ID APLF_MOUSE Reviewed; 499 AA. AC Q9D842; Q8BZL5; Q99LX6; DT 16-AUG-2005, integrated into UniProtKB/Swiss-Prot. DT 16-AUG-2005, sequence version 2. DT 24-JAN-2024, entry version 150. DE RecName: Full=Aprataxin and PNK-like factor; DE EC=3.1.-.- {ECO:0000250|UniProtKB:Q8IW19}; DE AltName: Full=Apurinic-apyrimidinic endonuclease APLF; GN Name=Aplf; OS Mus musculus (Mouse). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; OC Murinae; Mus; Mus. OX NCBI_TaxID=10090; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3). RC STRAIN=C57BL/6J; TISSUE=Diencephalon, and Small intestine; RX PubMed=16141072; DOI=10.1126/science.1112014; RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J., RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.; RT "The transcriptional landscape of the mammalian genome."; RL Science 309:1559-1563(2005). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). RC STRAIN=FVB/N; TISSUE=Mammary gland; RX PubMed=15489334; DOI=10.1101/gr.2596504; RG The MGC Project Team; RT "The status, quality, and expansion of the NIH full-length cDNA project: RT the Mammalian Gene Collection (MGC)."; RL Genome Res. 14:2121-2127(2004). RN [3] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-149, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Brain, Pancreas, Spleen, and Testis; RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001; RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R., RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.; RT "A tissue-specific atlas of mouse protein phosphorylation and expression."; RL Cell 143:1174-1189(2010). RN [4] RP FUNCTION. RX PubMed=21211721; DOI=10.1016/j.molcel.2010.12.006; RA Rulten S.L., Fisher A.E., Robert I., Zuma M.C., Rouleau M., Ju L., RA Poirier G., Reina-San-Martin B., Caldecott K.W.; RT "PARP-3 and APLF function together to accelerate nonhomologous end- RT joining."; RL Mol. Cell 41:33-45(2011). RN [5] RP FUNCTION. RX PubMed=27875275; DOI=10.1242/jcs.194035; RA Syed K.M., Joseph S., Mukherjee A., Majumder A., Teixeira J.M., Dutta D., RA Pillai M.R.; RT "Histone chaperone APLF regulates induction of pluripotency in murine RT fibroblasts."; RL J. Cell Sci. 129:4576-4591(2016). RN [6] RP FUNCTION, SUBCELLULAR LOCATION, AND DEVELOPMENTAL STAGE. RX PubMed=33277378; DOI=10.1242/jcs.246900; RA Varghese P.C., Rajam S.M., Nandy D., Jory A., Mukherjee A., Dutta D.; RT "Histone chaperone APLF level dictates the implantation of mouse embryos."; RL J. Cell Sci. 134:0-0(2021). CC -!- FUNCTION: Histone chaperone involved in single-strand and double-strand CC DNA break repair (By similarity). Recruited to sites of DNA damage CC through interaction with branched poly-ADP-ribose chains, a polymeric CC post-translational modification synthesized transiently at sites of CC chromosomal damage to accelerate DNA strand break repair reactions (By CC similarity). Following recruitment to DNA damage sites, acts as a CC histone chaperone that mediates histone eviction during DNA repair and CC promotes recruitment of histone variant MACROH2A1 (PubMed:27875275). CC Also has a nuclease activity: displays apurinic-apyrimidinic (AP) CC endonuclease and 3'-5' exonuclease activities in vitro (By similarity). CC Also able to introduce nicks at hydroxyuracil and other types of CC pyrimidine base damage (By similarity). Together with PARP3, promotes CC the retention of the LIG4-XRCC4 complex on chromatin and accelerate DNA CC ligation during non-homologous end-joining (NHEJ) (PubMed:21211721). CC Also acts as a negative regulator of cell pluripotency by promoting CC histone exchange (PubMed:27875275). Required for the embryo CC implantation during the epithelial to mesenchymal transition in females CC (PubMed:33277378). {ECO:0000250|UniProtKB:Q8IW19, CC ECO:0000269|PubMed:21211721, ECO:0000269|PubMed:27875275, CC ECO:0000269|PubMed:33277378}. CC -!