true2005-03-152024-03-27177ATG13_YEASTAnalyses of APG13 gene involved in autophagy in yeast, Saccharomyces cerevisiae.Funakoshi T.Matsuura A.Noda T.Ohsumi Y.doi:10.1016/s0378-1119(97)00031-01997Gene192207-213NUCLEOTIDE SEQUENCE [GENOMIC DNA]The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.Bussey H.Storms R.K.Ahmed A.Albermann K.Allen E.Ansorge W.Araujo R.Aparicio A.Barrell B.G.Badcock K.Benes V.Botstein D.Bowman S.Brueckner M.Carpenter J.Cherry J.M.Chung E.Churcher C.M.Coster F.Davis K.Davis R.W.Dietrich F.S.Delius H.DiPaolo T.Dubois E.Duesterhoeft A.Duncan M.Floeth M.Fortin N.Friesen J.D.Fritz C.Goffeau A.Hall J.Hebling U.Heumann K.Hilbert H.Hillier L.W.Hunicke-Smith S.Hyman R.W.Johnston M.Kalman S.Kleine K.Komp C.Kurdi O.Lashkari D.Lew H.Lin A.Lin D.Louis E.J.Marathe R.Messenguy F.Mewes H.-W.Mirtipati S.Moestl D.Mueller-Auer S.Namath A.Nentwich U.Oefner P.Pearson D.Petel F.X.Pohl T.M.Purnelle B.Rajandream M.A.Rechmann S.Rieger M.Riles L.Roberts D.Schaefer M.Scharfe M.Scherens B.Schramm S.Schroeder M.Sdicu A.-M.Tettelin H.Urrestarazu L.A.Ushinsky S.Vierendeels F.Vissers S.Voss H.Walsh S.V.Wambutt R.Wang Y.Wedler E.Wedler H.Winnett E.Zhong W.-W.Zollner A.Vo D.H.Hani J.1997Nature387103-105NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]ATCC 204508 / S288cThe reference genome sequence of Saccharomyces cerevisiae: Then and now.Engel S.R.Dietrich F.S.Fisk D.G.Binkley G.Balakrishnan R.Costanzo M.C.Dwight S.S.Hitz B.C.Karra K.Nash R.S.Weng S.Wong E.D.Lloyd P.Skrzypek M.S.Miyasato S.R.Simison M.Cherry J.M.doi:10.1534/g3.113.0089952014G3 (Bethesda)4389-398GENOME REANNOTATIONIsolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae.Tsukada M.Ohsumi Y.doi:10.1016/0014-5793(93)80398-e1993FEBS Lett.333169-174FUNCTIONApg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting.Scott S.V.Nice D.C. IIINau J.J.Weisman L.S.Kamada Y.Keizer-Gunnink I.Funakoshi T.Veenhuis M.Ohsumi Y.Klionsky D.J.doi:10.1074/jbc.m0028132002000J. Biol. Chem.27525840-25849FUNCTIONINTERACTION WITH VAC8PHOSPHORYLATIONDissection of autophagosome biogenesis into distinct nucleation and expansion steps.Abeliovich H.Dunn W.A. Jr.Kim J.Klionsky D.J.doi:10.1083/jcb.151.5.10252000J. Cell Biol.1511025-1034FUNCTIONTor-mediated induction of autophagy via an Apg1 protein kinase complex.Kamada Y.Funakoshi T.Shintani T.Nagano K.Ohsumi M.Ohsumi Y.doi:10.1083/jcb.150.6.15072000J. Cell Biol.1501507-1513FUNCTIONPHOSPHORYLATIONINTERACTION WITH ATG1Antagonistic controls of autophagy and glycogen accumulation by Snf1p, the yeast homolog of AMP-activated protein kinase, and the cyclin-dependent kinase Pho85p.Wang Z.Wilson W.A.Fujino M.A.Roach P.J.doi:10.1128/mcb.21.17.5742-5752.20012001Mol. Cell. Biol.215742-5752FUNCTIONA unified nomenclature for yeast autophagy-related genes.Klionsky D.J.Cregg J.M.Dunn W.A. Jr.Emr S.D.Sakai Y.Sandoval I.V.Sibirny A.Subramani S.Thumm M.Veenhuis M.Ohsumi Y.doi:10.1016/s1534-5807(03)00296-x2003Dev. Cell5539-545NOMENCLATUREGlobal analysis of protein localization in budding yeast.Huh W.-K.Falvo J.V.Gerke L.C.Carroll A.S.Howson R.W.Weissman J.S.O'Shea E.K.doi:10.1038/nature020262003Nature425686-691SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS]Global analysis of protein expression in yeast.Ghaemmaghami S.Huh W.