Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Cysteine protease ATG4B

Gene

ATG4B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the C-terminal amino acid of ATG8 family proteins MAP1LC3, GABARAPL1, GABARAPL2 and GABARAP, to reveal a C-terminal glycine. Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Has also an activity of delipidating enzyme for the PE-conjugated forms.6 Publications

Enzyme regulationi

Inhibited by N-ethylmaleimide. Redox-regulated during autophagy since reducing conditions activate ATG4A whereas an oxidizing environment such as the presence of H2O2 inhibits its activity.1 Publication

Kineticsi

  1. KM=5.1 µM for MAP1LC3B2 Publications
  2. KM=5.8 µM for GABARAP2 Publications
  3. KM=4.4 µM for GABARAPL12 Publications
  4. KM=6.1 µM for GABARAPL22 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei74 – 741Nucleophile
    Active sitei278 – 2781Sequence Analysis
    Active sitei280 – 2801

    GO - Molecular functioni

    • cysteine-type endopeptidase activity Source: GO_Central
    • cysteine-type peptidase activity Source: UniProtKB
    • endopeptidase activity Source: BHF-UCL

    GO - Biological processi

    • autophagic vacuole assembly Source: UniProtKB
    • autophagy Source: UniProtKB
    • cellular response to nitrogen starvation Source: GO_Central
    • C-terminal protein lipidation Source: GO_Central
    • mitochondrion degradation Source: GO_Central
    • nucleophagy Source: GO_Central
    • positive regulation of autophagy Source: BHF-UCL
    • positive regulation of protein catabolic process Source: Ensembl
    • protein delipidation Source: GO_Central
    • protein processing Source: GO_Central
    • protein targeting to membrane Source: GO_Central
    • proteolysis Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Autophagy, Protein transport, Transport, Ubl conjugation pathway

    Protein family/group databases

    MEROPSiC54.003.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cysteine protease ATG4B (EC:3.4.22.-)
    Alternative name(s):
    AUT-like 1 cysteine endopeptidase
    Autophagin-1
    Autophagy-related cysteine endopeptidase 1
    Autophagy-related protein 4 homolog B
    Short name:
    hAPG4B
    Gene namesi
    Name:ATG4B
    Synonyms:APG4B, AUTL1, KIAA0943
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640 Componenti: Chromosome 2

    Organism-specific databases

    HGNCiHGNC:20790. ATG4B.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: UniProtKB
    • cytosol Source: GO_Central
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi74 – 741C → S: Complete loss of protease activity. 4 Publications
    Mutagenesisi78 – 781C → A: Reduces the redox sensitivity and retains activity in presence of H(2)O(2). 1 Publication
    Mutagenesisi142 – 1421W → A: Strongly reduced protease activity. 1 Publication
    Mutagenesisi229 – 2291R → A: Strongly reduced protease activity. 1 Publication
    Mutagenesisi278 – 2781D → A: Complete loss of protease activity. 2 Publications
    Mutagenesisi280 – 2801H → A: Complete loss of protease activity. 2 Publications

    Organism-specific databases

    PharmGKBiPA134898340.

    Polymorphism and mutation databases

    BioMutaiATG4B.
    DMDMi296434400.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 393393Cysteine protease ATG4BPRO_0000215844Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine4 Publications
    Modified residuei383 – 3831Phosphoserine6 Publications

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiQ9Y4P1.
    PaxDbiQ9Y4P1.
    PRIDEiQ9Y4P1.

    PTM databases

    PhosphoSiteiQ9Y4P1.

    Expressioni

    Tissue specificityi

    Mainly expressed in the skeletal muscle, followed by brain, heart, liver and pancreas.2 Publications

    Gene expression databases

    BgeeiQ9Y4P1.
    CleanExiHS_ATG4B.
    ExpressionAtlasiQ9Y4P1. baseline and differential.
    GenevisibleiQ9Y4P1. HS.

    Organism-specific databases

    HPAiCAB037195.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    GABARAPO951668EBI-712014,EBI-712001
    GABARAPL1Q9H0R87EBI-712014,EBI-746969
    GABARAPL2P605207EBI-712014,EBI-720116
    MAP1LC3BQ9GZQ811EBI-712014,EBI-373144

    Protein-protein interaction databases

    BioGridi116801. 27 interactions.
    IntActiQ9Y4P1. 18 interactions.
    MINTiMINT-1414043.

