ATG4B_RAT
ID ATG4B_RAT Reviewed; 393 AA.
AC A0A0G2QC33; F1LRG2; Q4KM36;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 22-JUL-2015, sequence version 1.
DT 03-AUG-2022, entry version 41.
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 {ECO:0000312|RGD:1309664};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Spleen;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3] {ECO:0007744|PubMed:22673903}
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
RN [4]
RP S-NITROSYLATION.
RX PubMed=28633005; DOI=10.1080/15548627.2017.1320467;
RA Li Y., Zhang Y., Wang L., Wang P., Xue Y., Li X., Qiao X., Zhang X., Xu T.,
RA Liu G., Li P., Chen C.;
RT "Autophagy impairment mediated by S-nitrosation of ATG4B leads to
RT neurotoxicity in response to hyperglycemia.";
RL Autophagy 13:1145-1160(2017).
CC -!- FUNCTION: Cysteine protease that plays a key role in autophagy by
CC mediating both proteolytic activation and delipidation of ATG8 family
CC proteins. Required for canonical autophagy (macroautophagy), non-
CC canonical autophagy as well as for mitophagy. The protease activity is
CC required for proteolytic activation of ATG8 family proteins: cleaves
CC the C-terminal amino acid of ATG8 proteins MAP1LC3A, MAP1LC3B,
CC MAP1LC3C, GABARAPL1, GABARAPL2 and GABARAP, to reveal a C-terminal
CC glycine. Exposure of the glycine at the C-terminus is essential for
CC ATG8 proteins conjugation to phosphatidylethanolamine (PE) and
CC insertion to membranes, which is necessary for autophagy. Protease
CC activity is also required to counteract formation of high-molecular
CC weight conjugates of ATG8 proteins (ATG8ylation): acts as a
CC deubiquitinating-like enzyme that removes ATG8 conjugated to other
CC proteins, such as ATG3. In addition to the protease activity, also
CC mediates delipidation of ATG8 family proteins. Catalyzes delipidation
CC of PE-conjugated forms of ATG8 proteins during macroautophagy. Also
CC involved in non-canonical autophagy, a parallel pathway involving
CC conjugation of ATG8 proteins to single membranes at endolysosomal
CC compartments, by catalyzing delipidation of ATG8 proteins conjugated to
CC phosphatidylserine (PS). Compared to other members of the family
CC (ATG4A, ATG4C or ATG4C), constitutes the major protein for proteolytic
CC activation of ATG8 proteins, while it displays weaker delipidation
CC activity than other ATG4 paralogs. Involved in phagophore growth during
CC mitophagy independently of its protease activity and of ATG8 proteins:
CC acts by regulating ATG9A trafficking to mitochondria and promoting
CC phagophore-endoplasmic reticulum contacts during the lipid transfer
CC phase of mitophagy. {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 -!- CATALYTIC ACTIVITY:
CC Reaction=[protein]-C-terminal L-amino acid-glycyl-phosphatidylserine +
CC H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-
CC glycero-3-phospho-L-serine; Xref=Rhea:RHEA:67576, Rhea:RHEA-
CC COMP:17324, Rhea:RHEA-COMP:17326, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:57262, ChEBI:CHEBI:172940, ChEBI:CHEBI:172942;
CC Evidence={ECO:0000250|UniProtKB:Q9Y4P1};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67577;
CC Evidence={ECO:0000250|UniProtKB:Q9Y4P1};
CC -!- ACTIVITY REGULATION: Inhibited by N-ethylmaleimide. Redox-regulated
CC during autophagy since reducing conditions activate ATG4A whereas an
CC oxidizing environment such as the presence of H(2)O(2) inhibits its
CC activity. The cysteine protease activity compounds is inhibited by
CC styrylquinoline compounds 4-28 and LV-320.
CC {ECO:0000250|UniProtKB:Q9Y4P1}.
CC -!- SUBUNIT: Interacts with PFKP; promoting phosphorylation of ATG4B at
CC Ser-34 (By similarity). Interacts with GBP7 (By similarity).
CC {ECO:0000250|UniProtKB:Q8BGE6, ECO:0000250|UniProtKB:Q9Y4P1}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q9Y4P1}.