-K.Bower K.Howson R.W.Belle A.Dephoure N.O'Shea E.K.Weissman J.S.doi:10.1038/nature020462003Nature425737-741LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS]The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure.Reggiori F.Tucker K.A.Stromhaug P.E.Klionsky D.J.doi:10.1016/s1534-5807(03)00402-72004Dev. Cell679-90FUNCTIONAtg17 functions in cooperation with Atg1 and Atg13 in yeast autophagy.Kabeya Y.Kamada Y.Baba M.Takikawa H.Sasaki M.Ohsumi Y.doi:10.1091/mbc.e04-08-06692005Mol. Biol. Cell162544-2553FUNCTIONINTERACTION WITH ATG1 AND ATG17Atg17 regulates the magnitude of the autophagic response.Cheong H.Yorimitsu T.Reggiori F.Legakis J.E.Wang C.W.Klionsky D.J.doi:10.1091/mbc.e04-10-08942005Mol. Biol. Cell163438-3453INTERACTION WITH ATG1 AND ATG17Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.Gruhler A.Olsen J.V.Mohammed S.Mortensen P.Faergeman N.J.Mann M.Jensen O.N.doi:10.1074/mcp.m400219-mcp2002005Mol. Cell. Proteomics4310-327PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-649IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]YAL6BA cycling protein complex required for selective autophagy.Legakis J.E.Yen W.L.Klionsky D.J.doi:10.4161/auto.41292007Autophagy3422-432FUNCTIONHierarchy of Atg proteins in pre-autophagosomal structure organization.Suzuki K.Kubota Y.Sekito T.Ohsumi Y.doi:10.1111/j.1365-2443.2007.01050.x2007Genes Cells12209-218FUNCTIONSUBCELLULAR LOCATIONLarge-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.Li X.Gerber S.A.Rudner A.D.Beausoleil S.A.Haas W.Villen J.Elias J.E.Gygi S.P.doi:10.1021/pr060559j2007J. Proteome Res.61190-1197PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-355IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]ADR376Protein kinase A and Sch9 cooperatively regulate induction of autophagy in Saccharomyces cerevisiae.Yorimitsu T.Zaman S.Broach J.R.Klionsky D.J.doi:10.1091/mbc.e07-05-04852007Mol. Biol. Cell184180-4189FUNCTIONPHOSPHORYLATIONThe Atg1 kinase complex is involved in the regulation of protein recruitment to initiate sequestering vesicle formation for nonspecific autophagy in Saccharomyces cerevisiae.Cheong H.Nair U.Geng J.Klionsky D.J.doi:10.1091/mbc.e07-08-08262008Mol. Biol. Cell19668-681FUNCTIONOrganization of the pre-autophagosomal structure responsible for autophagosome formation.Kawamata T.Kamada Y.Kabeya Y.Sekito T.Ohsumi Y.doi:10.1091/mbc.e07-10-10482008Mol. Biol. Cell192039-2050FUNCTION OF THE ATG1-ATG13 COMPLEXSelf-interaction is critical for Atg9 transport and function at the phagophore assembly site during autophagy.He C.Baba M.Cao Y.Klionsky D.J.doi:10.1091/mbc.e08-05-05442008Mol. Biol. Cell195506-5516INTERACTION WITH ATG1A multidimensional chromatography technology for in-depth phosphoproteome analysis.Albuquerque C.P.Smolka M.B.Payne S.H.Bafna V.Eng J.Zhou H.doi:10.1074/mcp.m700468-mcp2002008Mol. Cell. Proteomics71389-1396PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-355; SER-461; SER-554 AND SER-649IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]Characterization of the Atg17-Atg29-Atg31 complex specifically required for starvation-induced autophagy in Saccharomyces cerevisiae.Kabeya Y.Noda N.N.Fujioka Y.Suzuki K.Inagaki F.Ohsumi Y.doi:10.1016/j.bbrc.2009.09.0342009Biochem. Biophys. Res. Commun.389612-615INTERACTION WITH THE ATG17-ATG29-ATG31 COMPLEXThe Tor and PKA signaling pathways independently target the Atg1/Atg13 protein kinase complex to control autophagy.Stephan J.S.Yeh Y.Y.Ramachandran V.Deminoff S.J.Herman P.K.doi:10.1073/pnas.09033161062009Proc. Natl. Acad. Sci. U.S.A.10617049-17054PHOSPHORYLATION AT SER-344; SER-437 AND SER-581 BY PKAMUTAGENESIS OF