ID   ATG4_PICPA              Reviewed;         533 AA.
AC   Q8NJJ3;
DT   26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2002, sequence version 1.
DT   03-AUG-2022, entry version 56.
DE   RecName: Full=Probable cysteine protease ATG4;
DE            EC=3.4.22.-;
DE   AltName: Full=Autophagy-related protein 4;
DE   AltName: Full=Pexophagy zeocin-resistant mutant protein 8;
GN   Name=ATG4; Synonyms=PAZ8;
OS   Komagataella pastoris (Yeast) (Pichia pastoris).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Phaffomycetaceae; Komagataella.
OX   NCBI_TaxID=4922;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=11856375; DOI=10.1046/j.1356-9597.2001.00499.x;
RA   Mukaiyama H., Oku M., Baba M., Samizo T., Hammond A.T., Glick B.S.,
RA   Kato N., Sakai Y.;
RT   "Paz2 and 13 other PAZ gene products regulate vacuolar engulfment of
RT   peroxisomes during micropexophagy.";
RL   Genes Cells 7:75-90(2002).
RN   [2]
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).
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. Required for selective autophagic
CC       degradation of the nucleus (nucleophagy) as well as for mitophagy which
CC       contributes to regulate mitochondrial quantity and quality by
CC       eliminating the mitochondria to a basal level to fulfill cellular
CC       energy requirements and preventing excess ROS production. The protease
CC       activity is required for proteolytic activation of ATG8: cleaves the C-
CC       terminal amino acid of ATG8 to reveal a C-terminal glycine. ATG8
CC       ubiquitin-like activity requires the exposure of the glycine at the C-
CC       terminus for its conjugation to phosphatidylethanolamine (PE) and its
CC       insertion to membranes, which is necessary for autophagy. The ATG8-PE
CC       conjugate mediates tethering between adjacent membranes and stimulates
CC       membrane hemifusion, leading to expansion of the autophagosomal
CC       membrane during autophagy. In addition to the protease activity, also
CC       catalyzes deconjugation of PE-conjugated forms of ATG8 during
CC       macroautophagy: ATG8 delipidation is required to release the protein
CC       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. {ECO:0000250|UniProtKB:P53867}.
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   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P53867}. Nucleus
CC       {ECO:0000250|UniProtKB:P53867}. Preautophagosomal structure
CC       {ECO:0000250|UniProtKB:P53867}.
CC   -!- SIMILARITY: Belongs to the peptidase C54 family. {ECO:0000305}.
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DR   EMBL; AY058220; AAL25849.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q8NJJ3; -.
DR   SMR; Q8NJJ3; -.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0000407; C:phagophore assembly site; IEA:UniProtKB-SubCell.
DR   GO; GO:0008234; F:cysteine-type peptidase activity; IEA:UniProtKB-KW.
DR   GO; GO:0006914; P:autophagy; IEA:UniProtKB-KW.
DR   GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
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..533
FT                   /note="Probable cysteine protease ATG4"
FT                   /id="PRO_0000215866"
FT   ACT_SITE        118
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
SQ   SEQUENCE   533 AA;  59883 MW;  1FBC063C9D518CCB CRC64;
     MYRFLGLGTH PNDDQNKIHV LGRQYDPIKT QETEGKDLDL NSRFQQVLDS IKDGNKKSTT
     YSQSFIDDVY SKIWLTYRAG FPPIARDKDS PTFTLGALLR GQFDFNEIGF TSDAGWGCMI
     RTSQSLLANA LLFLHLGRDW VFKAKDPANV EHDRIISWFV DIPDEPFSIH NFVQQGIKCC
     DKKPGEWFGP SAASRAIKNL CKEYPPCGLR VYFSSDCGDV YDTEVRELAY GDSDTFTPIL
     VLLGIRLGVE KVNLYIGDLL RECLSLKQSV GISGRKTSFL ALLSIGFQGD YLFYLIPTFP
     KKALTFGKHG EPVHRLQTKK TDENAAGQYP VFKYWIQIMK QTMMTAMKAS KTTASTLKFF
     RVLMSNQSTH QKVTKLHLSH MDPSMLIGFL ITSEDDFNDW KENIGKKDPS HKIVHITETK
     VSESTSNFQF NSLRSNSIAD YDNCSGEDCD SAAIASDSDD FVDLAADFAV TGLEPRTHTG
     VDDETSSDYV QHFPIRRFSQ PVIVSREDVV PTLSEDNGVI ALDDKMSGIS VGR