CC Cytoplasm, cytosol {ECO:0000250|UniProtKB:Q9Y4P1}. Cytoplasmic vesicle,
CC autophagosome {ECO:0000250|UniProtKB:Q9Y4P1}. Endoplasmic reticulum
CC {ECO:0000250|UniProtKB:Q9Y4P1}. Mitochondrion
CC {ECO:0000250|UniProtKB:Q9Y4P1}. Note=Mainly localizes to the cytoplasm,
CC including cytosol. A samll potion localizes to mitochondria;
CC phosphorylation at Ser-34 promotes localization to mitochondria.
CC {ECO:0000250|UniProtKB:Q9Y4P1}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=A0A0G2QC33-1; Sequence=Displayed;
CC Name=2;
CC IsoId=A0A0G2QC33-2; Sequence=VSP_061269;
CC -!- DOMAIN: The LIR motif (LC3-interacting region) is required for the
CC interaction with ATG8 family proteins MAP1LC3A, MAP1LC3B, MAP1LC3C and
CC GABARAPL1. Required for proteolytic activation and delipidation of ATG8
CC proteins. {ECO:0000250|UniProtKB:Q9Y4P1}.
CC -!- PTM: Phosphorylation at Ser-383 and Ser-392 promotes autophagy by
CC increasing protein delipidation activity without affecting proteolytic
CC activation of ATG8 proteins. Phosphorylation at Ser-316 by ULK1
CC inhibits autophagy by decreasing both proteolytic activation and
CC delipidation activities. Phosphorylation at Ser-316 is dephosphorylated
CC by protein phosphatase 2A (PP2A). Phosphorylation at Ser-34 by AKT2
CC promotes its hydrolase activity, leading to increased proteolytic
CC activation and delipidation of ATG8 family proteins. Phosphorylation at
CC Ser-34 by AKT1 promotes mitochondrial localization and inhibition of
CC the F1F0-ATP synthase activity, leading to elevation of mitochondrial
CC reactive oxygen species (ROS). {ECO:0000250|UniProtKB:Q9Y4P1}.
CC -!- PTM: Ubiquitinated by RNF5, leading to its degradation by the
CC proteasome. {ECO:0000250|UniProtKB:Q9Y4P1}.
CC -!- PTM: S-nitrosylation in response to high glucose decreases both
CC proteolytic activation and delipidation activities.
CC {ECO:0000269|PubMed:28633005}.
CC -!- PTM: O-glycosylated by OGT, leading to increase protease activity,
CC thereby promoting the proteolytic activation of ATG8 family proteins.
CC {ECO:0000250|UniProtKB:Q9Y4P1}.
CC -!- PTM: Forms reversible intrachain disulfide bonds in response to
CC oxidative stress. Forms interchain disulfide bonds, leading to
CC formation of homooligomers in response to oxidation.
CC {ECO:0000250|UniProtKB:Q9Y4P1}.
CC -!- SIMILARITY: Belongs to the peptidase C54 family. {ECO:0000305}.
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DR EMBL; AC109427; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC098833; AAH98833.1; -; mRNA.
DR RefSeq; XP_006245595.1; XM_006245533.3.
DR AlphaFoldDB; A0A0G2QC33; -.
DR SMR; A0A0G2QC33; -.
DR STRING; 10116.ENSRNOP00000025529; -.
DR MEROPS; C54.003; -.
DR iPTMnet; Q4KM36; -.
DR jPOST; A0A0G2QC33; -.
DR PaxDb; A0A0G2QC33; -.
DR Ensembl; ENSRNOT00000025529; ENSRNOP00000025529; ENSRNOG00000018403. [A0A0G2QC33-1]
DR GeneID; 316640; -.
DR CTD; 23192; -.
DR RGD; 1309664; Atg4b.
DR eggNOG; KOG2674; Eukaryota.
DR GeneTree; ENSGT00530000063000; -.
DR HOGENOM; CLU_021259_0_1_1; -.
DR OMA; CHTRRIR; -.
DR OrthoDB; 431748at2759; -.
DR TreeFam; TF314847; -.