SER-344; SER-437 AND SER-581FUNCTIONINTERACTION WITH ATG17Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.Holt L.J.Tuch B.B.Villen J.Johnson A.D.Gygi S.P.Morgan D.O.doi:10.1126/science.11728672009Science3251682-1686PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-355; SER-461 AND SER-649IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]Induction of autophagic flux by amino acid deprivation is distinct from nitrogen starvation-induced macroautophagy.Ecker N.Mor A.Journo D.Abeliovich H.doi:10.4161/auto.6.7.127532010Autophagy6879-890FUNCTIONActivation of Atg1 kinase in autophagy by regulated phosphorylation.Kijanska M.Dohnal I.Reiter W.Kaspar S.Stoffel I.Ammerer G.Kraft C.Peter M.doi:10.4161/auto.6.8.138492010Autophagy61168-1178INTERACTION WITH ATG1Autophosphorylation within the Atg1 activation loop is required for both kinase activity and the induction of autophagy in Saccharomyces cerevisiae.Yeh Y.Y.Wrasman K.Herman P.K.doi:10.1534/genetics.110.1165662010Genetics185871-882FUNCTIONINTERACTION WITH ATG1An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis.Mari M.Griffith J.Rieter E.Krishnappa L.Klionsky D.J.Reggiori F.doi:10.1083/jcb.2009120892010J. Cell Biol.1901005-1022FUNCTIONTor directly controls the Atg1 kinase complex to regulate autophagy.Kamada Y.Yoshino K.Kondo C.Kawamata T.Oshiro N.Yonezawa K.Ohsumi Y.doi:10.1128/mcb.01344-092010Mol. Cell. Biol.301049-1058PHOSPHORYLATION AT SER-348; SER-437; SER-438; SER-496; SER-535; SER-541; SER-646 AND SER-649MUTAGENESIS OF SER-348; SER-437; SER-438; SER-496; SER-535; SER-541; SER-646 AND SER-649FUNCTIONBidirectional regulation between TORC1 and autophagy in Saccharomyces cerevisiae.Shin C.S.Huh W.K.doi:10.4161/auto.7.8.156962011Autophagy7854-862PHOSPHORYLATION BY ATG1Mitochondria regulate autophagy by conserved signalling pathways.Graef M.Nunnari J.doi:10.1038/emboj.2011.1042011EMBO J.302101-2114FUNCTIONPHOSPHORYLATIONSUBCELLULAR LOCATION OF THE ATG1-ATG13 COMPLEXAntagonistic interactions between the cAMP-dependent protein kinase and Tor signaling pathways modulate cell growth in Saccharomyces cerevisiae.Ramachandran V.Herman P.K.doi:10.1534/genetics.110.1233722011Genetics187441-454PHOSPHORYLATIONDEPHOSPHORYLATIONAn Atg13 protein-mediated self-association of the Atg1 protein kinase is important for the induction of autophagy.Yeh Y.Y.Shah K.H.Herman P.K.doi:10.1074/jbc.m111.2503242011J. Biol. Chem.28628931-28939FUNCTIONINTERACTION WITH ATG1Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the absence of nitrogen starvation.Wu X.Tu B.P.doi:10.1091/mbc.e11-06-05252011Mol. Biol. Cell224124-4133PHOSPHORYLATIONDEPHOSPHORYLATIONArchitecture of the Atg17 complex as a scaffold for autophagosome biogenesis.Ragusa M.J.Stanley R.E.Hurley J.H.doi:10.1016/j.cell.2012.11.0282012Cell1511501-1512INTERACTION WITH THE ATG17-ATG29-ATG31 COMPLEXBinding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8 regulates autophagy.Kraft C.Kijanska M.Kalie E.Siergiejuk E.Lee S.S.Semplicio G.Stoffel I.Brezovich A.Verma M.Hansmann I.Ammerer G.Hofmann K.Tooze S.Peter M.doi:10.1038/emboj.2012.2252012EMBO J.313691-3703FUNCTIONINTERACTION WITH ATG1MUTAGENESIS OF PHE-468 AND VAL-469Ksp1 kinase regulates autophagy via the target of rapamycin complex 1 (TORC1) pathway.Umekawa M.Klionsky D.J.doi:10.1074/jbc.m112.3449522012J. Biol. Chem.28716300-16310FUNCTIONPHOSPHORYLATION BY TORC1 COMPLEXThe autophagy-related protein kinase Atg1 interacts with the ubiquitin-like