    Structurei

    Secondary structure

    1
    393
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 73Combined sources
    Helixi10 – 134Combined sources
    Helixi14 – 185Combined sources
    Beta strandi22 – 243Combined sources
    Beta strandi26 – 283Combined sources
    Beta strandi31 – 333Combined sources
    Turni35 – 373Combined sources
    Helixi39 – 4810Combined sources
    Beta strandi54 – 574Combined sources
    Turni61 – 644Combined sources
    Turni70 – 723Combined sources
    Helixi74 – 9118Combined sources
    Beta strandi100 – 1023Combined sources
    Helixi106 – 1138Combined sources
    Beta strandi116 – 1183Combined sources
    Helixi125 – 1339Combined sources
    Turni134 – 1363Combined sources
    Helixi145 – 15612Combined sources
    Turni160 – 1623Combined sources
    Beta strandi165 – 1684Combined sources
    Beta strandi173 – 1753Combined sources
    Helixi176 – 1838Combined sources
    Beta strandi184 – 1863Combined sources
    Beta strandi222 – 2298Combined sources
    Beta strandi232 – 2343Combined sources
    Helixi237 – 2393Combined sources
    Helixi240 – 2467Combined sources
    Beta strandi252 – 2576Combined sources
    Beta strandi264 – 2707Combined sources
    Beta strandi273 – 2775Combined sources
    Beta strandi281 – 2844Combined sources
    Beta strandi290 – 2923Combined sources
    Helixi297 – 2993Combined sources
    Beta strandi306 – 3094Combined sources
    Helixi310 – 3123Combined sources
    Beta strandi315 – 32511Combined sources
    Helixi326 – 34116Combined sources
    Beta strandi349 – 3535Combined sources
    Helixi371 – 3766Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2CY7X-ray1.90A1-393[»]
    2D1IX-ray2.00A/B1-393[»]
    2Z0DX-ray1.90A1-353[»]
    2Z0EX-ray1.90A1-353[»]
    2ZZPX-ray2.05A1-353[»]
    ProteinModelPortaliQ9Y4P1.
    SMRiQ9Y4P1. Positions 10-373.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9Y4P1.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase C54 family.Curated

    Phylogenomic databases

    eggNOGiNOG239662.
    GeneTreeiENSGT00530000063000.
    HOVERGENiHBG050536.
    InParanoidiQ9Y4P1.
    KOiK08342.
    OMAiDGMDSIN.
    OrthoDBiEOG73V6KD.
    PhylomeDBiQ9Y4P1.
    TreeFamiTF314847.

    Family and domain databases

    InterProiIPR005078. Peptidase_C54.
    [Graphical view]
    PANTHERiPTHR22624. PTHR22624. 1 hit.
    PfamiPF03416. Peptidase_C54. 1 hit.
    [Graphical view]

    Sequences (5)i

    Sequence statusi: Complete.

    This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q9Y4P1-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EILSDVASRL
    60 70 80 90 100
    WFTYRKNFPA IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ
    110 120 130 140 150
    RKRQPDSYFS VLNAFIDRKD SYYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ
    160 170 180 190 200
    VLKKLAVFDT WSSLAVHIAM DNTVVMEEIR RLCRTSVPCA GATAFPADSD
    210 220 230 240 250
    RHCNGFPAGA EVTNRPSPWR PLVLLIPLRL GLTDINEAYV ETLKHCFMMP
    260 270 280 290 300
    QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVEPTD GCFIPDESFH
    310 320 330 340 350
    CQHPPCRMSI AELDPSIAVG FFCKTEDDFN DWCQQVKKLS LLGGALPMFE
    360 370 380 390
    LVELQPSHLA CPDVLNLSLD SSDVERLERF FDSEDEDFEI LSL
    Length:393
    Mass (Da):44,294
    Last modified:May 18, 2010 - v2
    Checksum:iF4ADB3192176E0E5
    GO
    Isoform 2 (identifier: Q9Y4P1-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-1: M → MAHSVPSDSR...GSVGGRTGKM
         370-393: DSSDVERLERFFDSEDEDFEILSL → GESCQVQILLM

    Note: No experimental confirmation available.
    Show »
    Length:468
    Mass (Da):52,529
    Checksum:iF9731E7C406960D6
    GO
    Isoform 3 (identifier: Q9Y4P1-3) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-74: Missing.
         321-354: FFCKTEDDFNDWCQQVKKLSLLGGALPMFELVEL → KQGRLVRSLIPWAPRPSSWCAAVLGAAVVMCGTP
         355-393: Missing.

