ID   ATG4A_ORYSI             Reviewed;         473 AA.
AC   A2XHJ5;
DT   15-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT   20-MAR-2007, sequence version 1.
DT   03-AUG-2022, entry version 72.
DE   RecName: Full=Cysteine protease ATG4A {ECO:0000305};
DE            EC=3.4.22.- {ECO:0000250|UniProtKB:Q9Y4P1};
DE   AltName: Full=Autophagy-related protein 4 homolog A;
GN   Name=ATG4A; Synonyms=APG4A; ORFNames=OsI_011538;
OS   Oryza sativa subsp. indica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39946;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. 93-11;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
CC   -!- FUNCTION: Cysteine protease that plays a key role in autophagy by
CC       mediating both proteolytic activation and delipidation of ATG8 family
CC       proteins. The protease activity is required for proteolytic activation
CC       of ATG8 family proteins: cleaves the C-terminal amino acid of ATG8
CC       proteins to reveal a C-terminal glycine (By similarity). Exposure of
CC       the glycine at the C-terminus is essential for ATG8 proteins
CC       conjugation to phosphatidylethanolamine (PE) and insertion to
CC       membranes, which is necessary for autophagy. In addition to the
CC       protease activity, also mediates delipidation of PE-conjugated ATG8
CC       proteins (By similarity). {ECO:0000250|UniProtKB:Q2XPP4,
CC       ECO:0000250|UniProtKB:Q9Y4P1}.
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:Q9Y4P1};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67549;
CC         Evidence={ECO:0000250|UniProtKB:Q9Y4P1};
CC   -!- SUBUNIT: Interacts with ATG8. {ECO:0000250|UniProtKB:Q2XPP4}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q8BGE6}.
CC   -!- SIMILARITY: Belongs to the peptidase C54 family. {ECO:0000305}.
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DR   EMBL; CM000128; EAY90305.1; -; Genomic_DNA.
DR   AlphaFoldDB; A2XHJ5; -.
DR   SMR; A2XHJ5; -.
DR   STRING; 39946.A2XHJ5; -.
DR   EnsemblPlants; BGIOSGA012791-TA; BGIOSGA012791-PA; BGIOSGA012791.
DR   Gramene; BGIOSGA012791-TA; BGIOSGA012791-PA; BGIOSGA012791.
DR   HOGENOM; CLU_021259_1_0_1; -.
DR   OMA; NREHHEA; -.
DR   Proteomes; UP000007015; Chromosome 3.
DR   GO; GO:0005737; C:cytoplasm; 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; Protease; Protein transport;
KW   Reference proteome; Thiol protease; Transport; Ubl conjugation pathway.
FT   CHAIN           1..473
FT                   /note="Cysteine protease ATG4A"
FT                   /id="PRO_0000286901"
FT   REGION          1..33
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        160
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        357
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        359
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
SQ   SEQUENCE   473 AA;  51635 MW;  7B88C3E4CB762DEE CRC64;
     MTSLPGRGVS PSSSDPLCEG NAAPSSSSSG QDLKQSKNSI LSCVFSSPFS IFEAHQDSSA
     HRPLKPHSGS YAWSRFLRRI ACTGSMWRFL GASKALTSSD VWFLGKCYKL SSEELSNSSD
     CESGNAAFLE DFSSRIWITY RKGFDAISDS KYTSDVNWGC MVRSSQMLVA QALIFHHLGR
     SWRKPSQKPY SPEYIGILHM FGDSEACAFS IHNLLQAGKS YGLAAGSWVG PYAMCRAWQT
     LVRTNREHHE AVDGNGNFPM ALYVVSGDED GERGGAPVVC IDVAAQLCCD FNKGQSTWSP
     ILLLVPLVLG LDKLNPRYIP LLKETFTFPQ SLGILGGKPG TSTYVAGVQD DRVLYLDPHE
     VQLAVDIAAD NLEADTSSYH CSTVRDLALD LIDPSLAIGF YCRDKDDFDD FCSRASELVD
     KANGAPLFTV MQSVQPSKQM YNEESSSGDG MDIINVEGLD GSGETGEEEW QIL