ATG4A_ORYSJ
ID ATG4A_ORYSJ Reviewed; 474 AA.
AC Q75KP8; B7F9Q9; Q0DRE5; Q75KP9; Q75LS5;
DT 15-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 105.
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; OrderedLocusNames=Os03g0391000, LOC_Os03g27350;
GN ORFNames=OsJ_010666, OSJNBa0017N12.1, OSJNBa0065F09.1;
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=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
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 GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
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).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RG The rice full-length cDNA consortium;
RT "Oryza sativa full length cDNA.";
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q75KP8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q75KP8-2; Sequence=VSP_025236;
CC -!- SIMILARITY: Belongs to the peptidase C54 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF12193.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC092075; AAR06350.1; -; Genomic_DNA.
DR EMBL; AC099323; AAR87271.1; -; Genomic_DNA.
DR EMBL; AC099323; AAR87272.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF96366.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF96367.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF12193.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014959; BAS84522.1; -; Genomic_DNA.
DR EMBL; CM000140; EAZ27183.1; -; Genomic_DNA.
DR EMBL; AK242832; BAH01357.1; -; mRNA.
DR RefSeq; XP_015627879.1; XM_015772393.1. [Q75KP8-1]
DR AlphaFoldDB; Q75KP8; -.
DR SMR; Q75KP8; -.
DR STRING; 4530.OS03T0391000-01; -.
DR PRIDE; Q75KP8; -.
DR EnsemblPlants; Os03t0391000-01; Os03t0391000-01; Os03g0391000. [Q75KP8-1]
DR GeneID; 4333022; -.
DR Gramene; Os03t0391000-01; Os03t0391000-01; Os03g0391000. [Q75KP8-1]
DR KEGG; osa:4333022; -.
DR eggNOG; KOG2674; Eukaryota.
DR HOGENOM; CLU_021259_1_0_1; -.
DR InParanoid; Q75KP8; -.
DR OMA; NREHHEA; -.
DR OrthoDB; 431748at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; Q75KP8; 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 Alternative splicing; Autophagy; Cytoplasm; Hydrolase; Protease;
KW Protein transport; Reference proteome; Thiol protease; Transport;
KW Ubl conjugation pathway.
FT CHAIN 1..474
FT /note="Cysteine protease ATG4A"
FT /id="PRO_0000286902"
FT REGION 1..32
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 439..474
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 439..453
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 161
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT ACT_SITE 358
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT ACT_SITE 360
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT VAR_SEQ 406
FT /note="K -> KGELLLPDKMLGHHLSSLQSWFSYLLCLSAYV (in isoform
FT 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_025236"
SQ SEQUENCE 474 AA; 51555 MW; 555CFC256F92A4E9 CRC64;
MTSLPGRGVS PSSSDPLCEG NAAPSSSSSS GQDLKQLKNS ILSCVFSSPF SIFEAHQDSS
ANRSLKPHSG SYAWSRFLRR IACTGSMWRF LGASKALTSS DVWFLGKCYK LSSEELSNSS
DCESGNAAFL EDFSSRIWIT YRKGFDAISD SKYTSDVNWG CMVRSSQMLV AQALIFHHLG
RSWRKPSQKP YSPEYIGILH MFGDSEACAF SIHNLLQAGK SYGLAAGSWV GPYAMCRAWQ
TLVCTNREHH EAVDGNGNFP MALYVVSGDE DGERGGAPVV CIDVAAQLCC DFNKNQSTWS
PILLLVPLVL GLDKLNPRYI PLLKETLTFP QSLGILGGKP GTSTYIAGVQ DDRALYLDPH
EVQLAVDIAA DNLEAGTSSY HCSTVRDLAL DLIDPSLAIG FYCRDKDDFD DFCSRASELV
DKANGAPLFT VVQSVQPSKQ MYNEESSSGD GMDSINVEGL DGSGETGEEE WQIL
