ATG13_YEAST
ID ATG13_YEAST Reviewed; 738 AA.
AC Q06628; D6W4I5;
DT 15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=Autophagy-related protein 13;
GN Name=ATG13; Synonyms=APG13; OrderedLocusNames=YPR185W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9224892; DOI=10.1016/s0378-1119(97)00031-0;
RA Funakoshi T., Matsuura A., Noda T., Ohsumi Y.;
RT "Analyses of APG13 gene involved in autophagy in yeast, Saccharomyces
RT cerevisiae.";
RL Gene 192:207-213(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP FUNCTION.
RX PubMed=8224160; DOI=10.1016/0014-5793(93)80398-e;
RA Tsukada M., Ohsumi Y.;
RT "Isolation and characterization of autophagy-defective mutants of
RT Saccharomyces cerevisiae.";
RL FEBS Lett. 333:169-174(1993).
RN [5]
RP FUNCTION, INTERACTION WITH VAC8, AND PHOSPHORYLATION.
RX PubMed=10837477; DOI=10.1074/jbc.m002813200;
RA Scott S.V., Nice D.C. III, Nau J.J., Weisman L.S., Kamada Y.,
RA Keizer-Gunnink I., Funakoshi T., Veenhuis M., Ohsumi Y., Klionsky D.J.;
RT "Apg13p and Vac8p are part of a complex of phosphoproteins that are
RT required for cytoplasm to vacuole targeting.";
RL J. Biol. Chem. 275:25840-25849(2000).
RN [6]
RP FUNCTION.
RX PubMed=11086004; DOI=10.1083/jcb.151.5.1025;
RA Abeliovich H., Dunn W.A. Jr., Kim J., Klionsky D.J.;
RT "Dissection of autophagosome biogenesis into distinct nucleation and
RT expansion steps.";
RL J. Cell Biol. 151:1025-1034(2000).
RN [7]
RP FUNCTION, PHOSPHORYLATION, AND INTERACTION WITH ATG1.
RX PubMed=10995454; DOI=10.1083/jcb.150.6.1507;
RA Kamada Y., Funakoshi T., Shintani T., Nagano K., Ohsumi M., Ohsumi Y.;
RT "Tor-mediated induction of autophagy via an Apg1 protein kinase complex.";
RL J. Cell Biol. 150:1507-1513(2000).
RN [8]
RP FUNCTION.
RX PubMed=11486014; DOI=10.1128/mcb.21.17.5742-5752.2001;
RA Wang Z., Wilson W.A., Fujino M.A., Roach P.J.;
RT "Antagonistic controls of autophagy and glycogen accumulation by Snf1p, the
RT yeast homolog of AMP-activated protein kinase, and the cyclin-dependent
RT kinase Pho85p.";
RL Mol. Cell. Biol. 21:5742-5752(2001).
RN [9]
RP NOMENCLATURE.
RX PubMed=14536056; DOI=10.1016/s1534-5807(03)00296-x;
RA Klionsky D.J., Cregg J.M., Dunn W.A. Jr., Emr S.D., Sakai Y.,
RA Sandoval I.V., Sibirny A., Subramani S., Thumm M., Veenhuis M., Ohsumi Y.;
RT "A unified nomenclature for yeast autophagy-related genes.";
RL Dev. Cell 5:539-545(2003).
RN [10]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [11]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [12]
RP FUNCTION.
RX PubMed=14723849; DOI=10.1016/s1534-5807(03)00402-7;
RA Reggiori F., Tucker K.A., Stromhaug P.E., Klionsky D.J.;
RT "The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from
RT the pre-autophagosomal structure.";
RL Dev. Cell 6:79-90(2004).
RN [13]
RP FUNCTION, AND INTERACTION WITH ATG1 AND ATG17.
RX PubMed=15743910; DOI=10.1091/mbc.e04-08-0669;
RA Kabeya Y., Kamada Y., Baba M., Takikawa H., Sasaki M., Ohsumi Y.;
RT "Atg17 functions in cooperation with Atg1 and Atg13 in yeast autophagy.";
RL Mol. Biol. Cell 16:2544-2553(2005).