- SUBUNIT: Interacts with LIG4 (By similarity). Interacts with PARP1 (By CC similarity). Interacts with XRCC4. Interacts (via KBM motif) with XRCC5 CC and XRCC6; promoting recruitment to DNA damage sites (By similarity). CC Interacts with XRCC1 (By similarity). Interacts (via C-terminal CC disordered region) with histones; interacts with histone H2A, H2B and CC H3-H4 (By similarity). {ECO:0000250|UniProtKB:Q8IW19}. CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:33277378}. Chromosome CC {ECO:0000250|UniProtKB:Q8IW19}. Cytoplasm, cytosol CC {ECO:0000269|PubMed:33277378}. Note=Localizes to DNA damage sites. CC Accumulates at single-strand breaks and double-strand breaks via the CC PBZ-type zinc fingers. {ECO:0000250|UniProtKB:Q8IW19}. CC -!- ALTERNATIVE PRODUCTS: CC Event=Alternative splicing; Named isoforms=3; CC Name=1; CC IsoId=Q9D842-1; Sequence=Displayed; CC Name=2; CC IsoId=Q9D842-2; Sequence=VSP_014983, VSP_014984; CC Name=3; CC IsoId=Q9D842-3; Sequence=VSP_014982, VSP_014984; CC -!- DEVELOPMENTAL STAGE: Present in the 4-cell stage (PubMed:33277378). CC Expression is enhanced in early morula and late morula stage embryos CC (PubMed:33277378). Down-regulated during the first differentiation to CC form inner cell mass and trophectoderm within a blastocyst (32-cell CC stage) (PubMed:33277378). {ECO:0000269|PubMed:33277378}. CC -!- DOMAIN: The PBZ-type zinc fingers (also named CYR) mediate non-covalent CC poly-ADP-ribose-binding. Specifically recognizes branched poly-ADP- CC ribose chains generated by PARP2. Poly-ADP-ribose-binding is dependent CC on the presence of zinc and promotes its recruitment to DNA damage CC sites. {ECO:0000250|UniProtKB:Q8IW19}. CC -!- DOMAIN: The KBM (Ku-binding motif) mediates interaction with XRCC5/Ku80 CC and XRCC6/Ku70 and recruitment to DNA damage sites. CC {ECO:0000250|UniProtKB:Q8IW19}. CC -!- DOMAIN: The FHA-like domain mediates interaction with XRCC1 and XRCC4. CC {ECO:0000250|UniProtKB:Q8IW19}. CC -!- DOMAIN: The NAP1L motif is required for the histone chaperone activity. CC {ECO:0000250|UniProtKB:Q8IW19}. CC -!- PTM: Poly-ADP-ribosylated. In addition to binding non covalently poly- CC ADP-ribose via its PBZ-type zinc fingers, the protein is also CC covalently poly-ADP-ribosylated by PARP1. CC {ECO:0000250|UniProtKB:Q8IW19}. CC -!- PTM: Phosphorylated in an ATM-dependent manner upon double-strand DNA CC break. {ECO:0000250|UniProtKB:Q8IW19}. CC -!- SIMILARITY: Belongs to the APLF family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AK008513; BAB25711.1; -; mRNA. DR EMBL; AK034191; BAC28625.1; -; mRNA. DR EMBL; BC002179; AAH02179.1; -; mRNA. DR CCDS; CCDS20324.1; -. [Q9D842-3] DR CCDS; CCDS51839.1; -. [Q9D842-1] DR RefSeq; NP_001163960.1; NM_001170489.1. [Q9D842-1] DR RefSeq; NP_077213.2; NM_024251.4. [Q9D842-3] DR AlphaFoldDB; Q9D842; -. DR SMR; Q9D842; -. DR BioGRID; 215153; 5. DR STRING; 10090.ENSMUSP00000032130; -. DR iPTMnet; Q9D842; -. DR PhosphoSitePlus; Q9D842; -. DR SwissPalm; Q9D842; -. DR EPD; Q9D842; -. DR jPOST; Q9D842; -. DR MaxQB; Q9D842; -. DR PaxDb; 10090-ENSMUSP00000032130; -. DR PeptideAtlas; Q9D842; -. DR ProteomicsDB; 296375; -. [Q9D842-1] DR ProteomicsDB; 296376; -. [Q9D842-2] DR ProteomicsDB; 296377; -. [Q9D842-3] DR Pumba; Q9D842; -. DR Antibodypedia; 30942; 291 antibodies from 27 providers. DR Ensembl; ENSMUST00000032130.8; ENSMUSP00000032130.3; ENSMUSG00000030051.11. [Q9D842-1] DR