ID   ATG4_NEUCR              Reviewed;         506 AA.
AC   Q7S3X7;
DT   26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT   15-DEC-2003, sequence version 1.
DT   03-AUG-2022, entry version 96.
DE   RecName: Full=Cysteine protease 1;
DE            EC=3.4.22.-;
DE   AltName: Full=Autophagy-related protein 4;
GN   Name=cpr-1; Synonyms=atg4; ORFNames=NCU02433;
OS   Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 /
OS   FGSC 987).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes;
OC   Sordariomycetidae; Sordariales; Sordariaceae; Neurospora.
OX   NCBI_TaxID=367110;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987;
RX   PubMed=12712197; DOI=10.1038/nature01554;
RA   Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D.,
RA   Jaffe D.B., FitzHugh W., Ma L.-J., Smirnov S., Purcell S., Rehman B.,
RA   Elkins T., Engels R., Wang S., Nielsen C.B., Butler J., Endrizzi M.,
RA   Qui D., Ianakiev P., Bell-Pedersen D., Nelson M.A., Werner-Washburne M.,
RA   Selitrennikoff C.P., Kinsey J.A., Braun E.L., Zelter A., Schulte U.,
RA   Kothe G.O., Jedd G., Mewes H.-W., Staben C., Marcotte E., Greenberg D.,
RA   Roy A., Foley K., Naylor J., Stange-Thomann N., Barrett R., Gnerre S.,
RA   Kamal M., Kamvysselis M., Mauceli E.W., Bielke C., Rudd S., Frishman D.,
RA   Krystofova S., Rasmussen C., Metzenberg R.L., Perkins D.D., Kroken S.,
RA   Cogoni C., Macino G., Catcheside D.E.A., Li W., Pratt R.J., Osmani S.A.,
RA   DeSouza C.P.C., Glass N.L., Orbach M.J., Berglund J.A., Voelker R.,
RA   Yarden O., Plamann M., Seiler S., Dunlap J.C., Radford A., Aramayo R.,
RA   Natvig D.O., Alex L.A., Mannhaupt G., Ebbole D.J., Freitag M., Paulsen I.,
RA   Sachs M.S., Lander E.S., Nusbaum C., Birren B.W.;
RT   "The genome sequence of the filamentous fungus Neurospora crassa.";
RL   Nature 422:859-868(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; CM002242; EAA30202.1; -; Genomic_DNA.
DR   RefSeq; XP_959438.1; XM_954345.2.
DR   AlphaFoldDB; Q7S3X7; -.
DR   SMR; Q7S3X7; -.
DR   STRING; 5141.EFNCRP00000003085; -.
DR   MEROPS; C54.001; -.
DR   EnsemblFungi; EAA30202; EAA30202; NCU02433.
DR   GeneID; 3875585; -.
DR   KEGG; ncr:NCU02433; -.
DR   VEuPathDB; FungiDB:NCU02433; -.
DR   HOGENOM; CLU_021259_5_1_1; -.
DR   InParanoid; Q7S3X7; -.
DR   OMA; CHTRRIR; -.
DR   Proteomes; UP000001805; Chromosome 7, Linkage Group VII.
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   Reference proteome; Thiol protease; Transport.
FT   CHAIN           1..506
FT                   /note="Cysteine protease 1"
FT                   /id="PRO_0000215865"
FT   REGION          1..21
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        226
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        399
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        401
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
SQ   SEQUENCE   506 AA;  55356 MW;  9B5AC791CCFD2570 CRC64;
     MTSSRPSGRD STGWQETVSN TSPKLVNAME AARAGAAEVG RVGRRFLYRI WDWEPVNNRT
     INEPVWCLGC SYTLDIKQYG SPLSSSSLSQ LTADTPPLDK SQLAATHQHQ DFNGVRTTAT
     ATCLSDTSMS AAPTGSQLGS FDTVPDSVTS GYDSALAYEE PGQDGGWPPA FLDDFESRIW
     MTYRTDFALI PRSSDPQASS ALSFAMRIKT TFSDLTGFSS DTGWGCMIRS GQSLLANAIL
     IARLGREWRR GTDLDAEKDI IALFADDPRA PYSLHNFVKY GATACGKYPG EWFGPSATAR
     CIQALADEKQ SGLRVYSTGD LPDVYEDSFM AVANPDGRGF QPTLILVCTR LGIDKINQVY
     EEALISTLQL PQSIGIAGGR PSSSHYFVGV QGQRLFYLDP HHPRPALPYR EDPRGYTAEE
     LDTCHTRRLR QLHIGDMDPS MLIGFLIKDE DDWDTWKSSV KHVQGKSIIS VSPYDPARGQ
     GGGRAEAIDE VETLESDDDG EPALGA