RN [14]
RP INTERACTION WITH ATG1 AND ATG17.
RX PubMed=15901835; DOI=10.1091/mbc.e04-10-0894;
RA Cheong H., Yorimitsu T., Reggiori F., Legakis J.E., Wang C.W.,
RA Klionsky D.J.;
RT "Atg17 regulates the magnitude of the autophagic response.";
RL Mol. Biol. Cell 16:3438-3453(2005).
RN [15]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-649, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=YAL6B;
RX PubMed=15665377; DOI=10.1074/mcp.m400219-mcp200;
RA Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M.,
RA Jensen O.N.;
RT "Quantitative phosphoproteomics applied to the yeast pheromone signaling
RT pathway.";
RL Mol. Cell. Proteomics 4:310-327(2005).
RN [16]
RP FUNCTION.
RX PubMed=17426440; DOI=10.4161/auto.4129;
RA Legakis J.E., Yen W.L., Klionsky D.J.;
RT "A cycling protein complex required for selective autophagy.";
RL Autophagy 3:422-432(2007).
RN [17]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=17295840; DOI=10.1111/j.1365-2443.2007.01050.x;
RA Suzuki K., Kubota Y., Sekito T., Ohsumi Y.;
RT "Hierarchy of Atg proteins in pre-autophagosomal structure organization.";
RL Genes Cells 12:209-218(2007).
RN [18]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-355, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [19]
RP FUNCTION, AND PHOSPHORYLATION.
RX PubMed=17699586; DOI=10.1091/mbc.e07-05-0485;
RA Yorimitsu T., Zaman S., Broach J.R., Klionsky D.J.;
RT "Protein kinase A and Sch9 cooperatively regulate induction of autophagy in
RT Saccharomyces cerevisiae.";
RL Mol. Biol. Cell 18:4180-4189(2007).
RN [20]
RP FUNCTION.
RX PubMed=18077553; DOI=10.1091/mbc.e07-08-0826;
RA Cheong H., Nair U., Geng J., Klionsky D.J.;
RT "The Atg1 kinase complex is involved in the regulation of protein
RT recruitment to initiate sequestering vesicle formation for nonspecific
RT autophagy in Saccharomyces cerevisiae.";
RL Mol. Biol. Cell 19:668-681(2008).
RN [21]
RP FUNCTION OF THE ATG1-ATG13 COMPLEX.
RX PubMed=18287526; DOI=10.1091/mbc.e07-10-1048;
RA Kawamata T., Kamada Y., Kabeya Y., Sekito T., Ohsumi Y.;
RT "Organization of the pre-autophagosomal structure responsible for
RT autophagosome formation.";
RL Mol. Biol. Cell 19:2039-2050(2008).
RN [22]
RP INTERACTION WITH ATG1.
RX PubMed=18829864; DOI=10.1091/mbc.e08-05-0544;
RA He C., Baba M., Cao Y., Klionsky D.J.;
RT "Self-interaction is critical for Atg9 transport and function at the
RT phagophore assembly site during autophagy.";
RL Mol. Biol. Cell 19:5506-5516(2008).
RN [23]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-355; SER-461; SER-554 AND
RP SER-649, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [24]
RP INTERACTION WITH THE ATG17-ATG29-ATG31 COMPLEX.
RX PubMed=19755117; DOI=10.1016/j.bbrc.2009.09.034;
RA Kabeya Y., Noda N.N., Fujioka Y., Suzuki K., Inagaki F., Ohsumi Y.;
RT "Characterization of the Atg17-Atg29-Atg31 complex specifically required
RT for starvation-induced autophagy in Saccharomyces cerevisiae.";
RL Biochem. Biophys. Res. Commun. 389:612-615(2009).
RN [25]
RP PHOSPHORYLATION AT SER-344; SER-437 AND SER-581 BY PKA, MUTAGENESIS OF
RP SER-344; SER-437 AND SER-581, FUNCTION, AND INTERACTION WITH ATG17.
