AFSEHQPRPT QRKRILPAWM LAESLSDQSL 200
    STPAEGGDKD VIQRSGKAGT CEDRTPGNTS WHGKKRLSPS GNSKSVSAEQ 250
    DPGKKCRKAD QEGPGVSSEN VPESSSSNIV KDPDVDIVKT NKQKDGILIE 300
    ELGEVSKHKA ATKPTTNEEG ESCARVQSKS PPEKSQGCHP ESSSAPSSPD 350
    ALHTDTADPV LGCSEESKVR RTACMYGANC YRRNPLHFQH FSHPGDSDYG 400
    EVHGTDEGVI GDRPECPYGA SCYRKNPQHK MEYRHSALPA RVALDEDDDD 450
    VGQPSDDEDE EDYEPTDEDS DWHPGKDDEE QEDVDELLKE AKSSLHLKH 499
    Length:499
    Mass (Da):54,968
    Last modified:August 16, 2005 - v2
    Checksum:i4B41A9C0C8937963
    GO
    Isoform 2 (identifier: Q9D842-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-108: Missing.
         493-499: SSLHLKH → RFMRRKK

    Note: No experimental confirmation available.

    Show »
    Length:391
    Mass (Da):43,042
    Checksum:iD666D7635D0AFF78
    GO
    Isoform 3 (identifier: Q9D842-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-32: MPSDFFLQPLDGGPRVPVGPGQTVIGRGPLLG → MPSVPEGGGYE
         493-499: SSLHLKH → RFMRRKK

    Note: No experimental confirmation available.

    Show »
    Length:478
    Mass (Da):53,015
    Checksum:i44710524EAB5EFA4
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti178 – 1781R → H in AAH02179. (PubMed:15489334)Curated
    Sequence conflicti470 – 4701S → F in BAB25711. (PubMed:16141072)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 108108Missing in isoform 2. 1 PublicationVSP_014983Add
    BLAST
    Alternative sequencei1 – 3232MPSDF…GPLLG → MPSVPEGGGYE in isoform 3. 1 PublicationVSP_014982Add
    BLAST
    Alternative sequencei493 – 4997SSLHLKH → RFMRRKK in isoform 2 and isoform 3. 2 PublicationsVSP_014984

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK008513 mRNA. Translation: BAB25711.1.
    AK034191 mRNA. Translation: BAC28625.1.
    BC002179 mRNA. Translation: AAH02179.1.
    CCDSiCCDS20324.1. [Q9D842-3]
    CCDS51839.1. [Q9D842-1]
    RefSeqiNP_001163960.1. NM_001170489.1. [Q9D842-1]
    NP_077213.2. NM_024251.4. [Q9D842-3]
    UniGeneiMm.31770.

    Genome annotation databases

    EnsembliENSMUST00000032130; ENSMUSP00000032130; ENSMUSG00000030051. [Q9D842-1]
    ENSMUST00000065997; ENSMUSP00000066232; ENSMUSG00000030051. [Q9D842-3]
    GeneIDi72103.
    KEGGimmu:72103.
    UCSCiuc009ctq.2. mouse. [Q9D842-3]
    uc009ctr.2. mouse. [Q9D842-1]
    uc012eon.1. mouse. [Q9D842-2]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK008513 mRNA. Translation: BAB25711.1 .
    AK034191 mRNA. Translation: BAC28625.1 .
    BC002179 mRNA. Translation: AAH02179.1 .
    CCDSi CCDS20324.1. [Q9D842-3 ]
    CCDS51839.1. [Q9D842-1 ]
    RefSeqi NP_001163960.1. NM_001170489.1. [Q9D842-1 ]
    NP_077213.2. NM_024251.4. [Q9D842-3 ]
    UniGenei Mm.31770.

    3D structure databases

    ProteinModelPortali Q9D842.
    SMRi Q9D842. Positions 354-441.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 215153. 1 interaction.

    PTM databases

    PhosphoSitei Q9D842.

    Proteomic databases

    PRIDEi Q9D842.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000032130 ; ENSMUSP00000032130 ; ENSMUSG00000030051 . [Q9D842-1 ]
    ENSMUST00000065997 ; ENSMUSP00000066232 ; ENSMUSG00000030051 . [Q9D842-3 ]
    GeneIDi 72103.
    KEGGi mmu:72103.
    UCSCi uc009ctq.2. mouse. [Q9D842-3 ]
    uc009ctr.2. mouse. [Q9D842-1 ]
    uc012eon.1. mouse. [Q9D842-2 ]

    Organism-specific databases

    CTDi 200558.
    MGIi MGI:1919353. Aplf.

    Phylogenomic databases

    eggNOGi NOG85452.
    GeneTreei ENSGT00390000010591.
    HOGENOMi HOG000033995.
    HOVERGENi HBG095728.
    InParanoidi Q9D842.
    KOi K13295.
    OMAi KRILPAW.
    OrthoDBi EOG73805W.
    PhylomeDBi Q9D842.
    TreeFami TF326160.

    Miscellaneous databases

    NextBioi 335444.
    PROi Q9D842.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q9D842.
    Genevestigatori Q9D842.

    Family and domain databases

    Gene3Di 2.60.200.20. 1 hit.
    InterProi IPR000253. FHA_dom.
    IPR008984. SMAD_FHA_domain.
    IPR019406. Znf_C2H2_APLF-like.
    [Graphical view ]
    Pfami PF10283. zf-CCHH. 2 hits.
    [Graphical view ]
    SUPFAMi SSF49879. SSF49879. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
      Strain: C57BL/6J.
      Tissue: Diencephalon and Small intestine.
    2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Strain: FVB/N.
      Tissue: Mammary gland.

    Entry informationi

    Entry nameiAPLF_MOUSE
    AccessioniPrimary (citable) accession number: Q9D842
    Secondary accession number(s): Q8BZL5, Q99LX6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 16, 2005
    Last sequence update: August 16, 2005
    Last modified: October 1, 2014
    This is version 99 of the entry and version 2 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. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3