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Cysteine protease ATG4B (EC 3.4.22.-) (AUT-like 1 cysteine endopeptidase) (Autophagin-1) (Autophagy-related cysteine endopeptidase 1) (Autophagy-related protein 4 homolog B) (hAPG4B)

 ATG4B_HUMAN             Reviewed;         393 AA.
Q9Y4P1; B7WNK2; Q53NU4; Q6ZUV8; Q8WYM9; Q96K07; Q96K96; Q96SZ1;
Q9Y2F2;
15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
18-MAY-2010, sequence version 2.
23-MAY-2018, entry version 166.
RecName: Full=Cysteine protease ATG4B;
EC=3.4.22.-;
AltName: Full=AUT-like 1 cysteine endopeptidase;
AltName: Full=Autophagin-1;
AltName: Full=Autophagy-related cysteine endopeptidase 1;
AltName: Full=Autophagy-related protein 4 homolog B;
Short=hAPG4B;
Name=ATG4B; Synonyms=APG4B, AUTL1, KIAA0943;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, AND
VARIANT GLN-354.
TISSUE=Liver;
PubMed=12446702; DOI=10.1074/jbc.M208247200;
Marino G., Uria J.A., Puente X.S., Quesada V., Bordallo J.,
Lopez-Otin C.;
"Human autophagins, a family of cysteine proteinases potentially
implicated in cell degradation by autophagy.";
J. Biol. Chem. 278:3671-3678(2003).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, FUNCTION
IN GABARAPL2; GABARAP AND MAP1LC3A CLEAVAGE, MUTAGENESIS OF CYS-74,
AND VARIANT GLN-354.
PubMed=15169837; DOI=10.1242/jcs.01131;
Kabeya Y., Mizushima N., Yamamoto A., Oshitani-Okamoto S., Ohsumi Y.,
Yoshimori T.;
"LC3, GABARAP and GATE16 localize to autophagosomal membrane depending
on form-II formation.";
J. Cell Sci. 117:2805-2812(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT
GLN-354.
TISSUE=Brain;
PubMed=10231032; DOI=10.1093/dnares/6.1.63;
Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M.,
Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.;
"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.";
DNA Res. 6:63-70(1999).
[4]
SEQUENCE REVISION.
Ohara O., Nagase T., Kikuno R.;
Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2; 3; 4 AND 6).
TISSUE=Embryo, and Placenta;
PubMed=14702039; DOI=10.1038/ng1285;
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.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT
GLN-354.
TISSUE=Testis;
PubMed=17974005; DOI=10.1186/1471-2164-8-399;
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H.,
Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K.,
Ottenwaelder B., Poustka A., Wiemann S., Schupp I.;
"The full-ORF clone resource of the German cDNA consortium.";
BMC Genomics 8:399-399(2007).
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15815621; DOI=10.1038/nature03466;
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.;
"Generation and annotation of the DNA sequences of human chromosomes 2
and 4.";
Nature 434:724-731(2005).
[8]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT
GLN-354.
TISSUE=Placenta;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[9]
PROTEIN SEQUENCE OF 1-12; 33-49; 120-137; 185-201 AND 230-244,
ACETYLATION AT MET-1, AND IDENTIFICATION BY MASS SPECTROMETRY.
TISSUE=Ovarian carcinoma;
Bienvenut W.V.;
Submitted (JAN-2010) to UniProtKB.
[10]
FUNCTION, AND MUTAGENESIS OF CYS-74.
PubMed=15187094; DOI=10.1074/jbc.M401461200;
Tanida I., Sou Y.-S., Ezaki J., Minematsu-Ikeguchi N., Ueno T.,
Kominami E.;
"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.";
J. Biol. Chem. 279:36268-36276(2004).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=17081983; DOI=10.1016/j.cell.2006.09.026;
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P.,
Mann M.;
"Global, in vivo, and site-specific phosphorylation dynamics in
signaling networks.";
Cell 127:635-648(2006).
[12]
FUNCTION, ENZYME REGULATION, AND MUTAGENESIS OF CYS-78.