RX PubMed=19805182; DOI=10.1073/pnas.0903316106;
RA Stephan J.S., Yeh Y.Y., Ramachandran V., Deminoff S.J., Herman P.K.;
RT "The Tor and PKA signaling pathways independently target the Atg1/Atg13
RT protein kinase complex to control autophagy.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:17049-17054(2009).
RN [26]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-355; SER-461 AND SER-649, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [27]
RP FUNCTION.
RX PubMed=20647741; DOI=10.4161/auto.6.7.12753;
RA Ecker N., Mor A., Journo D., Abeliovich H.;
RT "Induction of autophagic flux by amino acid deprivation is distinct from
RT nitrogen starvation-induced macroautophagy.";
RL Autophagy 6:879-890(2010).
RN [28]
RP INTERACTION WITH ATG1.
RX PubMed=20953146; DOI=10.4161/auto.6.8.13849;
RA Kijanska M., Dohnal I., Reiter W., Kaspar S., Stoffel I., Ammerer G.,
RA Kraft C., Peter M.;
RT "Activation of Atg1 kinase in autophagy by regulated phosphorylation.";
RL Autophagy 6:1168-1178(2010).
RN [29]
RP FUNCTION, AND INTERACTION WITH ATG1.
RX PubMed=20439775; DOI=10.1534/genetics.110.116566;
RA Yeh Y.Y., Wrasman K., Herman P.K.;
RT "Autophosphorylation within the Atg1 activation loop is required for both
RT kinase activity and the induction of autophagy in Saccharomyces
RT cerevisiae.";
RL Genetics 185:871-882(2010).
RN [30]
RP FUNCTION.
RX PubMed=20855505; DOI=10.1083/jcb.200912089;
RA Mari M., Griffith J., Rieter E., Krishnappa L., Klionsky D.J., Reggiori F.;
RT "An Atg9-containing compartment that functions in the early steps of
RT autophagosome biogenesis.";
RL J. Cell Biol. 190:1005-1022(2010).
RN [31]
RP PHOSPHORYLATION AT SER-348; SER-437; SER-438; SER-496; SER-535; SER-541;
RP SER-646 AND SER-649, MUTAGENESIS OF SER-348; SER-437; SER-438; SER-496;
RP SER-535; SER-541; SER-646 AND SER-649, AND FUNCTION.
RX PubMed=19995911; DOI=10.1128/mcb.01344-09;
RA Kamada Y., Yoshino K., Kondo C., Kawamata T., Oshiro N., Yonezawa K.,
RA Ohsumi Y.;
RT "Tor directly controls the Atg1 kinase complex to regulate autophagy.";
RL Mol. Cell. Biol. 30:1049-1058(2010).
RN [32]
RP PHOSPHORYLATION BY ATG1.
RX PubMed=21490424; DOI=10.4161/auto.7.8.15696;
RA Shin C.S., Huh W.K.;
RT "Bidirectional regulation between TORC1 and autophagy in Saccharomyces
RT cerevisiae.";
RL Autophagy 7:854-862(2011).
RN [33]
RP FUNCTION, PHOSPHORYLATION, AND SUBCELLULAR LOCATION OF THE ATG1-ATG13
RP COMPLEX.
RX PubMed=21468027; DOI=10.1038/emboj.2011.104;
RA Graef M., Nunnari J.;
RT "Mitochondria regulate autophagy by conserved signalling pathways.";
RL EMBO J. 30:2101-2114(2011).
RN [34]
RP PHOSPHORYLATION, AND DEPHOSPHORYLATION.
RX PubMed=21078689; DOI=10.1534/genetics.110.123372;
RA Ramachandran V., Herman P.K.;
RT "Antagonistic interactions between the cAMP-dependent protein kinase and
RT Tor signaling pathways modulate cell growth in Saccharomyces cerevisiae.";
RL Genetics 187:441-454(2011).
RN [35]
RP FUNCTION, AND INTERACTION WITH ATG1.
