ATG13_KLUMD
ID ATG13_KLUMD Reviewed; 712 AA.
AC W0TA43;
DT 25-APR-2018, integrated into UniProtKB/Swiss-Prot.
DT 19-MAR-2014, sequence version 1.
DT 25-MAY-2022, entry version 40.
DE RecName: Full=Autophagy-related protein 13 {ECO:0000303|PubMed:26442587};
GN Name=ATG13 {ECO:0000303|PubMed:26442587}; ORFNames=KLMA_40473;
OS Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275)
OS (Yeast) (Candida kefyr).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Kluyveromyces.
OX NCBI_TaxID=1003335;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DMKU3-1042 / BCC 29191 / NBRC 104275;
RX PubMed=25834639; DOI=10.1186/s13068-015-0227-x;
RA Lertwattanasakul N., Kosaka T., Hosoyama A., Suzuki Y., Rodrussamee N.,
RA Matsutani M., Murata M., Fujimoto N., Suprayogi X., Tsuchikane K.,
RA Limtong S., Fujita N., Yamada M.;
RT "Genetic basis of the highly efficient yeast Kluyveromyces marxianus:
RT complete genome sequence and transcriptome analyses.";
RL Biotechnol. Biofuels 8:47-47(2015).
RN [2]
RP IDENTIFICATION, FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=26442587; DOI=10.1074/jbc.m115.684233;
RA Yamamoto H., Shima T., Yamaguchi M., Mochizuki Y., Hoshida H., Kakuta S.,
RA Kondo-Kakuta C., Noda N.N., Inagaki F., Itoh T., Akada R., Ohsumi Y.;
RT "The thermotolerant yeast Kluyveromyces marxianus is a useful organism for
RT structural and biochemical studies of autophagy.";
RL J. Biol. Chem. 290:29506-29518(2015).
RN [3] {ECO:0007744|PDB:4P1N}
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 441-500 IN COMPLEX WITH ATG1,
RP INTERACTION WITH ATG1 AND ATG17, DOMAIN, FUNCTION, DISRUPTION PHENOTYPE,
RP AND PHOSPHORYLATION.
RX PubMed=24793651; DOI=10.1038/nsmb.2822;
RA Fujioka Y., Suzuki S.W., Yamamoto H., Kondo-Kakuta C., Kimura Y.,
RA Hirano H., Akada R., Inagaki F., Ohsumi Y., Noda N.N.;
RT "Structural basis of starvation-induced assembly of the autophagy
RT initiation complex.";
RL Nat. Struct. Mol. Biol. 21:513-521(2014).
CC -!- FUNCTION: Activates the ATG1 kinase in a nutritional condition
CC dependent manner through the TOR pathway, leading to autophagy
CC (PubMed:26442587, PubMed:24793651). Involved in ATG9 and ATG23 cycling
CC through the pre-autophagosomal structure (By similarity). Also involved
CC in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt
CC vesicle formation (PubMed:24793651). Seems to play a role in the
CC switching machinery regulating the conversion between the Cvt pathway
CC and autophagy (By similarity). Finally, ATG13 is also required for
CC glycogen storage during stationary phase (By similarity).
CC {ECO:0000250|UniProtKB:Q06628, ECO:0000269|PubMed:24793651,
CC ECO:0000269|PubMed:26442587}.
CC -!- SUBUNIT: Hypophosphorylated form interacts with ATG1 to form the ATG1-
CC ATG13 kinase complex (PubMed:24793651). The ATG1-ATG13 complex
CC interacts with the ATG17-ATG29-ATG31 complex through direct interaction
CC with ATG17 (PubMed:24793651). Interacts with VAC8 (By similarity).
CC {ECO:0000250|UniProtKB:Q06628, ECO:0000269|PubMed:24793651}.
CC -!- INTERACTION:
CC W0TA43; W0T9X4: ATG1; NbExp=3; IntAct=EBI-16104996, EBI-16104970;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q06628}.
CC Preautophagosomal structure {ECO:0000250|UniProtKB:Q06628}.
CC -!- DOMAIN: The minimum ATG1-binding domain (residues 441 to 500) comprises
CC two alpha-helices and a linker connecting them (PubMed:24793651).
CC {ECO:0000269|PubMed:24793651}.
CC -!- PTM: Hyperphosphorylated under nutrient-rich conditions
CC (PubMed:24793651). Starvation and TOR inactivation results in ATG13
CC partial dephosphorylation leading to ATG1-binding (PubMed:24793651).
CC Dephosphorylation induces ATG17-binding (PubMed:24793651).
CC {ECO:0000269|PubMed:24793651}.
CC -!- DISRUPTION PHENOTYPE: Impairs ATG17 localization to the
CC preautophagosomal structure (PubMed:24793651). Still forms
CC preautophagosomal structures (PAS) in proximity to the vacuolar
CC membrane (PubMed:26442587). {ECO:0000269|PubMed:24793651,
CC ECO:0000269|PubMed:26442587}.