protein Atg8 via the Atg8 family interacting motif to facilitate autophagosome formation.Nakatogawa H.Ohbayashi S.Sakoh-Nakatogawa M.Kakuta S.Suzuki S.W.Kirisako H.Kondo-Kakuta C.Noda N.N.Yamamoto H.Ohsumi Y.doi:10.1074/jbc.c112.3875142012J. Biol. Chem.28728503-28507FUNCTIONINTERACTION WITH ATG1The protein factor-arrest 11 (Far11) is essential for the toxicity of human caspase-10 in yeast and participates in the regulation of autophagy and the DNA damage signaling.Lisa-Santamaria P.Jimenez A.Revuelta J.L.doi:10.1074/jbc.m112.3441922012J. Biol. Chem.28729636-29647FUNCTIONPHOSPHORYLATIONTransient sequestration of TORC1 into stress granules during heat stress.Takahara T.Maeda T.doi:10.1016/j.molcel.2012.05.0192012Mol. Cell47242-252PHOSPHORYLATIONGtr/Ego-independent TORC1 activation is achieved through a glutamine-sensitive interaction with Pib2 on the vacuolar membrane.Ukai H.Araki Y.Kira S.Oikawa Y.May A.I.Noda T.doi:10.1371/journal.pgen.10073342018PLoS Genet.14e1007334PHOSPHORYLATIONQuaternary structures of Vac8 differentially regulate the Cvt and PMN pathways.Park J.Kim H.I.Jeong H.Lee M.Jang S.H.Yoon S.Y.Kim H.Park Z.Y.Jun Y.Lee C.doi:10.1080/15548627.2019.16596152020Autophagy16991-1006X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) OF 567-695 IN COMPLEX WITH VA8FUNCTIONINTERACTION WITH ATG13DOMAIN2.90B=567-6953.20B/D=567-695210ATG1 protein kinase complex10the autophagy-related phagophore-formation transporter (apt) familyATG13EukaryotaMacroautophagy1 hit in 10 CRISPR screensProteinHORMA domainATG13Atg13_NHORMA_dom_sfAUTOPHAGY-RELATED PROTEIN 13UNCHARACTERIZEDATG13Autophagy-related protein 13ATG13APG13YPR185WActivates the ATG1 kinase in a nutritional condition dependent manner through the TOR pathway, leading to autophagy (PubMed:10995454, PubMed:11086004, PubMed:15743910, PubMed:17295840, PubMed:18077553, PubMed:18287526, PubMed:19805182, PubMed:19995911, PubMed:20647741, PubMed:20855505, PubMed:22447937, PubMed:22778255, PubMed:22782902, PubMed:22885598, PubMed:8224160, PubMed:21468027). Required for autophosphorylation of ATG1 at 'Thr-226' and its dimerization (PubMed:20439775, PubMed:17699586, PubMed:21712380). May also be involved in the regulation of autophagy through SNF1 (PubMed:11486014). Involved in ATG9 and ATG23 cycling through the pre-autophagosomal structure (PubMed:14723849, PubMed:17426440). Also involved in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt vesicle formation (PubMed:10837477). Seems to play a role in the switching machinery regulating the conversion between the Cvt pathway and autophagy (PubMed:10837477, PubMed:31512555). Finally, ATG13 is also required for glycogen storage during stationary phase (PubMed:11486014).Hypophosphorylated form interacts with ATG1 to form the ATG1-ATG13 kinase complex (PubMed:10995454, PubMed:15743910, PubMed:15901835, PubMed:18829864, PubMed:20439775, PubMed:20953146, PubMed:21712380, PubMed:22778255, PubMed:22885598). The ATG1-ATG13 complex interacts with the ATG17-ATG29-ATG31 complex through direct interaction with ATG17 (PubMed:23219485, PubMed:15743910, PubMed:15901835, PubMed:19755117, PubMed:19805182). Interacts with VAC8 and forms heterotetramers of two VAC8 and two ATG13 (PubMed:10837477, PubMed:31512555).The extended 70 Angstroms-longloop of ATG13 specifically binds the highly conserved innergroove formed by the armadillo repeats of VAC8.Phosphorylated; hyperphosphorylated by the TORC1 kinase complex