RX PubMed=21712380; DOI=10.1074/jbc.m111.250324;
RA Yeh Y.Y., Shah K.H., Herman P.K.;
RT "An Atg13 protein-mediated self-association of the Atg1 protein kinase is
RT important for the induction of autophagy.";
RL J. Biol. Chem. 286:28931-28939(2011).
RN [36]
RP PHOSPHORYLATION, AND DEPHOSPHORYLATION.
RX PubMed=21900499; DOI=10.1091/mbc.e11-06-0525;
RA Wu X., Tu B.P.;
RT "Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the
RT absence of nitrogen starvation.";
RL Mol. Biol. Cell 22:4124-4133(2011).
RN [37]
RP INTERACTION WITH THE ATG17-ATG29-ATG31 COMPLEX.
RX PubMed=23219485; DOI=10.1016/j.cell.2012.11.028;
RA Ragusa M.J., Stanley R.E., Hurley J.H.;
RT "Architecture of the Atg17 complex as a scaffold for autophagosome
RT biogenesis.";
RL Cell 151:1501-1512(2012).
RN [38]
RP FUNCTION, INTERACTION WITH ATG1, AND MUTAGENESIS OF PHE-468 AND VAL-469.
RX PubMed=22885598; DOI=10.1038/emboj.2012.225;
RA Kraft C., Kijanska M., Kalie E., Siergiejuk E., Lee S.S., Semplicio G.,
RA Stoffel I., Brezovich A., Verma M., Hansmann I., Ammerer G., Hofmann K.,
RA Tooze S., Peter M.;
RT "Binding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8
RT regulates autophagy.";
RL EMBO J. 31:3691-3703(2012).
RN [39]
RP FUNCTION, AND PHOSPHORYLATION BY TORC1 COMPLEX.
RX PubMed=22447937; DOI=10.1074/jbc.m112.344952;
RA Umekawa M., Klionsky D.J.;
RT "Ksp1 kinase regulates autophagy via the target of rapamycin complex 1
RT (TORC1) pathway.";
RL J. Biol. Chem. 287:16300-16310(2012).
RN [40]
RP FUNCTION, AND INTERACTION WITH ATG1.
RX PubMed=22778255; DOI=10.1074/jbc.c112.387514;
RA Nakatogawa H., Ohbayashi S., Sakoh-Nakatogawa M., Kakuta S., Suzuki S.W.,
RA Kirisako H., Kondo-Kakuta C., Noda N.N., Yamamoto H., Ohsumi Y.;
RT "The autophagy-related protein kinase Atg1 interacts with the ubiquitin-
RT like protein Atg8 via the Atg8 family interacting motif to facilitate
RT autophagosome formation.";
RL J. Biol. Chem. 287:28503-28507(2012).
RN [41]
RP FUNCTION, AND PHOSPHORYLATION.
RX PubMed=22782902; DOI=10.1074/jbc.m112.344192;
RA Lisa-Santamaria P., Jimenez A., Revuelta J.L.;
RT "The protein factor-arrest 11 (Far11) is essential for the toxicity of
RT human caspase-10 in yeast and participates in the regulation of autophagy
RT and the DNA damage signaling.";
RL J. Biol. Chem. 287:29636-29647(2012).
RN [42]
RP PHOSPHORYLATION.
RX PubMed=22727621; DOI=10.1016/j.molcel.2012.05.019;
RA Takahara T., Maeda T.;
RT "Transient sequestration of TORC1 into stress granules during heat
RT stress.";
RL Mol. Cell 47:242-252(2012).
RN [43]
RP PHOSPHORYLATION.
RX PubMed=29698392; DOI=10.1371/journal.pgen.1007334;
RA Ukai H., Araki Y., Kira S., Oikawa Y., May A.I., Noda T.;
RT "Gtr/Ego-independent TORC1 activation is achieved through a glutamine-
RT sensitive interaction with Pib2 on the vacuolar membrane.";
RL PLoS Genet. 14:e1007334-e1007334(2018).