PubMed=17347651; DOI=10.1038/sj.emboj.7601623;
Scherz-Shouval R., Shvets E., Fass E., Shorer H., Gil L., Elazar Z.;
"Reactive oxygen species are essential for autophagy and specifically
regulate the activity of Atg4.";
EMBO J. 26:1749-1760(2007).
[13]
ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19413330; DOI=10.1021/ac9004309;
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
Mohammed S.;
"Lys-N and trypsin cover complementary parts of the phosphoproteome in
a refined SCX-based approach.";
Anal. Chem. 81:4493-4501(2009).
[14]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19369195; DOI=10.1074/mcp.M800588-MCP200;
Oppermann F.S., Gnad F., Olsen J.V., Hornberger R., Greff Z., Keri G.,
Mann M., Daub H.;
"Large-scale proteomics analysis of the human kinome.";
Mol. Cell. Proteomics 8:1751-1764(2009).
[15]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Leukemic T-cell;
PubMed=19690332; DOI=10.1126/scisignal.2000007;
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
Rodionov V., Han D.K.;
"Quantitative phosphoproteomic analysis of T cell receptor signaling
reveals system-wide modulation of protein-protein interactions.";
Sci. Signal. 2:RA46-RA46(2009).
[16]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=20068231; DOI=10.1126/scisignal.2000475;
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.;
"Quantitative phosphoproteomics reveals widespread full
phosphorylation site occupancy during mitosis.";
Sci. Signal. 3:RA3-RA3(2010).
[17]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[18]
FUNCTION, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=21177865; DOI=10.1074/jbc.M110.199059;
Li M., Hou Y., Wang J., Chen X., Shao Z.M., Yin X.M.;
"Kinetics comparisons of mammalian Atg4 homologues indicate selective
preferences toward diverse Atg8 substrates.";
J. Biol. Chem. 286:7327-7338(2011).
[19]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21406692; DOI=10.1126/scisignal.2001570;
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
Blagoev B.;
"System-wide temporal characterization of the proteome and
phosphoproteome of human embryonic stem cell differentiation.";
Sci. Signal. 4:RS3-RS3(2011).
[20]
FUNCTION, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=22302004; DOI=10.4161/auto.18777;
Li M., Chen X., Ye Q.Z., Vogt A., Yin X.M.;
"A high-throughput FRET-based assay for determination of Atg4
activity.";
Autophagy 8:401-412(2012).
[21]
ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22223895; DOI=10.1074/mcp.M111.015131;
Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C.,
Meinnel T., Giglione C.;
"Comparative large-scale characterisation of plant vs. mammal proteins
reveals similar and idiosyncratic N-alpha acetylation features.";
Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
[22]
ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22814378; DOI=10.1073/pnas.1210303109;
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
Aldabe R.;
"N-terminal acetylome analyses and functional insights of the N-
terminal acetyltransferase NatB.";
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
[23]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D.,
Wang L., Ye M., Zou H.;
"An enzyme assisted RP-RPLC approach for in-depth analysis of human
liver phosphoproteome.";
J. Proteomics 96:253-262(2014).
[24]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), AND MUTAGENESIS OF CYS-74;
TRP-142; ARG-229; ASP-278 AND HIS-280.
PubMed=16183633; DOI=10.1074/jbc.M509158200;
Sugawara K., Suzuki N.N., Fujioka Y., Mizushima N., Ohsumi Y.,
Inagaki F.;
"Structural basis for the specificity and catalysis of human Atg4B
responsible for mammalian autophagy.";
J. Biol. Chem. 280:40058-40065(2005).
[25]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), AND MUTAGENESIS OF CYS-74;
ASP-278 AND HIS-280.
PubMed=16325851; DOI=10.1016/j.jmb.2005.11.018;
Kumanomidou T., Mizushima T., Komatsu M., Suzuki A., Tanida I.,
Sou Y.-S., Ueno T., Kominami E., Tanaka K., Yamane T.;
"The crystal structure of human Atg4b, a processing and de-conjugating
enzyme for autophagosome-forming modifiers.";
J. Mol. Biol. 355:612-618(2006).
[26]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-353 IN COMPLEX WITH RAT
MAP1LC3B/LC3, AND FUNCTION.