    Note: No experimental confirmation available.
    Show »
    Length:280
    Mass (Da):31,042
    Checksum:i0904A795A1B596B3
    GO
    Isoform 4 (identifier: Q9Y4P1-4) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-74: Missing.
         369-369: L → LGESCQVQVGSLG

    Show »
    Length:331
    Mass (Da):37,037
    Checksum:i97592E25838601B2
    GO
    Isoform 6 (identifier: Q9Y4P1-6) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         370-393: DSSDVERLERFFDSEDEDFEILSL → GESCQVQILLM

    Note: No experimental confirmation available.
    Show »
    Length:380
    Mass (Da):42,622
    Checksum:i48140873BCE7533D
    GO

    Sequence cautioni

    The sequence BAA76787.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
    The sequence BAC86110.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti136 – 1361Missing in BAB83890 (PubMed:15169837).Curated
    Sequence conflicti188 – 1881P → L in BAB55127 (PubMed:14702039).Curated
    Sequence conflicti247 – 2471F → Y in BAB55353 (PubMed:14702039).Curated
    Sequence conflicti273 – 2731E → G in BAB55042 (PubMed:14702039).Curated
    Sequence conflicti312 – 3121E → N in BAB83890 (PubMed:15169837).Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti354 – 3541L → Q.5 Publications
    Corresponds to variant rs7601000 [ dbSNP | Ensembl ].
    VAR_021486

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 7474Missing in isoform 3 and isoform 4. 1 PublicationVSP_013028Add
    BLAST
    Alternative sequencei1 – 11M → MAHSVPSDSRTSRRPTTRPH AARGAPRGSRRPGRTPKWRL PRISARAPYRLRRLRRHTYW PPRRPVAASRCWPVGATPLG SVGGRTGKM in isoform 2. 1 PublicationVSP_013029
    Alternative sequencei321 – 35434FFCKT…ELVEL → KQGRLVRSLIPWAPRPSSWC AAVLGAAVVMCGTP in isoform 3. 1 PublicationVSP_013031Add
    BLAST
    Alternative sequencei355 – 39339Missing in isoform 3. 1 PublicationVSP_013032Add
    BLAST
    Alternative sequencei369 – 3691L → LGESCQVQVGSLG in isoform 4. 1 PublicationVSP_013033
    Alternative sequencei370 – 39324DSSDV…EILSL → GESCQVQILLM in isoform 2 and isoform 6. 1 PublicationVSP_013034Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ504652 mRNA. Translation: CAD43219.1.
    AB066215 mRNA. Translation: BAB83890.1.
    AB023160 mRNA. Translation: BAA76787.2. Different initiation.
    AK027332 mRNA. Translation: BAB55042.1.
    AK027462 mRNA. Translation: BAB55127.1.
    AK027763 mRNA. Translation: BAB55353.1.
    AK125277 mRNA. Translation: BAC86110.1. Different initiation.
    AL080168 mRNA. Translation: CAB45756.1.
    AC133528 Genomic DNA. Translation: AAY14919.1.
    BC000719 mRNA. Translation: AAH00719.1.
    CCDSiCCDS46564.1. [Q9Y4P1-1]
    CCDS46565.1. [Q9Y4P1-6]
    PIRiT12492.
    RefSeqiNP_037457.3. NM_013325.4. [Q9Y4P1-1]
    NP_847896.1. NM_178326.2. [Q9Y4P1-6]
    UniGeneiHs.283610.

