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ATG4_CRYNB
ID   ATG4_CRYNB              Reviewed;        1193 AA.
AC   P0CQ11; Q55JY1; Q5K9L9;
DT   28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT   28-JUN-2011, sequence version 1.
DT   03-AUG-2022, entry version 40.
DE   RecName: Full=Cysteine protease ATG4;
DE            EC=3.4.22.-;
DE   AltName: Full=Autophagy-related protein 4;
GN   Name=ATG4; OrderedLocusNames=CNBK2020;
OS   Cryptococcus neoformans var. neoformans serotype D (strain B-3501A)
OS   (Filobasidiella neoformans).
OC   Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Tremellomycetes;
OC   Tremellales; Cryptococcaceae; Cryptococcus;
OC   Cryptococcus neoformans species complex.
OX   NCBI_TaxID=283643;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=B-3501A;
RX   PubMed=15653466; DOI=10.1126/science.1103773;
RA   Loftus B.J., Fung E., Roncaglia P., Rowley D., Amedeo P., Bruno D.,
RA   Vamathevan J., Miranda M., Anderson I.J., Fraser J.A., Allen J.E.,
RA   Bosdet I.E., Brent M.R., Chiu R., Doering T.L., Donlin M.J., D'Souza C.A.,
RA   Fox D.S., Grinberg V., Fu J., Fukushima M., Haas B.J., Huang J.C.,
RA   Janbon G., Jones S.J.M., Koo H.L., Krzywinski M.I., Kwon-Chung K.J.,
RA   Lengeler K.B., Maiti R., Marra M.A., Marra R.E., Mathewson C.A.,
RA   Mitchell T.G., Pertea M., Riggs F.R., Salzberg S.L., Schein J.E.,
RA   Shvartsbeyn A., Shin H., Shumway M., Specht C.A., Suh B.B., Tenney A.,
RA   Utterback T.R., Wickes B.L., Wortman J.R., Wye N.H., Kronstad J.W.,
RA   Lodge J.K., Heitman J., Davis R.W., Fraser C.M., Hyman R.W.;
RT   "The genome of the basidiomycetous yeast and human pathogen Cryptococcus
RT   neoformans.";
RL   Science 307:1321-1324(2005).
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; AAEY01000052; EAL18184.1; -; Genomic_DNA.
DR   RefSeq; XP_772831.1; XM_767738.1.
DR   AlphaFoldDB; P0CQ11; -.
DR   SMR; P0CQ11; -.
DR   EnsemblFungi; AAW46309; AAW46309; CNK01520.
DR   EnsemblFungi; EAL18184; EAL18184; CNBK2020.
DR   GeneID; 4938899; -.
DR   KEGG; cnb:CNBK2020; -.
DR   VEuPathDB; FungiDB:CNBK2020; -.
DR   HOGENOM; CLU_005225_0_0_1; -.
DR   Proteomes; UP000001435; Chromosome 11.
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; 2.
PE   3: Inferred from homology;
KW   Autophagy; Cytoplasm; Hydrolase; Nucleus; Protease; Protein transport;
KW   Thiol protease; Transport.
FT   CHAIN           1..1193
FT                   /note="Cysteine protease ATG4"
FT                   /id="PRO_0000410215"
FT   REGION          23..284
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          358..474
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          807..869
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          899..924
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1000..1171
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        33..48
FT                   /note="Pro residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        58..76
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        101..153
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        155..284
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        390..451
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        811..825
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        904..924
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1003..1026
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1037..1062
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1102..1116
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1130..1155
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        570
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        789
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        791
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
SQ   SEQUENCE   1193 AA;  130136 MW;  ECD91DB1D9543F25 CRC64;
     MSSPTSTSPK SSFVFSPTSF PHAAIASNNV RPRTNLPPPP PPDRIPPPKG RSHQQKFKIL
     RKEKDKDRRQ PIDLEDDWTI EDVTVNGDGV EQESQYLDDL QPEENELKPG PRFLEMANRE
     EKKEKTSKSR GLVKKTSRLF GRDKDKDRGK PEEPAVTGSS SSTLAAMRQS SSTSTDSTTS
     RSITSAFTRQ NSIQSRRSPR TSFGQAHSRR ASQDSQMSWP APRSIRSSTT SHDPSSDPQN
     SASSTGVPIP QRQGASMSSL SRYSLPHPNG GTSRSPDTFP NKMSTWFSHL LPVSSGSPPS
     SSYETSSSIR KQSSVAASLF NAARQKAVDG VRHLLDSEAQ PDKCMDTIWV RGVAHPGWRP
     ITPENSTSNL PALEPGGSGG GVEDRRASLS MNGPSPNSLR PSSWKRNTSL PPTGQPQSPA
     HVHTQASNQT TSPSKGFTGI WNPSTLSLGM PIGGSPNKEK ENGSGAESPS KKKSKEIVKW
     PEQFYDDFKS TVWFTYRNQY APISSLSPNL LIPSPEAYYA SFGPPLDATS PSSLRVTTPT
     AAAQQSASGS GGWGWSKEER GLTSDAGWGC MLRTGQSLLV NALIHIHLGR DWRVPSTPAS
     FSEATTTQEI AALKDYAKYA QMLSWFLDDP SPLCPFSVHR MALIGKELGK EVGEWFGPST
     AAGALKTLAN SFAPCGVAVA TATDSIIYKS DVYTASNLPS DDWNSISPTF NSSKKKRRGD
     NEAKEEKWGK RAVLILVGVR LGLDGVNPIY YDSIKALFTF PQSVGIAGGR PSSSYYFVGS
     QANHLFYLDP HLTRPAIPLQ IPPLPVHSAK EKGSTESSSI MSTAEEESEE GVMIRTPETP
     RSTTPSMFSA PEHVEDEDQE EWGQGSKYKL DVVDADGVEV EGIDDDKGRN EGKMIREEVP
     KSSFESNGAA QEQPKKQKGF TSTASIDSQV DSQVDPHMLW YTTAYPDPLL RTYHCEKIKK
     MPLSGLDPSM LLGFVCKDED DFEDFVERVA QLPKKIFTVQ DEMPSWEEDD DAGLESVSEP
     DFEGDEFEEP GTAKPRFDSS SPVNEDSLKG PRVVSASTTA TPLAAKEEDH LDVEEANSTD
     DDNESIGTTT AAGPMDIARH LNRVDLSSKR EQEGDDDDGE WVGGTPSSQG VLVEPPSLKG
     TPSKSRSSAF EPRYEQNGET EQERPVFPAR NRMESWVEPV CEGKEAPNGD NLL
 
 
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