CC -!- FUNCTION: Activates the ATG1 kinase in a nutritional condition
CC dependent manner through the TOR pathway, leading to autophagy
CC (PubMed:10995454, PubMed:11086004, PubMed:15743910, PubMed:17295840,
CC PubMed:18077553, PubMed:18287526, PubMed:19805182, PubMed:19995911,
CC PubMed:20647741, PubMed:20855505, PubMed:22447937, PubMed:22778255,
CC PubMed:22782902, PubMed:22885598, PubMed:8224160, PubMed:21468027).
CC Required for autophosphorylation of ATG1 at 'Thr-226' and its
CC dimerization (PubMed:20439775, PubMed:17699586, PubMed:21712380). May
CC also be involved in the regulation of autophagy through SNF1
CC (PubMed:11486014). Involved in ATG9 and ATG23 cycling through the pre-
CC autophagosomal structure (PubMed:14723849, PubMed:17426440). Also
CC involved in cytoplasm to vacuole transport (Cvt) and more specifically
CC in Cvt vesicle formation (PubMed:10837477). Seems to play a role in the
CC switching machinery regulating the conversion between the Cvt pathway
CC and autophagy (PubMed:10837477). Finally, ATG13 is also required for
CC glycogen storage during stationary phase (PubMed:11486014).
CC {ECO:0000269|PubMed:10837477, ECO:0000269|PubMed:10995454,
CC ECO:0000269|PubMed:11086004, ECO:0000269|PubMed:11486014,
CC ECO:0000269|PubMed:14723849, ECO:0000269|PubMed:15743910,
CC ECO:0000269|PubMed:17295840, ECO:0000269|PubMed:17426440,
CC ECO:0000269|PubMed:17699586, ECO:0000269|PubMed:18077553,
CC ECO:0000269|PubMed:18287526, ECO:0000269|PubMed:19805182,
CC ECO:0000269|PubMed:19995911, ECO:0000269|PubMed:20439775,
CC ECO:0000269|PubMed:20647741, ECO:0000269|PubMed:20855505,
CC ECO:0000269|PubMed:21468027, ECO:0000269|PubMed:21712380,
CC ECO:0000269|PubMed:22447937, ECO:0000269|PubMed:22778255,
CC ECO:0000269|PubMed:22782902, ECO:0000269|PubMed:22885598,
CC ECO:0000269|PubMed:8224160}.
CC -!- SUBUNIT: Hypophosphorylated form interacts with ATG1 to form the ATG1-
CC ATG13 kinase complex (PubMed:10995454, PubMed:15743910,
CC PubMed:15901835, PubMed:18829864, PubMed:20439775, PubMed:20953146,
CC PubMed:21712380, PubMed:22778255, PubMed:22885598). The ATG1-ATG13
CC complex interacts with the ATG17-ATG29-ATG31 complex through direct
CC interaction with ATG17 (PubMed:23219485, PubMed:15743910,
CC PubMed:15901835, PubMed:19755117, PubMed:19805182). Interacts with VAC8
CC (PubMed:10837477). {ECO:0000269|PubMed:10837477,
CC ECO:0000269|PubMed:10995454, ECO:0000269|PubMed:15743910,
CC ECO:0000269|PubMed:15901835, ECO:0000269|PubMed:18829864,
CC ECO:0000269|PubMed:19755117, ECO:0000269|PubMed:19805182,
CC ECO:0000269|PubMed:20439775, ECO:0000269|PubMed:20953146,
CC ECO:0000269|PubMed:21712380, ECO:0000269|PubMed:22778255,
CC ECO:0000269|PubMed:22885598, ECO:0000269|PubMed:23219485}.
CC -!- INTERACTION:
CC Q06628; P53104: ATG1; NbExp=18; IntAct=EBI-36188, EBI-2657;
CC Q06628; Q06410: ATG17; NbExp=6; IntAct=EBI-36188, EBI-30856;
CC Q06628; P39968: VAC8; NbExp=7; IntAct=EBI-36188, EBI-20212;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC Preautophagosomal structure {ECO:0000269|PubMed:17295840,
CC ECO:0000269|PubMed:21468027}.