DR Reactome; R-RNO-1632852; Macroautophagy.
DR PRO; PR:Q4KM36; -.
DR Proteomes; UP000002494; Chromosome 9.
DR Bgee; ENSRNOG00000018403; Expressed in thymus and 20 other tissues.
DR GO; GO:0005776; C:autophagosome; IEA:UniProtKB-SubCell.
DR GO; GO:0005737; C:cytoplasm; ISO:RGD.
DR GO; GO:0031410; C:cytoplasmic vesicle; IEA:UniProtKB-KW.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR GO; GO:0019786; F:Atg8-specific peptidase activity; ISO:RGD.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
DR GO; GO:0008234; F:cysteine-type peptidase activity; ISO:RGD.
DR GO; GO:0004175; F:endopeptidase activity; ISO:RGD.
DR GO; GO:0008233; F:peptidase activity; ISO:RGD.
DR GO; GO:0097110; F:scaffold protein binding; ISO:RGD.
DR GO; GO:0000045; P:autophagosome assembly; ISO:RGD.
DR GO; GO:0006914; P:autophagy; ISO:RGD.
DR GO; GO:0009267; P:cellular response to starvation; ISO:RGD.
DR GO; GO:0016237; P:lysosomal microautophagy; ISO:RGD.
DR GO; GO:0000423; P:mitophagy; ISO:RGD.
DR GO; GO:0031173; P:otolith mineralization completed early in development; ISO:RGD.
DR GO; GO:0045732; P:positive regulation of protein catabolic process; IMP:RGD.
DR GO; GO:0051697; P:protein delipidation; ISO:RGD.
DR GO; GO:0034497; P:protein localization to phagophore assembly site; ISO:RGD.
DR GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; ISO:RGD.
DR InterPro; IPR032916; ATG4B_met.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR005078; Peptidase_C54.
DR PANTHER; PTHR22624; PTHR22624; 1.
DR PANTHER; PTHR22624:SF39; PTHR22624:SF39; 1.
DR Pfam; PF03416; Peptidase_C54; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Autophagy; Cytoplasm;
KW Cytoplasmic vesicle; Disulfide bond; Endoplasmic reticulum; Glycoprotein;
KW Hydrolase; Isopeptide bond; Mitochondrion; Phosphoprotein; Protease;
KW Protein transport; Reference proteome; S-nitrosylation; Thiol protease;
KW Transport; Ubl conjugation; Ubl conjugation pathway.
FT CHAIN 1..393
FT /note="Cysteine protease ATG4B"
FT /id="PRO_0000454234"
FT MOTIF 388..391
FT /note="LIR"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT ACT_SITE 74
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT ACT_SITE 278
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT ACT_SITE 280
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT MOD_RES 34
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT MOD_RES 189
FT /note="S-nitrosocysteine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT MOD_RES 292
FT /note="S-nitrosocysteine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT MOD_RES 301
FT /note="S-nitrosocysteine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT MOD_RES 316
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT MOD_RES 383
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT MOD_RES 392
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT DISULFID 292..361
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT DISULFID 292
FT /note="Interchain (with C-361)"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT DISULFID 361
FT /note="Interchain (with C-292)"
FT /evidence="ECO:0000250|UniProtKB:Q9Y4P1"
FT VAR_SEQ 1..169
FT /note="Missing (in isoform 2)"
FT /id="VSP_061269"
SQ SEQUENCE 393 AA; 44364 MW; FDC50C2D15E4F598 CRC64;
MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EILSDVASRL WFTYRRNFPA
IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ RKRQPDSYFS VLNAFLDRKD
SYYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ VLKKLAVFDT WSSLAVHIAM DNTVVMEEIR
RLCRASLPCA GAAALSMESE RHCNGLPAGA EVTNRPLAWR PLVLLIPLRL GLTDINEAYV
ETLKHCFMMP QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVELTD SCFIPDESFH
CQHPPCRMGI GELDPSIAVG FFCKTEEDFN DWCQQVKKLS QLGGALPMFE LVEQQPSHLA
CQDVLNLSLD SSDVERLERF FDSEDEDFEI LSL
