ID   ATG4B_ORYSJ             Reviewed;         478 AA.
AC   Q7XPW8; B7EFR3;
DT   15-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2003, sequence version 1.
DT   03-AUG-2022, entry version 101.
DE   RecName: Full=Cysteine protease ATG4B {ECO:0000305};
DE            EC=3.4.22.- {ECO:0000250|UniProtKB:Q9Y4P1};
DE   AltName: Full=Autophagy-related protein 4 homolog B;
GN   Name=ATG4B; Synonyms=APG4B; OrderedLocusNames=Os04g0682000, LOC_Os04g58560;
GN   ORFNames=OSJNBa0032F06.13;
OS   Oryza sativa subsp. japonica (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=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12447439; DOI=10.1038/nature01183;
RA   Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y.,
RA   Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S., Tang Y., Weng Q.,
RA   Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T.,
RA   Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R.,
RA   Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G.,
RA   Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C.,
RA   Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J.,
RA   Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J.,
RA   Li J., Hong G., Xue Y., Han B.;
RT   "Sequence and analysis of rice chromosome 4.";
RL   Nature 420:316-320(2002).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
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; AL606641; CAE03430.1; -; Genomic_DNA.
DR   EMBL; AP008210; BAF16207.1; -; Genomic_DNA.
DR   EMBL; AP014960; BAS91684.1; -; Genomic_DNA.
DR   EMBL; AK069012; BAG91210.1; -; mRNA.
DR   RefSeq; XP_015637247.1; XM_015781761.1.
DR   RefSeq; XP_015637248.1; XM_015781762.1.
DR   RefSeq; XP_015637249.1; XM_015781763.1.
DR   AlphaFoldDB; Q7XPW8; -.
DR   SMR; Q7XPW8; -.
DR   STRING; 4530.OS04T0682000-01; -.
DR   PaxDb; Q7XPW8; -.
DR   PRIDE; Q7XPW8; -.
DR   EnsemblPlants; Os04t0682000-01; Os04t0682000-01; Os04g0682000.
DR   GeneID; 4337435; -.
DR   Gramene; Os04t0682000-01; Os04t0682000-01; Os04g0682000.
DR   KEGG; osa:4337435; -.
DR   eggNOG; KOG2674; Eukaryota.
DR   HOGENOM; CLU_021259_1_0_1; -.
DR   InParanoid; Q7XPW8; -.
DR   OMA; CHTRRIR; -.
DR   OrthoDB; 431748at2759; -.
DR   Proteomes; UP000000763; Chromosome 4.
DR   Proteomes; UP000059680; Chromosome 4.
DR   Genevisible; Q7XPW8; OS.
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   2: Evidence at transcript level;
KW   Autophagy; Cytoplasm; Hydrolase; Protease; Protein transport;
KW   Reference proteome; Thiol protease; Transport; Ubl conjugation pathway.
FT   CHAIN           1..478
FT                   /note="Cysteine protease ATG4B"
FT                   /id="PRO_0000286904"
FT   REGION          1..31
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        164
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        361
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT   ACT_SITE        363
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
SQ   SEQUENCE   478 AA;  52526 MW;  0D7A20E821665C38 CRC64;
     MTSLPDRGVS SSSSDPLCEG NIAPCSSSSE QKEDCSLKQS KTSILSCVFN SPFNIFEAHQ
     DSSANKSPKS SSGSYDWSRV LRRIVCSGSM WRFLGTSKVL TSSDVWFLGK CYKLSSEESS
     SDSDSESGHA TFLEDFSSRI WITYRRGFDA ISDSKYTSDV NWGCMVRSSQ MLVAQALIFH
     HLGRSWRRPL EKPYNPEYIG ILHMFGDSEA CAFSIHNLLQ AGNSYGLAAG SWVGPYAMCR
     AWQTLVRTNR EQHEVVDGNE SFPMALYVVS GDEDGERGGA PVVCIDVAAQ LCCDFNKGQS
     TWSPILLLVP LVLGLDKINP RYIPLLKETF TFPQSLGILG GKPGTSTYIA GVQDDRALYL
     DPHEVQMAVD IAADNIEADT SSYHCSTVRD LALDLIDPSL AIGFYCRDKD DFDDFCSRAT
     ELVDKANGAP LFTVVQSVQP SKQMYNQDDV LGISGDGNIN VEDLDASGET GEEEWQIL