ATG16_YEAST
ID ATG16_YEAST Reviewed; 150 AA.
AC Q03818; D6VZY1;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 163.
DE RecName: Full=Autophagy protein 16;
DE AltName: Full=Cytoplasm to vacuole targeting protein 11;
DE AltName: Full=SAP18 homolog;
GN Name=ATG16; Synonyms=APG15, APG16, CVT11, SAP18; OrderedLocusNames=YMR159C;
GN ORFNames=YM8520.08C;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [2]
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 [3]
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 [4]
RP FUNCTION.
RX PubMed=8663607; DOI=10.1074/jbc.271.30.17621;
RA Harding T.M., Hefner-Gravink A., Thumm M., Klionsky D.J.;
RT "Genetic and phenotypic overlap between autophagy and the cytoplasm to
RT vacuole protein targeting pathway.";
RL J. Biol. Chem. 271:17621-17624(1996).
RN [5]
RP FUNCTION, AND INTERACTION WITH ATG5 AND ATG12.
RX PubMed=10406794; DOI=10.1093/emboj/18.14.3888;
RA Mizushima N., Noda T., Ohsumi Y.;
RT "Apg16p is required for the function of the Apg12p-Apg5p conjugate in the
RT yeast autophagy pathway.";
RL EMBO J. 18:3888-3896(1999).
RN [6]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=11689437; DOI=10.1093/emboj/20.21.5971;
RA Suzuki K., Kirisako T., Kamada Y., Mizushima N., Noda T., Ohsumi Y.;
RT "The pre-autophagosomal structure organized by concerted functions of APG
RT genes is essential for autophagosome formation.";
RL EMBO J. 20:5971-5981(2001).
RN [7]
RP FUNCTION, AND IDENTIFICATION IN THE COMPLEX.
RX PubMed=11897782; DOI=10.1074/jbc.m111889200;
RA Kuma A., Mizushima N., Ishihara N., Ohsumi Y.;
RT "Formation of the approximately 350-kDa Apg12-Apg5.Apg16 multimeric
RT complex, mediated by Apg16 oligomerization, is essential for autophagy in
RT yeast.";
RL J. Biol. Chem. 277:18619-18625(2002).
RN [8]
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 [9]
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 [10]
RP PHENOTYPIC CHARACTERIZATION.
RX PubMed=15277759; DOI=10.1271/bbb.68.1541;
RA Okazaki H., Ono B., Ohsumi Y., Ohsumi M.;
RT "apg15-1, a UGA mutant allele in the Saccharomyces cerevisiae APG16 gene,
RT and its suppression by a cytoplasmic factor.";
RL Biosci. Biotechnol. Biochem. 68:1541-1548(2004).
RN [11]
RP IDENTIFICATION IN THE ATG5-ATG12/ATG16 COMPLEX.
RX PubMed=16874032; DOI=10.4161/auto.1.2.1858;
RA Hanada T., Ohsumi Y.;
RT "Structure-function relationship of Atg12, a ubiquitin-like modifier
RT essential for autophagy.";
RL Autophagy 1:110-118(2005).
RN [12]
RP FUNCTION.
RX PubMed=15569245; DOI=10.1111/j.1600-0854.2004.00245.x;
RA Hamasaki M., Noda T., Baba M., Ohsumi Y.;
RT "Starvation triggers the delivery of the endoplasmic reticulum to the
RT vacuole via autophagy in yeast.";
RL Traffic 6:56-65(2005).
RN [13]
RP FUNCTION.
RX PubMed=17132049; DOI=10.1371/journal.pbio.0040423;
RA Bernales S., McDonald K.L., Walter P.;
RT "Autophagy counterbalances endoplasmic reticulum expansion during the
RT unfolded protein response.";
RL PLoS Biol. 4:E423-E423(2006).
RN [14]
RP SUBCELLULAR LOCATION.
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 [15]
RP SUBCELLULAR LOCATION.
RX PubMed=20154084; DOI=10.1074/jbc.m109.080374;
RA Nair U., Cao Y., Xie Z., Klionsky D.J.;
RT "Roles of the lipid-binding motifs of Atg18 and Atg21 in the cytoplasm to
RT vacuole targeting pathway and autophagy.";
RL J. Biol. Chem. 285:11476-11488(2010).
RN [16]
RP FUNCTION.
RX PubMed=22652539; DOI=10.4161/auto.19652;
RA Yu Z.Q., Ni T., Hong B., Wang H.Y., Jiang F.J., Zou S., Chen Y.,
RA Zheng X.L., Klionsky D.J., Liang Y., Xie Z.;
RT "Dual roles of Atg8-PE deconjugation by Atg4 in autophagy.";
RL Autophagy 8:883-892(2012).
RN [17]
RP FUNCTION, AND SUBCELLULAR LOCATION OF THE ATG5-ATG2/ATG16 COMPLEX.