CC -!- MISCELLANEOUS: Kluyveromyces marxianus proteins are shorter in length
CC and have a more ordered secondary structure than their S.cerevisiae
CC counterparts, which might contribute to the superior thermotolerance
CC and solubility (PubMed:26442587). K.marxianus could be therefore useful
CC as a new model organism for further elucidation of the molecular
CC details of autophagy (PubMed:26442587). {ECO:0000269|PubMed:26442587}.
CC -!- SIMILARITY: Belongs to the ATG13 family. Fungi subfamily.
CC {ECO:0000305}.
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DR EMBL; AP012216; BAO40497.1; -; Genomic_DNA.
DR PDB; 4P1N; X-ray; 2.20 A; C/D=440-500.
DR PDBsum; 4P1N; -.
DR AlphaFoldDB; W0TA43; -.
DR SMR; W0TA43; -.
DR DIP; DIP-60844N; -.
DR IntAct; W0TA43; 1.
DR EnsemblFungi; BAO40497; BAO40497; KLMA_40473.
DR OrthoDB; 490734at2759; -.
DR Proteomes; UP000065495; Chromosome 4.
DR GO; GO:1990316; C:Atg1/ULK1 kinase complex; IEA:EnsemblFungi.
DR GO; GO:0019898; C:extrinsic component of membrane; IEA:EnsemblFungi.
DR GO; GO:0000407; C:phagophore assembly site; IEA:UniProtKB-SubCell.
DR GO; GO:0120095; C:vacuole-isolation membrane contact site; IEA:EnsemblFungi.
DR GO; GO:0019887; F:protein kinase regulator activity; IEA:EnsemblFungi.
DR GO; GO:0032147; P:activation of protein kinase activity; IEA:EnsemblFungi.
DR GO; GO:0000422; P:autophagy of mitochondrion; IEA:EnsemblFungi.
DR GO; GO:0071255; P:Cvt vesicle assembly; IEA:EnsemblFungi.
DR GO; GO:0044805; P:late nucleophagy; IEA:EnsemblFungi.
DR GO; GO:0034727; P:piecemeal microautophagy of the nucleus; IEA:EnsemblFungi.
DR GO; GO:0034497; P:protein localization to phagophore assembly site; IEA:EnsemblFungi.
DR GO; GO:0071211; P:protein targeting to vacuole involved in autophagy; IEA:EnsemblFungi.
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 Transport.
FT CHAIN 1..712
FT /note="Autophagy-related protein 13"
FT /id="PRO_0000443908"
FT REGION 388..443
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 412..420
FT /note="ATG17-binding"
FT /evidence="ECO:0000269|PubMed:24793651"
FT REGION 441..500
FT /note="ATG1-binding"
FT /evidence="ECO:0000269|PubMed:24793651"
FT REGION 568..611
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 388..417
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 420..443
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 576..590
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 447..454
FT /evidence="ECO:0007829|PDB:4P1N"
FT HELIX 464..466
FT /evidence="ECO:0007829|PDB:4P1N"
FT HELIX 472..496
FT /evidence="ECO:0007829|PDB:4P1N"
SQ SEQUENCE 712 AA; 78683 MW; B743AA3C348A5CA3 CRC64;
MSDSDREIIG LINNFFLKAA LLLEQCKVVA RGGGFDGEEP LRDGNHLFNI ETRGDPTLEA
QIQPWTTFDG EKSMPPLVLE TFLDLRGLHS NQTVYLHDSD GNPWMVCKGG KKSEIVLERW
LIELDRQFSS TTGSTDAAED DEYNEFNDPE NLHKQLVLLF RYLYTLTQLL PANDIITKLQ
ASQQGTAQAT TTTGTLKPLH IHTRLLDGSK PILSKGRVGL SKPIIASYSN TMNETNIASH
LEQRKITPIK TKFGSLRITV SYRKDVDFYV IDQEDPYKRT TNVSALQDTV TATDRRISSN
SNISISVSPK TTNMLNANHI PVDSSGGGFA RRQSISSKLQ PFKVGSVGSG SFVQSGSLQS
VTNPNPSLSR NVSSSSVAAA LKVQRGSAGS TVLNSDLPPE LSSVGSGSKY SSSFGRIRRH
SSVRRSESID RTAKPRKSNE TPPEDLLEFV KLLEDKKELN MKPSTILPQQ DISSSLIKFQ
SMKPNNDTLS DNLSMSMSID QPNMRMGSNS HSPIPSFSPN YGSIPSRLSQ GSRNNSNVEL
ITSRKSSLDR HRLSLLNRTG SNVDIRRGSV GTMETTNEDS KEDEDSHVHG LRFNSGTVND
KTEDNNEDDD EEEILIKRSS NAVASSTEHF SVSPRSARSI SVSSYTRSQL PLKHPNFSYP
TTSATTAHAK FHKSEVIPDQ LHREGSHHHN SSHKNDEDDD LLFVMSDMNL TN
