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ATG4B_BOVIN
ID   ATG4B_BOVIN             Reviewed;         393 AA.
AC   Q6PZ03; Q6PZ04;
DT   15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   03-AUG-2022, entry version 96.
DE   RecName: Full=Cysteine protease ATG4B;
DE            EC=3.4.22.-;
DE   AltName: Full=Autophagy-related cysteine endopeptidase 2B;
DE            Short=Autophagin-2B;
DE            Short=bAut2B {ECO:0000303|PubMed:15140988};
DE   AltName: Full=Autophagy-related protein 4 homolog B;
GN   Name=ATG4B; Synonyms=APG4B, AUT2B;
OS   Bos taurus (Bovine).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC   Bovinae; Bos.
OX   NCBI_TaxID=9913;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), AND FUNCTION (MICROBIAL
RP   INFECTION).
RX   PubMed=15140988; DOI=10.1128/jvi.78.11.5900-5912.2004;
RA   Fricke J., Voss C., Thumm M., Meyers G.;
RT   "Processing of a pestivirus protein by a cellular protease specific for
RT   light chain 3 of microtubule-associated proteins.";
RL   J. Virol. 78:5900-5912(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. 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   -!- FUNCTION: (Microbial infection) Mediates cleavage of an ATG8 protein
CC       homolog coded in the genome of cytopathogenic bovine viral diarrhea
CC       virus (BVDV). {ECO:0000269|PubMed:15140988}.
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; Synonyms=Aut2B2 {ECO:0000303|PubMed:15140988};
CC         IsoId=Q6PZ03-1; Sequence=Displayed;
CC       Name=2; Synonyms=Aut2B1 {ECO:0000303|PubMed:15140988};
CC         IsoId=Q6PZ03-2; Sequence=VSP_013026, VSP_013027;
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 at Cys-189 and Cys-292 in response to high glucose
CC       decreases both proteolytic activation and delipidation activities.
CC       {ECO:0000250|UniProtKB:Q9Y4P1}.
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; AY570550; AAS78582.1; -; mRNA.
DR   EMBL; AY570551; AAS78583.1; -; mRNA.
DR   RefSeq; NP_001001170.1; NM_001001170.1. [Q6PZ03-1]
DR   AlphaFoldDB; Q6PZ03; -.
DR   SMR; Q6PZ03; -.
DR   STRING; 9913.ENSBTAP00000020474; -.
DR   MEROPS; C54.003; -.
DR   PaxDb; Q6PZ03; -.
DR   PRIDE; Q6PZ03; -.
DR   Ensembl; ENSBTAT00000020474; ENSBTAP00000020474; ENSBTAG00000015401. [Q6PZ03-1]
DR   GeneID; 408002; -.
DR   KEGG; bta:408002; -.
DR   CTD; 23192; -.
DR   VEuPathDB; HostDB:ENSBTAG00000015401; -.
DR   eggNOG; KOG2674; Eukaryota.
DR   GeneTree; ENSGT00530000063000; -.
DR   InParanoid; Q6PZ03; -.
DR   OMA; CHTRRIR; -.
DR   OrthoDB; 431748at2759; -.
DR   Proteomes; UP000009136; Chromosome 3.
DR   Bgee; ENSBTAG00000015401; Expressed in retina and 104 other tissues.
DR   GO; GO:0005776; C:autophagosome; IEA:UniProtKB-SubCell.
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; IEA:Ensembl.
DR   GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
DR   GO; GO:0097110; F:scaffold protein binding; IEA:Ensembl.
DR   GO; GO:0006914; P:autophagy; ISS:UniProtKB.
DR   GO; GO:0016237; P:lysosomal microautophagy; ISS:UniProtKB.
DR   GO; GO:0000423; P:mitophagy; ISS:UniProtKB.
DR   GO; GO:0031173; P:otolith mineralization completed early in development; ISS:UniProtKB.
DR   GO; GO:0051697; P:protein delipidation; IEA:Ensembl.
DR   GO; GO:0034497; P:protein localization to phagophore assembly site; IEA:Ensembl.
DR   GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
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   2: Evidence at transcript 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_0000215843"
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         320..342
FT                   /note="GFFCETEDDFNDWCQQVSKLSLL -> VRPPCPAIGAVLLLLQEGGPLLP
FT                   (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:15140988"
FT                   /id="VSP_013026"
FT   VAR_SEQ         343..393
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:15140988"
FT                   /id="VSP_013027"
SQ   SEQUENCE   393 AA;  43539 MW;  4777962CC6E08CE3 CRC64;
     MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSVLTEKD EILADVASRL WFTYRKNFPA
     IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ RKRQPDSYCS VLQAFLDRKD
     SCYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ VLKKLAVFDT WSALAVHVAM DNTVVMADIR
     RLCRSSLPCA GAEAFPADSE RHCNGFPAGA EGGGRAAPWR PLVLLIPLRL GLADVNAAYA
     GTLKHCFRMP QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVAAAD RCPVPDESFH
     CQHPPGRMSI AELDPSIAVG FFCETEDDFN DWCQQVSKLS LLGGALPMFE LVEQQPSHLA
     CPDVLNLSLD SSDAERLERF FDSEDEDFEI LSL
 
 
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