RX PubMed=23064152; DOI=10.1038/emboj.2012.278;
RA Romanov J., Walczak M., Ibiricu I., Schuchner S., Ogris E., Kraft C.,
RA Martens S.;
RT "Mechanism and functions of membrane binding by the Atg5-Atg12/Atg16
RT complex during autophagosome formation.";
RL EMBO J. 31:4304-4317(2012).
RN [18]
RP X-RAY CRYSTALLOGRAPHY (1.97 ANGSTROMS) OF 1-57 IN COMPLEX WITH ATG5,
RP MUTAGENESIS OF ARG-35 AND PHE-46, AND FUNCTION.
RX PubMed=17192262; DOI=10.1074/jbc.m609876200;
RA Matsushita M., Suzuki N.N., Obara K., Fujioka Y., Ohsumi Y., Inagaki F.;
RT "Structure of Atg5.Atg16, a complex essential for autophagy.";
RL J. Biol. Chem. 282:6763-6772(2007).
RN [19]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT, AND MUTAGENESIS OF ASP-101;
RP GLU-102; ILE-104; ILE-108 AND VAL-112.
RX PubMed=19889643; DOI=10.1074/jbc.m109.053520;
RA Fujioka Y., Noda N.N., Nakatogawa H., Ohsumi Y., Inagaki F.;
RT "Dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its
RT functional significance in autophagy.";
RL J. Biol. Chem. 285:1508-1515(2010).
RN [20]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-46 IN COMPLEX WITH ATG5 AND
RP ATG12.
RX PubMed=23238393; DOI=10.1038/embor.2012.208;
RA Noda N.N., Fujioka Y., Hanada T., Ohsumi Y., Inagaki F.;
RT "Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating
RT Atg8-PE conjugation.";
RL EMBO Rep. 14:206-211(2013).
CC -!- FUNCTION: Stabilizes the ATG5-ATG12 conjugate and mediates the
CC formation of the 350 kDa complex, which is necessary for autophagy. The
CC ATG5-ATG12/ATG16 complex is required for efficient promotion of ATG8-
CC conjugation to phosphatidylethanolamine and ATG8 localization to the
CC pre-autophagosomal structure (PAS). Recruits also ATG3 to the PAS.
CC Involved in endoplasmic reticulum-specific autophagic process and is
CC essential for the survival of cells subjected to severe ER stress.
CC {ECO:0000269|PubMed:10406794, ECO:0000269|PubMed:11689437,
CC ECO:0000269|PubMed:11897782, ECO:0000269|PubMed:15569245,
CC ECO:0000269|PubMed:17132049, ECO:0000269|PubMed:17192262,
CC ECO:0000269|PubMed:22652539, ECO:0000269|PubMed:23064152,
CC ECO:0000269|PubMed:8224160, ECO:0000269|PubMed:8663607}.
CC -!- SUBUNIT: Homodimer. Part of the 350 kDa complex which is at least
CC composed of ATG5, ATG12 and ATG16. Several units of each may be present
CC in this complex. Interacts directly with ATG12.
CC {ECO:0000269|PubMed:10406794, ECO:0000269|PubMed:11897782,
CC ECO:0000269|PubMed:16874032, ECO:0000269|PubMed:17192262,
CC ECO:0000269|PubMed:19889643, ECO:0000269|PubMed:23238393}.
CC -!- INTERACTION:
CC Q03818; P38316: ATG12; NbExp=10; IntAct=EBI-27344, EBI-2692;
CC Q03818; Q03818: ATG16; NbExp=3; IntAct=EBI-27344, EBI-27344;
CC Q03818; Q12380: ATG5; NbExp=4; IntAct=EBI-27344, EBI-2664;
CC -!- SUBCELLULAR LOCATION: Preautophagosomal structure membrane
CC {ECO:0000269|PubMed:11689437, ECO:0000269|PubMed:18077553,
CC ECO:0000269|PubMed:20154084, ECO:0000269|PubMed:23064152}; Peripheral
CC membrane protein {ECO:0000269|PubMed:11689437,
CC ECO:0000269|PubMed:18077553, ECO:0000269|PubMed:20154084,
CC ECO:0000269|PubMed:23064152}.
CC -!- MISCELLANEOUS: Present with 573 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the ATG16 family. {ECO:0000305}.
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DR EMBL; Z49705; CAA89795.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA10055.1; -; Genomic_DNA.
DR PIR; S54517; S54517.
DR RefSeq; NP_013882.1; NM_001182663.1.
DR PDB; 2DYM; X-ray; 2.20 A; B/D/F/H=1-46.
DR PDB; 2DYO; X-ray; 1.97 A; B=1-57.
DR PDB; 3A7O; X-ray; 2.50 A; A/B/C/D/E/F=50-123.
DR PDB; 3A7P; X-ray; 2.80 A; A/B=1-150.
DR PDB; 3W1S; X-ray; 2.60 A; B=1-46.
DR PDBsum; 2DYM; -.
DR PDBsum; 2DYO; -.
DR PDBsum; 3A7O; -.
DR PDBsum; 3A7P; -.
DR PDBsum; 3W1S; -.
