ATG13_MOUSE
ID ATG13_MOUSE Reviewed; 516 AA.
AC Q91YI1; A2AH18; Q80TU9;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 02-SEP-2008, sequence version 2.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Autophagy-related protein 13;
GN Name=Atg13; Synonyms=D2Ertd391e, Kiaa0652;
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] (ISOFORM 2).
RC STRAIN=C57BL/6J, and NOD; TISSUE=Bone marrow, and Dendritic cell;
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 GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND ALTERNATIVE SPLICING.
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=129, and FVB/N; TISSUE=Eye, and Mammary tumor;
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 91-516 (ISOFORM 1).
RC TISSUE=Brain;
RX PubMed=12693553; DOI=10.1093/dnares/10.1.35;
RA Okazaki N., Kikuno R., Ohara R., Inamoto S., Aizawa H., Yuasa S.,
RA Nakajima D., Nagase T., Ohara O., Koga H.;
RT "Prediction of the coding sequences of mouse homologues of KIAA gene: II.
RT The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs
RT identified by screening of terminal sequences of cDNA clones randomly
RT sampled from size-fractionated libraries.";
RL DNA Res. 10:35-48(2003).
RN [6]
RP FUNCTION, INTERACTION WITH ULK1 AND RB1CC1, PHOSPHORYLATION, AND
RP SUBCELLULAR LOCATION.
RX PubMed=19258318; DOI=10.1074/jbc.m900573200;
RA Ganley I.G., Lam du H., Wang J., Ding X., Chen S., Jiang X.;
RT "ULK1.ATG13.FIP200 complex mediates mTOR signaling and is essential for
RT autophagy.";
RL J. Biol. Chem. 284:12297-12305(2009).
RN [7]
RP SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=19211835; DOI=10.1091/mbc.e08-12-1248;
RA Hosokawa N., Hara T., Kaizuka T., Kishi C., Takamura A., Miura Y.,
RA Iemura S., Natsume T., Takehana K., Yamada N., Guan J.L., Oshiro N.,
RA Mizushima N.;
RT "Nutrient-dependent mTORC1 association with the ULK1-Atg13-FIP200 complex
RT required for autophagy.";
RL Mol. Biol. Cell 20:1981-1991(2009).
CC -!- FUNCTION: Autophagy factor required for autophagosome formation and
CC mitophagy. Target of the TOR kinase signaling pathway that regulates
CC autophagy through the control of the phosphorylation status of ATG13
CC and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through
CC its regulation of ULK1 activity, plays a role in the regulation of the
CC kinase activity of mTORC1 and cell proliferation.
CC {ECO:0000269|PubMed:19258318}.
CC -!- SUBUNIT: Part of a complex consisting of ATG13, ULK1 and RB1CC1
CC (PubMed:19258318, PubMed:19211835). Interacts with ATG101 (By
CC similarity). Interacts with ULK1 (via C-terminus); this interaction is
CC increased in the absence of TMEM39A (By similarity). Interacts with
CC ULK2 (via C-terminus) (By similarity). Interacts (via the LIR motif)
CC with GABARAP, GABARAPL and GABARAPL2 (By similarity). Interacts (via
CC the LIR motif) with MAP1LC3A, MAP1LC3B and MAP1LC3C (By similarity).
CC Interacts with TAB2 and TAB3 (By similarity). Interacts with C9orf72
CC (By similarity). Interacts with RB1CC1; this interaction is increased
CC in the absence of TMEM39A (By similarity).
CC {ECO:0000250|UniProtKB:O75143, ECO:0000269|PubMed:19211835,
CC ECO:0000269|PubMed:19258318}.
CC -!- INTERACTION:
CC Q91YI1; Q9BSB4: ATG101; Xeno; NbExp=2; IntAct=EBI-8391007, EBI-2946739;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:19211835,
CC ECO:0000269|PubMed:19258318}. Preautophagosomal structure
CC {ECO:0000269|PubMed:19211835, ECO:0000269|PubMed:19258318}. Note=Under
CC starvation conditions, is localized to puncate structures primarily
CC representing the isolation membrane that sequesters a portion of the
CC cytoplasm resulting in the formation of an autophagosome.