    Genome annotation databases

    EnsembliENST00000402096; ENSP00000384661; ENSG00000168397. [Q9Y4P1-4]
    ENST00000404914; ENSP00000384259; ENSG00000168397. [Q9Y4P1-1]
    ENST00000405546; ENSP00000383964; ENSG00000168397. [Q9Y4P1-6]
    GeneIDi23192.
    KEGGihsa:23192.
    UCSCiuc002wbu.3. human. [Q9Y4P1-4]
    uc002wbv.3. human. [Q9Y4P1-1]
    uc002wbw.3. human. [Q9Y4P1-6]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ504652 mRNA. Translation: CAD43219.1.
    AB066215 mRNA. Translation: BAB83890.1.
    AB023160 mRNA. Translation: BAA76787.2. Different initiation.
    AK027332 mRNA. Translation: BAB55042.1.
    AK027462 mRNA. Translation: BAB55127.1.
    AK027763 mRNA. Translation: BAB55353.1.
    AK125277 mRNA. Translation: BAC86110.1. Different initiation.
    AL080168 mRNA. Translation: CAB45756.1.
    AC133528 Genomic DNA. Translation: AAY14919.1.
    BC000719 mRNA. Translation: AAH00719.1.
    CCDSiCCDS46564.1. [Q9Y4P1-1]
    CCDS46565.1. [Q9Y4P1-6]
    PIRiT12492.
    RefSeqiNP_037457.3. NM_013325.4. [Q9Y4P1-1]
    NP_847896.1. NM_178326.2. [Q9Y4P1-6]
    UniGeneiHs.283610.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2CY7X-ray1.90A1-393[»]
    2D1IX-ray2.00A/B1-393[»]
    2Z0DX-ray1.90A1-353[»]
    2Z0EX-ray1.90A1-353[»]
    2ZZPX-ray2.05A1-353[»]
    ProteinModelPortaliQ9Y4P1.
    SMRiQ9Y4P1. Positions 10-373.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi116801. 27 interactions.
    IntActiQ9Y4P1. 18 interactions.
    MINTiMINT-1414043.

    Chemistry

    BindingDBiQ9Y4P1.
    ChEMBLiCHEMBL1741221.

    Protein family/group databases

    MEROPSiC54.003.

    PTM databases

    PhosphoSiteiQ9Y4P1.

    Polymorphism and mutation databases

    BioMutaiATG4B.
    DMDMi296434400.

    Proteomic databases

    MaxQBiQ9Y4P1.
    PaxDbiQ9Y4P1.
    PRIDEiQ9Y4P1.

    Protocols and materials databases

    DNASUi23192.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000402096; ENSP00000384661; ENSG00000168397. [Q9Y4P1-4]
    ENST00000404914; ENSP00000384259; ENSG00000168397. [Q9Y4P1-1]
    ENST00000405546; ENSP00000383964; ENSG00000168397. [Q9Y4P1-6]
    GeneIDi23192.
    KEGGihsa:23192.
    UCSCiuc002wbu.3. human. [Q9Y4P1-4]
    uc002wbv.3. human. [Q9Y4P1-1]
    uc002wbw.3. human. [Q9Y4P1-6]

    Organism-specific databases

    CTDi23192.
    GeneCardsiGC02P242578.
    H-InvDBHIX0180188.
    HGNCiHGNC:20790. ATG4B.
    HPAiCAB037195.
    MIMi611338. gene.
    neXtProtiNX_Q9Y4P1.
    PharmGKBiPA134898340.
    HUGEiSearch...
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiNOG239662.
    GeneTreeiENSGT00530000063000.
    HOVERGENiHBG050536.
    InParanoidiQ9Y4P1.
    KOiK08342.
    OMAiDGMDSIN.
    OrthoDBiEOG73V6KD.
    PhylomeDBiQ9Y4P1.
    TreeFamiTF314847.

    Miscellaneous databases

    ChiTaRSiATG4B. human.
    EvolutionaryTraceiQ9Y4P1.
    GeneWikiiATG4B.
    GenomeRNAii23192.
    NextBioi44679.
    PROiQ9Y4P1.
    SOURCEiSearch...

    Gene expression databases

    BgeeiQ9Y4P1.
    CleanExiHS_ATG4B.
    ExpressionAtlasiQ9Y4P1. baseline and differential.
    GenevisibleiQ9Y4P1. HS.

    Family and domain databases

    InterProiIPR005078. Peptidase_C54.
    [Graphical view]
    PANTHERiPTHR22624. PTHR22624. 1 hit.
    PfamiPF03416. Peptidase_C54. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy."
      Marino G., Uria J.A., Puente X.S., Quesada V., Bordallo J., Lopez-Otin C.
      J. Biol. Chem. 278:3671-3678(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, VARIANT GLN-354.
      Tissue: Liver.
    2. "LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation."
      Kabeya Y., Mizushima N., Yamamoto A., Oshitani-Okamoto S., Ohsumi Y., Yoshimori T.
      J. Cell Sci. 117:2805-2812(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, FUNCTION IN GABARAPL2; GABARAP AND MAP1LC3A CLEAVAGE, MUTAGENESIS OF CYS-74, VARIANT GLN-354.
    3. "Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
      Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
      DNA Res. 6:63-70(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT GLN-354.
      Tissue: Brain.
    4. Ohara O., Nagase T., Kikuno R.
      Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION.
    5. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2; 3; 4 AND 6).
      Tissue: Embryo and Placenta.
    6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT GLN-354.
      Tissue: Testis.
    7. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
      Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
      , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
      Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    8. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT GLN-354.
      Tissue: Placenta.
    9. Bienvenut W.V.
      Submitted (JAN-2010) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 1-12; 33-49; 120-137; 185-201 AND 230-244, ACETYLATION AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY.
      Tissue: Ovarian carcinoma.
    10. "HsAtg4B/HsApg4B/autophagin-1 cleaves the carboxyl termini of three human Atg8 homologues and delipidates microtubule-associated protein light chain 3- and GABAA receptor-associated protein-phospholipid conjugates."
      Tanida I., Sou Y.-S., Ezaki J., Minematsu-Ikeguchi N., Ueno T., Kominami E.
      J. Biol. Chem. 279:36268-36276(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF CYS-74.
    11. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
      Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
      Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    12. "Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4."
      Scherz-Shouval R., Shvets E., Fass E., Shorer H., Gil L., Elazar Z.
      EMBO J. 26:1749-1760(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ENZYME REGULATION, MUTAGENESIS OF CYS-78.
    13. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
      Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
      Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Leukemic T-cell.
    16. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
      Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
      Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    17. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    18. "Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates."
      Li M., Hou Y., Wang J., Chen X., Shao Z.M., Yin X.M.
      J. Biol. Chem. 286:7327-7338(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    19. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
      Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
      Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    20. "A high-throughput FRET-based assay for determination of Atg4 activity."
      Li M., Chen X., Ye Q.Z., Vogt A., Yin X.M.
      Autophagy 8:401-412(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    21. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
      Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
      Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    22. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    23. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
      Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
      J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.
    24. "Structural basis for the specificity and catalysis of human Atg4B responsible for mammalian autophagy."
      Sugawara K., Suzuki N.N., Fujioka Y., Mizushima N., Ohsumi Y., Inagaki F.
      J. Biol. Chem. 280:40058-40065(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), MUTAGENESIS OF CYS-74; TRP-142; ARG-229; ASP-278 AND HIS-280.
    25. "The crystal structure of human Atg4b, a processing and de-conjugating enzyme for autophagosome-forming modifiers."
      Kumanomidou T., Mizushima T., Komatsu M., Suzuki A., Tanida I., Sou Y.-S., Ueno T., Kominami E., Tanaka K., Yamane T.
      J. Mol. Biol. 355:612-618(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), MUTAGENESIS OF CYS-74; ASP-278 AND HIS-280.
    26. "The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy."
      Satoo K., Noda N.N., Kumeta H., Fujioka Y., Mizushima N., Ohsumi Y., Inagaki F.
      EMBO J. 28:1341-1350(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-353 IN COMPLEX WITH RAT MAP1LC3B/LC3, FUNCTION.

    Entry informationi

    Entry nameiATG4B_HUMAN
    AccessioniPrimary (citable) accession number: Q9Y4P1
    Secondary accession number(s): B7WNK2
    , Q53NU4, Q6ZUV8, Q8WYM9, Q96K07, Q96K96, Q96SZ1, Q9Y2F2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 15, 2005
    Last sequence update: May 18, 2010
    Last modified: June 24, 2015
    This is version 138 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome 2
      Human chromosome 2: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. Peptidase families
      Classification of peptidase families and list of entries
    7. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.