DR AlphaFoldDB; Q03818; -.
DR SMR; Q03818; -.
DR BioGRID; 35336; 108.
DR ComplexPortal; CPX-1849; ATG12-ATG5-ATG16 complex.
DR DIP; DIP-2144N; -.
DR IntAct; Q03818; 8.
DR MINT; Q03818; -.
DR STRING; 4932.YMR159C; -.
DR PaxDb; Q03818; -.
DR PRIDE; Q03818; -.
DR EnsemblFungi; YMR159C_mRNA; YMR159C; YMR159C.
DR GeneID; 855194; -.
DR KEGG; sce:YMR159C; -.
DR SGD; S000004769; ATG16.
DR VEuPathDB; FungiDB:YMR159C; -.
DR eggNOG; ENOG502S6TV; Eukaryota.
DR HOGENOM; CLU_158825_0_0_1; -.
DR InParanoid; Q03818; -.
DR OMA; QLRNKDY; -.
DR BioCyc; YEAST:G3O-32849-MON; -.
DR EvolutionaryTrace; Q03818; -.
DR PRO; PR:Q03818; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; Q03818; protein.
DR GO; GO:0034274; C:Atg12-Atg5-Atg16 complex; IDA:SGD.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005829; C:cytosol; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0061908; C:phagophore; IDA:SGD.
DR GO; GO:0000407; C:phagophore assembly site; IDA:SGD.
DR GO; GO:0034045; C:phagophore assembly site membrane; IC:ComplexPortal.
DR GO; GO:0120095; C:vacuole-isolation membrane contact site; IDA:SGD.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0030674; F:protein-macromolecule adaptor activity; IMP:SGD.
DR GO; GO:0000045; P:autophagosome assembly; IC:ComplexPortal.
DR GO; GO:1905037; P:autophagosome organization; IMP:SGD.
DR GO; GO:0006914; P:autophagy; IMP:UniProtKB.
DR GO; GO:0000422; P:autophagy of mitochondrion; IMP:SGD.
DR GO; GO:0006501; P:C-terminal protein lipidation; IMP:SGD.
DR GO; GO:0032258; P:cytoplasm to vacuole transport by the Cvt pathway; IMP:SGD.
DR GO; GO:0044805; P:late nucleophagy; IMP:SGD.
DR GO; GO:0016236; P:macroautophagy; IDA:SGD.
DR GO; GO:0034727; P:piecemeal microautophagy of the nucleus; IMP:SGD.
DR GO; GO:0006497; P:protein lipidation; IDA:ComplexPortal.
DR IDEAL; IID50085; -.
DR InterPro; IPR013923; Autophagy-rel_prot_16_dom.
DR Pfam; PF08614; ATG16; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Autophagy; Coiled coil; Membrane; Protein transport;
KW Reference proteome; Transport.
FT CHAIN 1..150
FT /note="Autophagy protein 16"
FT /id="PRO_0000218595"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 58..130
FT /evidence="ECO:0000255"
FT COMPBIAS 7..23
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 35
FT /note="R->A: Impairs interaction with ATG5and autophagy."
FT /evidence="ECO:0000269|PubMed:17192262"
FT MUTAGEN 46
FT /note="F->A: Impairs interaction with ATG5and autophagy."
FT /evidence="ECO:0000269|PubMed:17192262"
FT MUTAGEN 101
FT /note="D->A: Significantly reduces autophagic activity;
FT when associated with A-102."
FT /evidence="ECO:0000269|PubMed:19889643"
FT MUTAGEN 102
FT /note="E->A: Significantly reduces autophagic activity;
FT when associated with A-101."
FT /evidence="ECO:0000269|PubMed:19889643"
FT MUTAGEN 104
FT /note="I->A: Significantly reduces autophagic activity;
FT when associated with A-108 and A-112."
FT /evidence="ECO:0000269|PubMed:19889643"
FT MUTAGEN 108
FT /note="I->A: Significantly reduces autophagic activity;
FT when associated with A-104 and A-112."
FT /evidence="ECO:0000269|PubMed:19889643"
FT MUTAGEN 112
FT /note="V->A: Significantly reduces autophagic activity;
FT when associated with A-104 and A-108."
FT /evidence="ECO:0000269|PubMed:19889643"
FT HELIX 23..40
FT /evidence="ECO:0007829|PDB:2DYO"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:2DYO"
FT TURN 48..51
FT /evidence="ECO:0007829|PDB:2DYO"
FT HELIX 61..117
FT /evidence="ECO:0007829|PDB:3A7O"
SQ SEQUENCE 150 AA; 17222 MW; 6D4308298D4DBB59 CRC64;
MGNFIITERK KAKEERSNPQ TDSMDDLLIR RLTDRNDKEA HLNELFQDNS GAIGGNIVSH
DDALLNTLAI LQKELKSKEQ EIRRLKEVIA LKNKNTERLN DELISGTIEN NVLQQKLSDL
KKEHSQLVAR WLKKTEKETE AMNSEIDGTK