to repress the induction of autophagy in nutrient-replete conditions (PubMed:10995454, PubMed:19995911, PubMed:19805182, PubMed:22447937, PubMed:22727621, PubMed:29698392). Starvation and TOR inactivation results in ATG13 partial dephosphorylation leading to ATG1-binding (PubMed:10995454). Rephosphorylated by ATG1 during prolonged nitrogen starvation (PubMed:21490424). Also phosphorylated by PKA (PubMed:17699586, PubMed:19805182, PubMed:21078689). PKA phosphorylation regulates the association of ATG13 with the PAS (PubMed:21900499). Within this regulatory network, mitochondrial respiratory deficiency suppresses autophagic flux (PubMed:21468027). Hyperphosphorylation in rich medium is impaired in the absence of VAC8 (PubMed:10837477). Dephosphorylation is dependent on FAR11 (PubMed:22782902).Present with 149 molecules/cell in log phase SD medium.Belongs to the ATG13 family. Fungi subfamily.Autophagy-related protein 13832811738Disordered279359Disordered377462Interaction with ATG1432520Disordered521599Disordered690719Polar residues438Polar residues532592Polar residues692710Phosphoserine; by PKA344Phosphoserine; by TORC1348Phosphoserine355Phosphoserine; by TORC1 and PKA437Phosphoserine; by TORC1Phosphoserine461Phosphoserine; by TORC1496Phosphoserine; by TORC1535Phosphoserine; by TORC1541Phosphoserine554Phosphoserine; by PKA581Phosphoserine; by TORC1646Phosphoserine; by TORC1649Decreases phosphorylation by PKA.ALeads to constitutive activation of autophagy; when associated with A-437; A-438; A-496; A-535; A-541; A-646 and A-649.ADecreases phosphorylation by PKA. Leads to constitutive activation of autophagy; when associated with A-348; A-438; A-496; A-535; A-541; A-646 and A-649.ALeads to constitutive activation of autophagy; when associated with A-348; A-437; A-496; A-535; A-541; A-646 and A-649.AImpairs binding to ATG1; when associated with A-469.A468Impairs binding to ATG1; when associated with A-468.A469Leads to constitutive activation of autophagy; when associated with A-348; A-437; A-438; A-535; A-541; A-646 and A-649.ALeads to constitutive activation of autophagy; when associated with A-348; A-437; A-438; A-496; A-541; A-646 and A-649.ALeads to constitutive activation of autophagy; when associated with A-348; A-437; A-438; A-496; A-535; A-646 and A-649.ADecreases phosphorylation by PKA.ALeads to constitutive activation of autophagy; when associated with A-348; A-437; A-438; A-496; A-535; A-541 and A-649.ALeads to constitutive activation of autophagy; when associated with A-348; A-437; A-438; A-496; A-535; A-541, and A-646.Afalse18false6false7ATG1ATG17VAC81996-11-01183281496bbc4eee7890477521fd0c705159ecMVAEEDIEKQVLQLIDSFFLKTTLLICSTESSRYQSSTENIFLFDDTWFEDHSELVSELPEIISKWSHYDGRKELPPLVVETYLDLRQLNSSHLVRLKDHEGHLWNVCKGTKKQEIVMERWLIELDNSSPTFKSYSEDETDVNELSKQLVLLFRYLLTLIQLLPTTELYQLLIKSYNGPQNEGSSNPITSTGPLVSIRTCVLDGSKPILSKGRIGLSKPIINTYSNALNESNLPAHLDQKKITPVWTKFGLLRVSVSYRRDWKFEINNTNDELFSARHASVSHNSQGPQNQPEQEGQSDQDIGKRQPQFQQQQQPQQQQQQQQQQQRQHQVQTQQQRQIPDRRSLSLSPCTRANSFEPQSWQKKVYPISRPVQPFKVGSIGSQSASRNPSNSSFFNQPPVHRPSMSSNYGPQMNIEGTSVGSTSKYSSSFGNIRRHSSVKTTENAEKVSKAVKSPLQPQESQEDLMDFVKLLEEKPDLTIKKTSGNNPPNINISDSLIRYQNLKPSNDLLSEDLSVSLSMDPNHTYHRGRSDSHSPLPSISPSMHYGSLNSRMSQGANASHLIARGGGNSSTSALNSRRNSLDKSSNKQGMSGLPPIFGGESTSYHHDNKIQKYNQLGVEEDDDDENDRLLNQMGNSATKFKSSISPRSIDSISSSFIKSRIPIRQPYHYSQPTTAPFQAQAKFHKPANKLIDNGNRSNSNNNNHNGNDAVGVMHNDEDDQDDDLVFFMSDMNLSKEGtruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetrue