ID   ATG4_KLUMD              Reviewed;         451 AA.
AC   W0TGM7;
DT   25-APR-2018, integrated into UniProtKB/Swiss-Prot.
DT   19-MAR-2014, sequence version 1.
DT   03-AUG-2022, entry version 30.
DE   RecName: Full=Cysteine protease ATG4 {ECO:0000250|UniProtKB:P53867};
DE            EC=3.4.22.- {ECO:0000250|UniProtKB:P53867};
DE   AltName: Full=Autophagy-related protein 4 {ECO:0000303|PubMed:26442587};
GN   Name=ATG4 {ECO:0000303|PubMed:26442587}; ORFNames=KLMA_50615;
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).
CC   -!- FUNCTION: Cysteine protease that plays a key role in cytoplasm to
CC       vacuole transport (Cvt) and autophagy by mediating both proteolytic
CC       activation and delipidation of ATG8 (PubMed:26442587). Required for
CC       selective autophagic degradation of the nucleus (nucleophagy) as well
CC       as for mitophagy which contributes to regulate mitochondrial quantity
CC       and quality by eliminating the mitochondria to a basal level to fulfill
CC       cellular energy requirements and preventing excess ROS production (By
CC       similarity). The protease activity is required for proteolytic
CC       activation of ATG8: cleaves the C-terminal amino acid of ATG8 to reveal
CC       a C-terminal glycine (PubMed:26442587). ATG8 ubiquitin-like activity
CC       requires the exposure of the glycine at the C-terminus for its
CC       conjugation to phosphatidylethanolamine (PE) and its insertion to
CC       membranes, which is necessary for autophagy (PubMed:26442587). The
CC       ATG8-PE conjugate mediates tethering between adjacent membranes and
CC       stimulates membrane hemifusion, leading to expansion of the
CC       autophagosomal membrane during autophagy. In addition to the protease
CC       activity, also catalyzes deconjugation of PE-conjugated forms of ATG8
CC       during macroautophagy: ATG8 delipidation is required to release the
CC       protein from membranes, which facilitates multiple events during
CC       macroautophagy, and especially for efficient autophagosome biogenesis,
CC       the assembly of ATG9-containing tubulovesicular clusters into
CC       phagophores/autophagosomes, and for the disassembly of PAS-associated
CC       ATG components. ATG8 delipidation by ATG4 also recycles ATG8-PE
CC       generated on inappropriate membranes to maintain a reservoir of
CC       unlipidated ATG8 that is required for autophagosome formation at the
CC       PAS (By similarity). {ECO:0000250|UniProtKB:P53867,
CC       ECO:0000269|PubMed:26442587}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=[protein]-C-terminal L-amino acid-glycyl-
CC         phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-
CC         glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine;
CC         Xref=Rhea:RHEA:67548, Rhea:RHEA-COMP:17323, Rhea:RHEA-COMP:17324,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:64612, ChEBI:CHEBI:172940,
CC         ChEBI:CHEBI:172941; Evidence={ECO:0000250|UniProtKB:P53867};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67549;
CC         Evidence={ECO:0000250|UniProtKB:P53867};
CC   -!- SUBUNIT: Interacts with ATG8 (By similarity).
CC       {ECO:0000250|UniProtKB:P53867}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P53867}. Nucleus
CC       {ECO:0000250|UniProtKB:P53867}. Preautophagosomal structure
CC       {ECO:0000250|UniProtKB:P53867}.
CC   -!- DISRUPTION PHENOTYPE: Impairs the formation of preautophagosomal
CC       structures (PubMed:26442587). Blocks the maturation and subsequent
CC       localization of ATG8 to autophagic membranes (PubMed:26442587).
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 peptidase C54 family. {ECO:0000305}.
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DR   EMBL; AP012217; BAO41269.1; -; Genomic_DNA.
DR   AlphaFoldDB; W0TGM7; -.
DR   SMR; W0TGM7; -.
DR   EnsemblFungi; BAO41269; BAO41269; KLMA_50615.
DR   OrthoDB; 431748at2759; -.
DR   Proteomes; UP000065495; Chromosome 5.
DR   GO; GO:0005829; C:cytosol; IEA:EnsemblFungi.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0000407; C:phagophore assembly site; IEA:UniProtKB-SubCell.
DR   GO; GO:0019786; F:Atg8-specific peptidase activity; IEA:EnsemblFungi.
DR   GO; GO:0000045; P:autophagosome assembly; IEA:EnsemblFungi.
DR   GO; GO:0000422; P:autophagy of mitochondrion; IEA:EnsemblFungi.
DR   GO; GO:0006501; P:C-terminal protein lipidation; IEA:EnsemblFungi.
DR   GO; GO:0032258; P:cytoplasm to vacuole transport by the Cvt pathway; 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:0051697; P:protein delipidation; IEA:EnsemblFungi.
DR   GO; GO:0006612; P:protein targeting to membrane; IEA:EnsemblFungi.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   InterPro; IPR038765; Papain-like_cys_pep_sf.
DR   InterPro; IPR005078; Peptidase_C54.
DR   PANTHER; PTHR22624; PTHR22624; 1.
DR   Pfam; PF03416; Peptidase_C54; 1.
DR   SUPFAM; SSF54001; SSF54001; 1.
PE   3: Inferred from homology;
KW   Autophagy; Cytoplasm; Hydrolase; Nucleus; Protease; Protein transport;
KW   Thiol protease; Transport.
FT   CHAIN           1..451
FT                   /note="Cysteine protease ATG4"
FT                   /id="PRO_0000443874"
FT   ACT_SITE        122
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        297
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        299
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
SQ   SEQUENCE   451 AA;  51288 MW;  86440A395A2DA2B1 CRC64;
     MEFLTKITQQ LGLVGEIDKV GSVFVLGEEY RPYIFKTQGK ADDAETAFGS FLGNAQTNPQ
     LLSDIETRIF FTYRTQFTPI PRDEEGPSPI NLTLFFRDNP INTLENVLTD PDSFYSDIGW
     GCMIRTGQSL LANAIQRVKQ TREFRVNLEN IDIKEMSIIQ WFQDDWKYPL SLHNFVKVEG
     KKSGMKPGQW FGPSSTARSI QSLINDFPDC GIDRCLISPQ SADIYEDEMI RVFEENKRAN
     VLLLFATRLG VNEINSIYWS DIFQILKSSY SVGIAGGKPS SSLYFFGYQN DYLFYLDPHQ
     TQSSSLDMDD NSYYRSCHGH RFSKIHISET DPSMLLGMLI SGKAEWDLFK DEFKNSRIIQ
     FVASKPSDDI YEGVDLSPGS VSVHSIQSDL QDTGDYIDVG NFMSEKANSS QPSKNEEFEN
     VKCKNQRILI CENPSETEIE QVLVEDSTTD N