PubMed=19322194; DOI=10.1038/emboj.2009.80;
Satoo K., Noda N.N., Kumeta H., Fujioka Y., Mizushima N., Ohsumi Y.,
Inagaki F.;
"The structure of Atg4B-LC3 complex reveals the mechanism of LC3
processing and delipidation during autophagy.";
EMBO J. 28:1341-1350(2009).
-!- FUNCTION: 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. {ECO:0000269|PubMed:15169837,
ECO:0000269|PubMed:15187094, ECO:0000269|PubMed:17347651,
ECO:0000269|PubMed:19322194, ECO:0000269|PubMed:21177865,
ECO:0000269|PubMed:22302004}.
-!- ENZYME REGULATION: Inhibited by N-ethylmaleimide. Redox-regulated
during autophagy since reducing conditions activate ATG4A whereas
an oxidizing environment such as the presence of H(2)O(2) inhibits
its activity. {ECO:0000269|PubMed:17347651}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=5.1 uM for MAP1LC3B {ECO:0000269|PubMed:21177865,
ECO:0000269|PubMed:22302004};
KM=5.8 uM for GABARAP {ECO:0000269|PubMed:21177865,
ECO:0000269|PubMed:22302004};
KM=4.4 uM for GABARAPL1 {ECO:0000269|PubMed:21177865,
ECO:0000269|PubMed:22302004};
KM=6.1 uM for GABARAPL2 {ECO:0000269|PubMed:21177865,
ECO:0000269|PubMed:22302004};
-!- INTERACTION:
O95166:GABARAP; NbExp=8; IntAct=EBI-712014, EBI-712001;
Q9H0R8:GABARAPL1; NbExp=9; IntAct=EBI-712014, EBI-746969;
P60520:GABARAPL2; NbExp=9; IntAct=EBI-712014, EBI-720116;
Q9H492:MAP1LC3A; NbExp=5; IntAct=EBI-712014, EBI-720768;
Q9GZQ8:MAP1LC3B; NbExp=13; IntAct=EBI-712014, EBI-373144;
Q9BXW4:MAP1LC3C; NbExp=3; IntAct=EBI-712014, EBI-2603996;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=5;
Name=1;
IsoId=Q9Y4P1-1; Sequence=Displayed;
Name=2;
IsoId=Q9Y4P1-2; Sequence=VSP_013029, VSP_013034;
Note=No experimental confirmation available.;
Name=3;
IsoId=Q9Y4P1-3; Sequence=VSP_013028, VSP_013031, VSP_013032;
Note=No experimental confirmation available.;
Name=4;
IsoId=Q9Y4P1-4; Sequence=VSP_013028, VSP_013033;
Name=6;
IsoId=Q9Y4P1-6; Sequence=VSP_013034;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Mainly expressed in the skeletal muscle,
followed by brain, heart, liver and pancreas.
{ECO:0000269|PubMed:12446702, ECO:0000269|PubMed:15169837}.
-!- SIMILARITY: Belongs to the peptidase C54 family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAA76787.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
Sequence=BAC86110.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
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EMBL; AJ504652; CAD43219.1; -; mRNA.
EMBL; AB066215; BAB83890.1; -; mRNA.
EMBL; AB023160; BAA76787.2; ALT_INIT; mRNA.
EMBL; AK027332; BAB55042.1; -; mRNA.
EMBL; AK027462; BAB55127.1; -; mRNA.
EMBL; AK027763; BAB55353.1; -; mRNA.
EMBL; AK125277; BAC86110.1; ALT_INIT; mRNA.
EMBL; AL080168; CAB45756.1; -; mRNA.
EMBL; AC133528; AAY14919.1; -; Genomic_DNA.
EMBL; BC000719; AAH00719.1; -; mRNA.
CCDS; CCDS46564.1; -. [Q9Y4P1-1]
CCDS; CCDS46565.1; -. [Q9Y4P1-6]
PIR; T12492; T12492.
RefSeq; NP_037457.3; NM_013325.4. [Q9Y4P1-1]
RefSeq; NP_847896.1; NM_178326.2. [Q9Y4P1-6]
UniGene; Hs.283610; -.
PDB; 2CY7; X-ray; 1.90 A; A=1-393.
PDB; 2D1I; X-ray; 2.00 A; A/B=1-393.