Ensembl; ENSMUST00000065997.5; ENSMUSP00000066232.3; ENSMUSG00000030051.11. [Q9D842-3] DR GeneID; 72103; -. DR KEGG; mmu:72103; -. DR UCSC; uc009ctq.2; mouse. [Q9D842-3] DR UCSC; uc009ctr.2; mouse. [Q9D842-1] DR UCSC; uc012eon.1; mouse. [Q9D842-2] DR AGR; MGI:1919353; -. DR CTD; 200558; -. DR MGI; MGI:1919353; Aplf. DR VEuPathDB; HostDB:ENSMUSG00000030051; -. DR eggNOG; ENOG502R7QZ; Eukaryota. DR GeneTree; ENSGT00390000010591; -. DR HOGENOM; CLU_043152_0_0_1; -. DR InParanoid; Q9D842; -. DR OMA; PCFYRSS; -. DR OrthoDB; 2971338at2759; -. DR PhylomeDB; Q9D842; -. DR TreeFam; TF326160; -. DR BioGRID-ORCS; 72103; 1 hit in 114 CRISPR screens. DR ChiTaRS; Aplf; mouse. DR PRO; PR:Q9D842; -. DR Proteomes; UP000000589; Chromosome 6. DR RNAct; Q9D842; Protein. DR Bgee; ENSMUSG00000030051; Expressed in otic placode and 166 other cell types or tissues. DR ExpressionAtlas; Q9D842; baseline and differential. DR GO; GO:0005829; C:cytosol; IDA:UniProtKB. DR GO; GO:0005654; C:nucleoplasm; ISO:MGI. DR GO; GO:0005634; C:nucleus; IDA:UniProtKB. DR GO; GO:0090734; C:site of DNA damage; ISS:UniProtKB. DR GO; GO:0035861; C:site of double-strand break; ISS:UniProtKB. DR GO; GO:0008408; F:3'-5' exonuclease activity; ISS:UniProtKB. DR GO; GO:0160002; F:ADP-D-ribose modification-dependent protein binding; ISS:UniProtKB. DR GO; GO:0004520; F:DNA endonuclease activity; ISS:UniProtKB. DR GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; ISS:UniProtKB. DR GO; GO:0042393; F:histone binding; ISS:UniProtKB. DR GO; GO:0140713; F:histone chaperone activity; ISS:UniProtKB. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0000166; F:nucleotide binding; ISS:UniProtKB. DR GO; GO:0072572; F:poly-ADP-D-ribose binding; ISS:UniProtKB. DR GO; GO:0044183; F:protein folding chaperone; ISO:MGI. DR GO; GO:0006974; P:DNA damage response; ISS:UniProtKB. DR GO; GO:0006281; P:DNA repair; ISO:MGI. DR GO; GO:0140861; P:DNA repair-dependent chromatin remodeling; ISS:UniProtKB. DR GO; GO:0006302; P:double-strand break repair; IMP:MGI. DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; ISS:UniProtKB. DR GO; GO:0007566; P:embryo implantation; IMP:UniProtKB. DR GO; GO:0051106; P:positive regulation of DNA ligation; ISO:MGI. DR GO; GO:0071168; P:protein localization to chromatin; ISO:MGI. DR GO; GO:0010717; P:regulation of epithelial to mesenchymal transition; IMP:UniProtKB. DR GO; GO:0045191; P:regulation of isotype switching; IMP:MGI. DR GO; GO:0000012; P:single strand break repair; ISS:UniProtKB. DR CDD; cd22717; FHA_APLF; 1. DR Gene3D; 2.60.200.20; -; 1. DR InterPro; IPR039253; APLF. DR InterPro; IPR019406; APLF_PBZ. DR InterPro; IPR041388; FHA_2. DR InterPro; IPR008984; SMAD_FHA_dom_sf. DR PANTHER; PTHR21315:SF2; APRATAXIN AND PNK-LIKE FACTOR; 1. DR PANTHER; PTHR21315; UNCHARACTERIZED; 1. DR Pfam; PF17913; FHA_2; 1. DR Pfam; PF10283; zf-CCHH; 2. DR SUPFAM; SSF49879; SMAD/FHA domain; 1. DR Genevisible; Q9D842; MM. PE 1: Evidence at protein level; KW ADP-ribosylation; Alternative splicing; Chromosome; Coiled coil; Cytoplasm; KW DNA damage; DNA repair; Hydrolase; Metal-binding; Nucleotide-binding; KW Nucleus; Phosphoprotein; Reference proteome; Repeat; Zinc; Zinc-finger. FT CHAIN 1..499 FT /note="Aprataxin and PNK-like factor" FT /id="PRO_0000089343" FT DOMAIN 1..108 FT /note="FHA-like" FT ZN_FING 372..393 FT /note="PBZ-type 1" FT ZN_FING 414..435 FT /note="PBZ-type 2" FT REGION 134..183 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 197..292 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 305..358 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 401..411 FT /note="Flexible