CC -!- PTM: Phosphorylated; hyperphosphorylated by the TORC1 kinase complex to
CC repress the induction of autophagy in nutrient-replete conditions
CC (PubMed:10995454, PubMed:19995911, PubMed:19805182, PubMed:22447937,
CC PubMed:22727621, PubMed:29698392). Starvation and TOR inactivation
CC results in ATG13 partial dephosphorylation leading to ATG1-binding
CC (PubMed:10995454). Rephosphorylated by ATG1 during prolonged nitrogen
CC starvation (PubMed:21490424). Also phosphorylated by PKA
CC (PubMed:17699586, PubMed:19805182, PubMed:21078689). PKA
CC phosphorylation regulates the association of ATG13 with the PAS
CC (PubMed:21900499). Within this regulatory network, mitochondrial
CC respiratory deficiency suppresses autophagic flux (PubMed:21468027).
CC Hyperphosphorylation in rich medium is impaired in the absence of VAC8
CC (PubMed:10837477). Dephosphorylation is dependent on FAR11
CC (PubMed:22782902). {ECO:0000269|PubMed:10837477,
CC ECO:0000269|PubMed:10995454, ECO:0000269|PubMed:17699586,
CC ECO:0000269|PubMed:19805182, ECO:0000269|PubMed:19995911,
CC ECO:0000269|PubMed:21078689, ECO:0000269|PubMed:21468027,
CC ECO:0000269|PubMed:21490424, ECO:0000269|PubMed:21900499,
CC ECO:0000269|PubMed:22447937, ECO:0000269|PubMed:22727621,
CC ECO:0000269|PubMed:22782902, ECO:0000269|PubMed:29698392}.
CC -!- MISCELLANEOUS: Present with 149 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the ATG13 family. Fungi subfamily.
CC {ECO:0000305}.
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DR EMBL; U25842; AAB68118.1; -; Genomic_DNA.
DR EMBL; D88025; BAA21485.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11601.1; -; Genomic_DNA.
DR PIR; S59842; S59842.
DR RefSeq; NP_015511.1; NM_001184282.1.
DR PDB; 6KBM; X-ray; 2.90 A; B=567-695.
DR PDB; 6KBN; X-ray; 3.20 A; B/D=567-695.
DR PDBsum; 6KBM; -.
DR PDBsum; 6KBN; -.
DR AlphaFoldDB; Q06628; -.
DR SMR; Q06628; -.
DR BioGRID; 36357; 200.
DR ComplexPortal; CPX-1676; ATG1 kinase complex.
DR DIP; DIP-1191N; -.
DR IntAct; Q06628; 10.
DR MINT; Q06628; -.
DR STRING; 4932.YPR185W; -.
DR TCDB; 9.A.15.1.1; the autophagy-related phagophore-formation transporter (apt) family.
DR iPTMnet; Q06628; -.
DR MaxQB; Q06628; -.
DR PaxDb; Q06628; -.
DR PRIDE; Q06628; -.
DR TopDownProteomics; Q06628; -.
DR EnsemblFungi; YPR185W_mRNA; YPR185W; YPR185W.
DR GeneID; 856315; -.
DR KEGG; sce:YPR185W; -.
DR SGD; S000006389; ATG13.
DR VEuPathDB; FungiDB:YPR185W; -.
DR eggNOG; KOG4573; Eukaryota.
DR HOGENOM; CLU_411076_0_0_1; -.
DR InParanoid; Q06628; -.
DR OMA; MHQHPRS; -.
DR BioCyc; YEAST:G3O-34308-MON; -.
DR Reactome; R-SCE-1632852; Macroautophagy.
DR PRO; PR:Q06628; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q06628; protein.
DR GO; GO:1990316; C:Atg1/ULK1 kinase complex; IDA:SGD.
DR GO; GO:0005829; C:cytosol; HDA:SGD.
DR GO; GO:0019898; C:extrinsic component of membrane; IDA:SGD.
DR GO; GO:0000407; C:phagophore assembly site; IDA:SGD.