PDB; 2Z0D; X-ray; 1.90 A; A=1-353.
PDB; 2Z0E; X-ray; 1.90 A; A=1-353.
PDB; 2ZZP; X-ray; 2.05 A; A=1-353.
PDB; 5LXH; X-ray; 1.58 A; E/F/G=384-393.
PDB; 5LXI; X-ray; 1.44 A; C/E=384-393.
PDBsum; 2CY7; -.
PDBsum; 2D1I; -.
PDBsum; 2Z0D; -.
PDBsum; 2Z0E; -.
PDBsum; 2ZZP; -.
PDBsum; 5LXH; -.
PDBsum; 5LXI; -.
ProteinModelPortal; Q9Y4P1; -.
SMR; Q9Y4P1; -.
BioGrid; 116801; 28.
IntAct; Q9Y4P1; 18.
MINT; Q9Y4P1; -.
STRING; 9606.ENSP00000384259; -.
BindingDB; Q9Y4P1; -.
ChEMBL; CHEMBL1741221; -.
MEROPS; C54.003; -.
TCDB; 9.A.15.2.1; the autophagy-related phagophore-formation transporter (apt) family.
iPTMnet; Q9Y4P1; -.
PhosphoSitePlus; Q9Y4P1; -.
BioMuta; ATG4B; -.
DMDM; 296434400; -.
EPD; Q9Y4P1; -.
PaxDb; Q9Y4P1; -.
PeptideAtlas; Q9Y4P1; -.
PRIDE; Q9Y4P1; -.
DNASU; 23192; -.
Ensembl; ENST00000402096; ENSP00000384661; ENSG00000168397. [Q9Y4P1-4]
Ensembl; ENST00000404914; ENSP00000384259; ENSG00000168397. [Q9Y4P1-1]
Ensembl; ENST00000405546; ENSP00000383964; ENSG00000168397. [Q9Y4P1-6]
GeneID; 23192; -.
KEGG; hsa:23192; -.
UCSC; uc002wbv.4; human. [Q9Y4P1-1]
CTD; 23192; -.
DisGeNET; 23192; -.
EuPathDB; HostDB:ENSG00000168397.16; -.
GeneCards; ATG4B; -.
H-InvDB; HIX0180188; -.
HGNC; HGNC:20790; ATG4B.
HPA; CAB037195; -.
HPA; HPA069803; -.
MIM; 611338; gene.
neXtProt; NX_Q9Y4P1; -.
OpenTargets; ENSG00000168397; -.
PharmGKB; PA134898340; -.
eggNOG; KOG2674; Eukaryota.
eggNOG; ENOG410XPQ0; LUCA.
GeneTree; ENSGT00530000063000; -.
HOVERGEN; HBG050536; -.
InParanoid; Q9Y4P1; -.
KO; K08342; -.
OMA; LMGESQN; -.
OrthoDB; EOG091G0995; -.
PhylomeDB; Q9Y4P1; -.
TreeFam; TF314847; -.
Reactome; R-HSA-1632852; Macroautophagy.
SIGNOR; Q9Y4P1; -.
ChiTaRS; ATG4B; human.
EvolutionaryTrace; Q9Y4P1; -.
GeneWiki; ATG4B; -.
GenomeRNAi; 23192; -.
PRO; PR:Q9Y4P1; -.
Proteomes; UP000005640; Chromosome 2.
Bgee; ENSG00000168397; -.
CleanEx; HS_ATG4B; -.
ExpressionAtlas; Q9Y4P1; baseline and differential.
Genevisible; Q9Y4P1; HS.
GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
GO; GO:0005829; C:cytosol; IBA:GO_Central.
GO; GO:0004197; F:cysteine-type endopeptidase activity; IBA:GO_Central.
GO; GO:0008234; F:cysteine-type peptidase activity; IDA:UniProtKB.
GO; GO:0004175; F:endopeptidase activity; IDA:BHF-UCL.
GO; GO:0000045; P:autophagosome assembly; IGI:UniProtKB.
GO; GO:0006914; P:autophagy; IDA:BHF-UCL.
GO; GO:0000422; P:autophagy of mitochondrion; IBA:GO_Central.