CC {ECO:0000269|PubMed:19211835, ECO:0000269|PubMed:19258318}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q91YI1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q91YI1-2; Sequence=VSP_034922;
CC -!- DOMAIN: The LIR motif (LC3-interacting region) is required for the
CC interaction with the ATG8 family proteins GABARAP, GABARAPL, GABARAPL2,
CC and MAP1LC3A. {ECO:0000250|UniProtKB:O75143}.
CC -!- PTM: Phosphorylated by ULK1, ULK2 and mTOR. Phosphorylation status
CC depends on nutrient-rich conditions; dephosphorylated during starvation
CC or following treatment with rapamycin. ULK1-mediated phosphorylation of
CC ATG13 at Ser-354 is required for efficient clearance of depolarized
CC mitochondria. {ECO:0000250|UniProtKB:O75143}.
CC -!- SIMILARITY: Belongs to the ATG13 family. Metazoan subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC65621.3; Type=Miscellaneous discrepancy; Note=The sequence differs from that shown because it seems to be derived from a pre-mRNA.; Evidence={ECO:0000305};
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DR EMBL; AK149672; BAE29016.1; -; mRNA.
DR EMBL; AK171206; BAE42312.1; -; mRNA.
DR EMBL; AK171440; BAE42453.1; -; mRNA.
DR EMBL; AL714023; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH466519; EDL27574.1; -; Genomic_DNA.
DR EMBL; BC016669; AAH16669.1; -; mRNA.
DR EMBL; BC023673; AAH23673.1; -; mRNA.
DR EMBL; BC023712; AAH23712.1; -; mRNA.
DR EMBL; BC033419; AAH33419.1; -; mRNA.
DR EMBL; AK122339; BAC65621.3; ALT_SEQ; Transcribed_RNA.
DR CCDS; CCDS16438.1; -. [Q91YI1-2]
DR CCDS; CCDS89517.1; -. [Q91YI1-1]
DR RefSeq; NP_663503.1; NM_145528.3. [Q91YI1-2]
DR RefSeq; XP_006499953.1; XM_006499890.3.
DR AlphaFoldDB; Q91YI1; -.
DR SMR; Q91YI1; -.
DR BioGRID; 206251; 4.
DR ComplexPortal; CPX-380; ULK1-ATG13-RB1CC1-ATG101 autophagy initiation complex.
DR DIP; DIP-60542N; -.
DR IntAct; Q91YI1; 4.
DR MINT; Q91YI1; -.
DR STRING; 10090.ENSMUSP00000076081; -.
DR iPTMnet; Q91YI1; -.
DR PhosphoSitePlus; Q91YI1; -.
DR EPD; Q91YI1; -.
DR MaxQB; Q91YI1; -.
DR PeptideAtlas; Q91YI1; -.
DR PRIDE; Q91YI1; -.
DR ProteomicsDB; 265161; -. [Q91YI1-1]
DR ProteomicsDB; 265162; -. [Q91YI1-2]
DR Antibodypedia; 26361; 633 antibodies from 38 providers.
DR DNASU; 51897; -.
DR Ensembl; ENSMUST00000028678; ENSMUSP00000028678; ENSMUSG00000027244. [Q91YI1-1]
DR Ensembl; ENSMUST00000076803; ENSMUSP00000076081; ENSMUSG00000027244. [Q91YI1-2]
DR GeneID; 51897; -.
DR KEGG; mmu:51897; -.
DR UCSC; uc008kwn.2; mouse. [Q91YI1-2]
DR CTD; 9776; -.
DR MGI; MGI:1196429; Atg13.
DR VEuPathDB; HostDB:ENSMUSG00000027244; -.
DR eggNOG; KOG3874; Eukaryota.
DR GeneTree; ENSGT00390000007055; -.
DR HOGENOM; CLU_036365_0_0_1; -.
DR InParanoid; Q91YI1; -.
DR OMA; ICYRIYM; -.
DR OrthoDB; 926357at2759; -.
DR PhylomeDB; Q91YI1; -.
DR TreeFam; TF321599; -.
DR Reactome; R-MMU-1632852; Macroautophagy.
DR BioGRID-ORCS; 51897; 13 hits in 76 CRISPR screens.
DR ChiTaRS; Atg13; mouse.
DR PRO; PR:Q91YI1; -.