DR GO; GO:0120095; C:vacuole-isolation membrane contact site; IDA:SGD.
DR GO; GO:0019887; F:protein kinase regulator activity; IDA:SGD.
DR GO; GO:0032147; P:activation of protein kinase activity; IMP:SGD.
DR GO; GO:0000045; P:autophagosome assembly; IDA:SGD.
DR GO; GO:0006914; P:autophagy; IMP:UniProtKB.
DR GO; GO:0000422; P:autophagy of mitochondrion; IMP:SGD.
DR GO; GO:0071255; P:Cvt vesicle assembly; IMP:SGD.
DR GO; GO:0044805; P:late nucleophagy; IMP:SGD.
DR GO; GO:0016236; P:macroautophagy; IMP:SGD.
DR GO; GO:0000423; P:mitophagy; IBA:GO_Central.
DR GO; GO:0034727; P:piecemeal microautophagy of the nucleus; IMP:SGD.
DR GO; GO:0034497; P:protein localization to phagophore assembly site; IGI:SGD.
DR GO; GO:0006468; P:protein phosphorylation; IC:ComplexPortal.
DR GO; GO:0071211; P:protein targeting to vacuole involved in autophagy; IMP:SGD.
DR GO; GO:0042594; P:response to starvation; IC:ComplexPortal.
DR DisProt; DP01732; -.
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 3D-structure; Autophagy; Cytoplasm; Phosphoprotein; Protein transport;
KW Reference proteome; Transport.
FT CHAIN 1..738
FT /note="Autophagy-related protein 13"
FT /id="PRO_0000157972"
FT REGION 279..359
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 377..462
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 432..520
FT /note="Interaction with ATG1"
FT REGION 521..599
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 690..719
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 377..438
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 532..592
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 692..710
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 344
FT /note="Phosphoserine; by PKA"
FT /evidence="ECO:0000269|PubMed:19805182"
FT MOD_RES 348
FT /note="Phosphoserine; by TORC1"
FT /evidence="ECO:0000269|PubMed:19995911"
FT MOD_RES 355
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 437
FT /note="Phosphoserine; by TORC1 and PKA"
FT /evidence="ECO:0000269|PubMed:19805182,
FT ECO:0000269|PubMed:19995911"
FT MOD_RES 438
FT /note="Phosphoserine; by TORC1"
FT /evidence="ECO:0000269|PubMed:19995911"
FT MOD_RES 461
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 496
FT /note="Phosphoserine; by TORC1"
FT /evidence="ECO:0000269|PubMed:19995911"
FT MOD_RES 535
FT /note="Phosphoserine; by TORC1"
FT /evidence="ECO:0000269|PubMed:19995911"
FT MOD_RES 541
FT /note="Phosphoserine; by TORC1"
FT /evidence="ECO:0000269|PubMed:19995911"
FT MOD_RES 554
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 581
FT /note="Phosphoserine; by PKA"
FT /evidence="ECO:0000269|PubMed:19805182"
FT MOD_RES 646
FT /note="Phosphoserine; by TORC1"
FT /evidence="ECO:0000269|PubMed:19995911"
FT MOD_RES 649
FT /note="Phosphoserine; by TORC1"
FT /evidence="ECO:0000269|PubMed:19995911,
FT ECO:0007744|PubMed:15665377, ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT MUTAGEN 344
FT /note="S->A: Decreases phosphorylation by PKA."
FT /evidence="ECO:0000269|PubMed:19805182"
FT MUTAGEN 348
FT /note="S->A: Leads to constitutive activation of autophagy;
FT when associated with A-437; A-438; A-496; A-535; A-541; A-
FT 646 and A-649."
FT /evidence="ECO:0000269|PubMed:19995911"
FT MUTAGEN 437
FT /note="S->A: Decreases phosphorylation by PKA. Leads to
FT constitutive activation of autophagy; when associated with
FT A-348; A-438; A-496; A-535; A-541; A-646 and A-649."