GO; GO:0044804; P:autophagy of nucleus; IBA:GO_Central.
GO; GO:0006501; P:C-terminal protein lipidation; IBA:GO_Central.
GO; GO:0016236; P:macroautophagy; TAS:Reactome.
GO; GO:0045732; P:positive regulation of protein catabolic process; IEA:Ensembl.
GO; GO:0051697; P:protein delipidation; IDA:MGI.
GO; GO:0006612; P:protein targeting to membrane; IBA:GO_Central.
GO; GO:0006508; P:proteolysis; IDA:UniProtKB.
InterPro; IPR032916; ATG4B_met.
InterPro; IPR005078; Peptidase_C54.
PANTHER; PTHR22624; PTHR22624; 1.
PANTHER; PTHR22624:SF39; PTHR22624:SF39; 1.
Pfam; PF03416; Peptidase_C54; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Alternative splicing; Autophagy;
Complete proteome; Cytoplasm; Direct protein sequencing; Hydrolase;
Phosphoprotein; Polymorphism; Protease; Protein transport;
Reference proteome; Thiol protease; Transport;
Ubl conjugation pathway.
CHAIN 1 393 Cysteine protease ATG4B.
/FTId=PRO_0000215844.
ACT_SITE 74 74 Nucleophile.
ACT_SITE 278 278 {ECO:0000255}.
ACT_SITE 280 280
MOD_RES 1 1 N-acetylmethionine.
{ECO:0000244|PubMed:19413330,
ECO:0000244|PubMed:22223895,
ECO:0000244|PubMed:22814378,
ECO:0000269|Ref.9}.
MOD_RES 383 383 Phosphoserine.
{ECO:0000244|PubMed:17081983,
ECO:0000244|PubMed:19369195,
ECO:0000244|PubMed:19690332,
ECO:0000244|PubMed:20068231,
ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:24275569}.
VAR_SEQ 1 74 Missing (in isoform 3 and isoform 4).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_013028.
VAR_SEQ 1 1 M -> MAHSVPSDSRTSRRPTTRPHAARGAPRGSRRPGRTP
KWRLPRISARAPYRLRRLRRHTYWPPRRPVAASRCWPVGAT
PLGSVGGRTGKM (in isoform 2).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_013029.
VAR_SEQ 321 354 FFCKTEDDFNDWCQQVKKLSLLGGALPMFELVEL -> KQG
RLVRSLIPWAPRPSSWCAAVLGAAVVMCGTP (in
isoform 3).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_013031.
VAR_SEQ 355 393 Missing (in isoform 3).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_013032.
VAR_SEQ 369 369 L -> LGESCQVQVGSLG (in isoform 4).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_013033.
VAR_SEQ 370 393 DSSDVERLERFFDSEDEDFEILSL -> GESCQVQILLM
(in isoform 2 and isoform 6).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_013034.
VARIANT 354 354 L -> Q (in dbSNP:rs7601000).
{ECO:0000269|PubMed:10231032,
ECO:0000269|PubMed:12446702,
ECO:0000269|PubMed:15169837,
ECO:0000269|PubMed:15489334,
ECO:0000269|PubMed:17974005}.
/FTId=VAR_021486.
MUTAGEN 74 74 C->S: Complete loss of protease activity.
{ECO:0000269|PubMed:15169837,
ECO:0000269|PubMed:15187094,
ECO:0000269|PubMed:16183633,
ECO:0000269|PubMed:16325851}.
MUTAGEN 78 78 C->A: Reduces the redox sensitivity and
retains activity in presence of H(2)O(2).
{ECO:0000269|PubMed:17347651}.
MUTAGEN 142 142 W->A: Strongly reduced protease activity.
{ECO:0000269|PubMed:16183633}.
MUTAGEN 229 229 R->A: Strongly reduced protease activity.
{ECO:0000269|PubMed:16183633}.
MUTAGEN 278 278 D->A: Complete loss of protease activity.
{ECO:0000269|PubMed:16183633,
ECO:0000269|PubMed:16325851}.
MUTAGEN 280 280 H->A: Complete loss of protease activity.
{ECO:0000269|PubMed:16183633,
ECO:0000269|PubMed:16325851}.