linker" FT /evidence="ECO:0000250, ECO:0000250|UniProtKB:Q8IW19" FT REGION 440..499 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT MOTIF 182..191 FT /note="KBM" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT MOTIF 463..487 FT /note="NAP1L motif" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT COMPBIAS 134..162 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 222..249 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 267..281 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 316..351 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 449..485 FT /note="Acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT BINDING 371 FT /ligand="a glycoprotein" FT /ligand_id="ChEBI:CHEBI:17089" FT /ligand_part="poly[(1''->2')-ADP-alpha-D-ribose] group" FT /ligand_part_id="ChEBI:CHEBI:157741" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT BINDING 376 FT /ligand="a glycoprotein" FT /ligand_id="ChEBI:CHEBI:17089" FT /ligand_part="poly[(1''->2')-ADP-alpha-D-ribose] group" FT /ligand_part_id="ChEBI:CHEBI:157741" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT BINDING 381 FT /ligand="a glycoprotein" FT /ligand_id="ChEBI:CHEBI:17089" FT /ligand_part="poly[(1''->2')-ADP-alpha-D-ribose] group" FT /ligand_part_id="ChEBI:CHEBI:157741" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT BINDING 382 FT /ligand="a glycoprotein" FT /ligand_id="ChEBI:CHEBI:17089" FT /ligand_part="poly[(1''->2')-ADP-alpha-D-ribose] group" FT /ligand_part_id="ChEBI:CHEBI:157741" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT BINDING 418 FT /ligand="a glycoprotein" FT /ligand_id="ChEBI:CHEBI:17089" FT /ligand_part="poly[(1''->2')-ADP-alpha-D-ribose] group" FT /ligand_part_id="ChEBI:CHEBI:157741" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT BINDING 423 FT /ligand="a glycoprotein" FT /ligand_id="ChEBI:CHEBI:17089" FT /ligand_part="poly[(1''->2')-ADP-alpha-D-ribose] group" FT /ligand_part_id="ChEBI:CHEBI:157741" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT BINDING 424 FT /ligand="a glycoprotein" FT /ligand_id="ChEBI:CHEBI:17089" FT /ligand_part="poly[(1''->2')-ADP-alpha-D-ribose] group" FT /ligand_part_id="ChEBI:CHEBI:157741" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT MOD_RES 116 FT /note="Phosphoserine; by ATM" FT /evidence="ECO:0000250|UniProtKB:Q8IW19" FT MOD_RES 149 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:21183079" FT VAR_SEQ 1..108 FT /note="Missing (in isoform 2)" FT /evidence="ECO:0000303|PubMed:15489334" FT /id="VSP_014983" FT VAR_SEQ 1..32 FT /note="MPSDFFLQPLDGGPRVPVGPGQTVIGRGPLLG -> MPSVPEGGGYE (in FT isoform 3)" FT /evidence="ECO:0000303|PubMed:16141072" FT /id="VSP_014982" FT VAR_SEQ 493..499 FT /note="SSLHLKH -> RFMRRKK (in isoform 2 and isoform 3)" FT /evidence="ECO:0000303|PubMed:15489334, FT ECO:0000303|PubMed:16141072" FT /id="VSP_014984" FT CONFLICT 178 FT /note="R -> H (in Ref. 2; AAH02179)" FT /evidence="ECO:0000305" FT CONFLICT 470 FT /note="S -> F (in Ref. 1; BAB25711)" FT /evidence="ECO:0000305" SQ SEQUENCE 499 AA; 54968 MW; 4B41A9C0C8937963 CRC64; MPSDFFLQPL DGGPRVPVGP GQTVIGRGPL LGITDKRVSR RHAILEVVDS QLRIKPIHRN PCFYQSSEKS QHSPMETQVW SQLHPGDSFS LLLDKYAFRV FSAESEVEME CTLRNSQMLD EDDILSEMQK SPVVNLPDKT TGASQLQGSP EITKTKCPTI DPMSSSGECR AFSEHQPRPT QRKRILPAWM LAESLSDQSL STPAEGGDKD VIQRSGKAGT CEDRTPGNTS WHGKKRLSPS GNSKSVSAEQ DPGKKCRKAD QEGPGVSSEN VPESSSSNIV KDPDVDIVKT NKQKDGILIE ELGEVSKHKA ATKPTTNEEG ESCARVQSKS PPEKSQGCHP ESSSAPSSPD ALHTDTADPV LGCSEESKVR RTACMYGANC YRRNPLHFQH FSHPGDSDYG EVHGTDEGVI GDRPECPYGA SCYRKNPQHK MEYRHSALPA RVALDEDDDD VGQPSDDEDE EDYEPTDEDS DWHPGKDDEE QEDVDELLKE AKSSLHLKH //