ATG4B_ARATH
ID ATG4B_ARATH Reviewed; 477 AA.
AC Q9M1Y0; Q570T6;
DT 15-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 117.
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;
DE Short=AtAPG4b {ECO:0000303|PubMed:12114572};
DE Short=Protein autophagy 4b {ECO:0000303|PubMed:12114572};
GN Name=ATG4B {ECO:0000303|PubMed:12114572};
GN Synonyms=APG4B {ECO:0000303|PubMed:12114572}; OrderedLocusNames=At3g59950;
GN ORFNames=F24G16.220;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), NOMENCLATURE, AND GENE FAMILY.
RX PubMed=12114572; DOI=10.1104/pp.011024;
RA Hanaoka H., Noda T., Shirano Y., Kato T., Hayashi H., Shibata D.,
RA Tabata S., Ohsumi Y.;
RT "Leaf senescence and starvation-induced chlorosis are accelerated by the
RT disruption of an Arabidopsis autophagy gene.";
RL Plant Physiol. 129:1181-1193(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP INTERACTION WITH ATG8A AND ATG8D.
RX PubMed=15178341; DOI=10.1016/j.febslet.2004.04.088;
RA Ketelaar T., Voss C., Dimmock S.A., Thumm M., Hussey P.J.;
RT "Arabidopsis homologues of the autophagy protein Atg8 are a novel family of
RT microtubule binding proteins.";
RL FEBS Lett. 567:302-306(2004).
RN [6]
RP TISSUE SPECIFICITY.
RX PubMed=15494556; DOI=10.1105/tpc.104.025395;
RA Yoshimoto K., Hanaoka H., Sato S., Kato T., Tabata S., Noda T., Ohsumi Y.;
RT "Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by
RT ATG4s are essential for plant autophagy.";
RL Plant Cell 16:2967-2983(2004).
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 ATG8a and ATG8d. {ECO:0000269|PubMed:15178341}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q8BGE6}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9M1Y0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9M1Y0-2; Sequence=VSP_025233, VSP_025234, VSP_025235;
CC -!- TISSUE SPECIFICITY: Constitutively expressed.
CC {ECO:0000269|PubMed:15494556}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to intron retention.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the peptidase C54 family. {ECO:0000305}.
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DR EMBL; AB073172; BAB88384.1; -; mRNA.
DR EMBL; AL138647; CAB75814.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79989.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79990.1; -; Genomic_DNA.
DR EMBL; AK226932; BAE99003.1; -; mRNA.
DR EMBL; AK220621; BAD95023.1; -; mRNA.
DR PIR; T47819; T47819.
DR RefSeq; NP_001118859.1; NM_001125387.1. [Q9M1Y0-2]
DR RefSeq; NP_191554.1; NM_115858.6. [Q9M1Y0-1]
DR AlphaFoldDB; Q9M1Y0; -.
DR SMR; Q9M1Y0; -.
DR STRING; 3702.AT3G59950.1; -.
DR MEROPS; C54.012; -.
DR TCDB; 9.A.15.3.1; the autophagy-related phagophore-formation transporter (apt) family.
DR iPTMnet; Q9M1Y0; -.
DR PaxDb; Q9M1Y0; -.
DR EnsemblPlants; AT3G59950.1; AT3G59950.1; AT3G59950. [Q9M1Y0-1]
DR EnsemblPlants; AT3G59950.3; AT3G59950.3; AT3G59950. [Q9M1Y0-2]
DR GeneID; 825165; -.
DR Gramene; AT3G59950.1; AT3G59950.1; AT3G59950. [Q9M1Y0-1]
DR Gramene; AT3G59950.3; AT3G59950.3; AT3G59950. [Q9M1Y0-2]
DR KEGG; ath:AT3G59950; -.
DR Araport; AT3G59950; -.
DR TAIR; locus:2080447; AT3G59950.
DR eggNOG; KOG2674; Eukaryota.
DR HOGENOM; CLU_021259_1_0_1; -.
DR InParanoid; Q9M1Y0; -.
DR PhylomeDB; Q9M1Y0; -.
DR PRO; PR:Q9M1Y0; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9M1Y0; baseline and differential.
DR Genevisible; Q9M1Y0; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008234; F:cysteine-type peptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0004175; F:endopeptidase activity; IDA:TAIR.
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 1: Evidence at protein level;
KW Alternative splicing; Autophagy; Cytoplasm; Hydrolase; Protease;
KW Protein transport; Reference proteome; Thiol protease; Transport;
KW Ubl conjugation pathway.
FT CHAIN 1..477
FT /note="Cysteine protease ATG4b"
FT /id="PRO_0000286899"
FT REGION 11..39
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 453..477
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 173
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT ACT_SITE 368
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT ACT_SITE 370
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT VAR_SEQ 1..86
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.4"
FT /id="VSP_025233"
FT VAR_SEQ 329..353
FT /note="YIPSLIATFTFPQSLGILGGKPGAS -> FVTLSKRFLDDKCYRRQEFSFSF
FT SS (in isoform 2)"
FT /evidence="ECO:0000303|Ref.4"
FT /id="VSP_025234"
FT VAR_SEQ 354..477
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.4"
FT /id="VSP_025235"
SQ SEQUENCE 477 AA; 52202 MW; 81D17B95E77280A7 CRC64;
MKAICDRFVP SKCSSSSTSE KRDISSPTSL VSDSASSDNK SNLTLCSDVV ASSSPVSQLC
REASTSGHNP VCTTHSSWTV ILKTASMASG AIRRFQDRVL GPSRTGISSS TSEIWLLGVC
YKISEGESSE EADAGRVLAA FRQDFSSLIL MTYRRGFEPI GDTTYTSDVN WGCMLRSGQM
LFAQALLFQR LGRSWRKKDS EPADEKYLEI LELFGDTEAS AFSIHNLILA GESYGLAAGS
WVGPYAVCRS WESLARKNKE ETDDKHKSFS MAVHIVSGSE DGERGGAPIL CIEDVTKTCL
EFSEGETEWP PILLLVPLVL GLDRVNPRYI PSLIATFTFP QSLGILGGKP GASTYIVGVQ
EDKGFYLDPH DVQQVVTVKK ENQDVDTSSY HCNTLRYVPL ESLDPSLALG FYCQHKDDFD
DFCIRATKLA GDSNGAPLFT VTQSHRRNDC GIAETSSSTE TSTEISGEEH EDDWQLL