CONFLICT 136 136 Missing (in Ref. 2; BAB83890).
{ECO:0000305}.
CONFLICT 188 188 P -> L (in Ref. 5; BAB55127).
{ECO:0000305}.
CONFLICT 247 247 F -> Y (in Ref. 5; BAB55353).
{ECO:0000305}.
CONFLICT 273 273 E -> G (in Ref. 5; BAB55042).
{ECO:0000305}.
CONFLICT 312 312 E -> N (in Ref. 2; BAB83890).
{ECO:0000305}.
HELIX 5 7 {ECO:0000244|PDB:2Z0E}.
HELIX 10 13 {ECO:0000244|PDB:2CY7}.
HELIX 14 18 {ECO:0000244|PDB:2Z0E}.
STRAND 22 24 {ECO:0000244|PDB:2D1I}.
STRAND 26 28 {ECO:0000244|PDB:2CY7}.
STRAND 31 33 {ECO:0000244|PDB:2CY7}.
TURN 35 37 {ECO:0000244|PDB:2CY7}.
HELIX 39 48 {ECO:0000244|PDB:2CY7}.
STRAND 54 57 {ECO:0000244|PDB:2CY7}.
TURN 61 64 {ECO:0000244|PDB:2CY7}.
TURN 70 72 {ECO:0000244|PDB:2CY7}.
HELIX 74 91 {ECO:0000244|PDB:2CY7}.
STRAND 100 102 {ECO:0000244|PDB:2Z0E}.
HELIX 106 113 {ECO:0000244|PDB:2CY7}.
STRAND 116 118 {ECO:0000244|PDB:2CY7}.
HELIX 125 133 {ECO:0000244|PDB:2CY7}.
TURN 134 136 {ECO:0000244|PDB:2CY7}.
HELIX 145 156 {ECO:0000244|PDB:2CY7}.
TURN 160 162 {ECO:0000244|PDB:2CY7}.
STRAND 165 168 {ECO:0000244|PDB:2CY7}.
STRAND 173 175 {ECO:0000244|PDB:2CY7}.
HELIX 176 183 {ECO:0000244|PDB:2CY7}.
STRAND 184 186 {ECO:0000244|PDB:2CY7}.
STRAND 222 229 {ECO:0000244|PDB:2CY7}.
STRAND 232 234 {ECO:0000244|PDB:2CY7}.
HELIX 237 239 {ECO:0000244|PDB:2CY7}.
HELIX 240 246 {ECO:0000244|PDB:2CY7}.
STRAND 252 257 {ECO:0000244|PDB:2CY7}.
STRAND 264 270 {ECO:0000244|PDB:2CY7}.
STRAND 273 277 {ECO:0000244|PDB:2CY7}.
STRAND 281 284 {ECO:0000244|PDB:2CY7}.
STRAND 290 292 {ECO:0000244|PDB:2D1I}.
HELIX 297 299 {ECO:0000244|PDB:2CY7}.
STRAND 306 309 {ECO:0000244|PDB:2CY7}.
HELIX 310 312 {ECO:0000244|PDB:2CY7}.
STRAND 315 325 {ECO:0000244|PDB:2CY7}.
HELIX 326 341 {ECO:0000244|PDB:2CY7}.
STRAND 349 353 {ECO:0000244|PDB:2CY7}.
HELIX 371 376 {ECO:0000244|PDB:2CY7}.
STRAND 388 390 {ECO:0000244|PDB:5LXH}.
SEQUENCE 393 AA; 44294 MW; F4ADB3192176E0E5 CRC64;
MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EILSDVASRL WFTYRKNFPA
IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ RKRQPDSYFS VLNAFIDRKD
SYYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ VLKKLAVFDT WSSLAVHIAM DNTVVMEEIR
RLCRTSVPCA GATAFPADSD RHCNGFPAGA EVTNRPSPWR PLVLLIPLRL GLTDINEAYV
ETLKHCFMMP QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVEPTD GCFIPDESFH
CQHPPCRMSI AELDPSIAVG FFCKTEDDFN DWCQQVKKLS LLGGALPMFE LVELQPSHLA
CPDVLNLSLD SSDVERLERF FDSEDEDFEI LSL


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