DR Proteomes; UP000000589; Chromosome 2.
DR RNAct; Q91YI1; protein.
DR Bgee; ENSMUSG00000027244; Expressed in retinal neural layer and 239 other tissues.
DR Genevisible; Q91YI1; MM.
DR GO; GO:1990316; C:Atg1/ULK1 kinase complex; IDA:MGI.
DR GO; GO:0005829; C:cytosol; IDA:UniProtKB.
DR GO; GO:0019898; C:extrinsic component of membrane; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; ISO:MGI.
DR GO; GO:0000407; C:phagophore assembly site; IDA:UniProtKB.
DR GO; GO:0019901; F:protein kinase binding; ISO:MGI.
DR GO; GO:0000045; P:autophagosome assembly; IDA:ComplexPortal.
DR GO; GO:0000423; P:mitophagy; IMP:ParkinsonsUK-UCL.
DR GO; GO:0008285; P:negative regulation of cell population proliferation; IDA:ComplexPortal.
DR GO; GO:0034727; P:piecemeal microautophagy of the nucleus; IBA:GO_Central.
DR GO; GO:0010508; P:positive regulation of autophagy; IDA:ComplexPortal.
DR GO; GO:0046777; P:protein autophosphorylation; IDA:ComplexPortal.
DR GO; GO:0034497; P:protein localization to phagophore assembly site; IBA:GO_Central.
DR GO; GO:0006468; P:protein phosphorylation; IDA:ComplexPortal.
DR GO; GO:1903059; P:regulation of protein lipidation; IDA:ComplexPortal.
DR GO; GO:0098780; P:response to mitochondrial depolarisation; IMP:BHF-UCL.
DR Gene3D; 3.30.900.10; -; 1.
DR InterPro; IPR040182; ATG13.
DR InterPro; IPR018731; Atg13_N.
DR InterPro; IPR036570; HORMA_dom_sf.
DR PANTHER; PTHR13430; PTHR13430; 1.
DR Pfam; PF10033; ATG13; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Autophagy; Cytoplasm; Phosphoprotein;
KW Reference proteome.
FT CHAIN 1..516
FT /note="Autophagy-related protein 13"
FT /id="PRO_0000345151"
FT REGION 127..134
FT /note="Important for interaction with ATG101"
FT /evidence="ECO:0000250|UniProtKB:O75143"
FT REGION 336..359
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 405..438
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 443..446
FT /note="LIR"
FT COMPBIAS 337..359
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 416..438
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000250|UniProtKB:O75143"
FT MOD_RES 354
FT /note="Phosphoserine; by ULK1"
FT /evidence="ECO:0000250|UniProtKB:O75143"
FT MOD_RES 355
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O75143"
FT MOD_RES 360
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O75143"
FT VAR_SEQ 263..299
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334,
FT ECO:0000303|PubMed:16141072"
FT /id="VSP_034922"
SQ SEQUENCE 516 AA; 56441 MW; 04B4E49BB19449F2 CRC64;
METELSSQDR KDLDKFIKFF ALKTVQVIVQ ARLGEKICTR SSSSPTGSDW FNLAIKDIPE
VTHEAKKALS GQLPAVGRSM CVEISLKTSE GDSMELEIWC LEMNEKCDKE IKVSYTVYNR
LSLLLKSLLA ITRVTPAYRL SRKQGHEYVI LYRIYFGEVQ LNGLGEGFQT VRVGTVGTPV
GTLTLSCAYR INLAFMSTRQ FERTPPIMGI IIDHFVDRPY PSSSPMHPCN YRTAEDAGVA
YPSVEDSQEV CTTSFSTSPP SQLSSSRLSY QPAVLGLGSA DLAYPVVFTA GLNTTHAHQL
MVPGKEGGVT LAPSHPTHGA QADPERLVMH MPSDGTHCAA TPSSSEDTET VSNSSEGRAS
PHDILETIFV RKVGAFVNKP INQVTVTSLD IPFAMFAPKN LELEDADPMV NPPESPETTS
PLHGSLHSDG SSGGSGGSTH DDFVMIDFKP AFSKDDILPM DLGTFYREFQ NPPQLSSLSI
DFGAQSMAED LDSLPEKLAV HEKNVREFDA FVETLQ