FT /evidence="ECO:0000269|PubMed:19805182,
FT ECO:0000269|PubMed:19995911"
FT MUTAGEN 438
FT /note="S->A: Leads to constitutive activation of autophagy;
FT when associated with A-348; A-437; A-496; A-535; A-541; A-
FT 646 and A-649."
FT /evidence="ECO:0000269|PubMed:19995911"
FT MUTAGEN 468
FT /note="F->A: Impairs binding to ATG1; when associated with
FT A-469."
FT /evidence="ECO:0000269|PubMed:22885598"
FT MUTAGEN 469
FT /note="V->A: Impairs binding to ATG1; when associated with
FT A-468."
FT /evidence="ECO:0000269|PubMed:22885598"
FT MUTAGEN 496
FT /note="S->A: Leads to constitutive activation of autophagy;
FT when associated with A-348; A-437; A-438; A-535; A-541; A-
FT 646 and A-649."
FT /evidence="ECO:0000269|PubMed:19995911"
FT MUTAGEN 535
FT /note="S->A: Leads to constitutive activation of autophagy;
FT when associated with A-348; A-437; A-438; A-496; A-541; A-
FT 646 and A-649."
FT /evidence="ECO:0000269|PubMed:19995911"
FT MUTAGEN 541
FT /note="S->A: Leads to constitutive activation of autophagy;
FT when associated with A-348; A-437; A-438; A-496; A-535; A-
FT 646 and A-649."
FT /evidence="ECO:0000269|PubMed:19995911"
FT MUTAGEN 581
FT /note="S->A: Decreases phosphorylation by PKA."
FT /evidence="ECO:0000269|PubMed:19805182"
FT MUTAGEN 646
FT /note="S->A: Leads to constitutive activation of autophagy;
FT when associated with A-348; A-437; A-438; A-496; A-535; A-
FT 541 and A-649."
FT /evidence="ECO:0000269|PubMed:19995911"
FT MUTAGEN 649
FT /note="S->A: Leads to constitutive activation of autophagy;
FT when associated with A-348; A-437; A-438; A-496; A-535; A-
FT 541, and A-646."
FT /evidence="ECO:0000269|PubMed:19995911"
SQ SEQUENCE 738 AA; 83281 MW; 45CD16F69B795E62 CRC64;
MVAEEDIEKQ VLQLIDSFFL KTTLLICSTE SSRYQSSTEN IFLFDDTWFE DHSELVSELP
EIISKWSHYD GRKELPPLVV ETYLDLRQLN SSHLVRLKDH EGHLWNVCKG TKKQEIVMER
WLIELDNSSP TFKSYSEDET DVNELSKQLV LLFRYLLTLI QLLPTTELYQ LLIKSYNGPQ
NEGSSNPITS TGPLVSIRTC VLDGSKPILS KGRIGLSKPI INTYSNALNE SNLPAHLDQK
KITPVWTKFG LLRVSVSYRR DWKFEINNTN DELFSARHAS VSHNSQGPQN QPEQEGQSDQ
DIGKRQPQFQ QQQQPQQQQQ QQQQQQRQHQ VQTQQQRQIP DRRSLSLSPC TRANSFEPQS
WQKKVYPISR PVQPFKVGSI GSQSASRNPS NSSFFNQPPV HRPSMSSNYG PQMNIEGTSV
GSTSKYSSSF GNIRRHSSVK TTENAEKVSK AVKSPLQPQE SQEDLMDFVK LLEEKPDLTI
KKTSGNNPPN INISDSLIRY QNLKPSNDLL SEDLSVSLSM DPNHTYHRGR SDSHSPLPSI
SPSMHYGSLN SRMSQGANAS HLIARGGGNS STSALNSRRN SLDKSSNKQG MSGLPPIFGG
ESTSYHHDNK IQKYNQLGVE EDDDDENDRL LNQMGNSATK FKSSISPRSI DSISSSFIKS
RIPIRQPYHY SQPTTAPFQA QAKFHKPANK LIDNGNRSNS NNNNHNGNDA VGVMHNDEDD
QDDDLVFFMS DMNLSKEG
