Q9Y4P1 (ATG4B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	ATG4B
Synonyms:	APG4B, AUTL1, KIAA0943

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	393 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cysteine protease required for autophagy, which cleaves the C-terminal part of MAP1LC3, GABARAPL1, GABARAPL2 and GABARAP, allowing the liberation of form I. A subpopulation of form I is subsequently converted to a smaller form (form II). Form II, with a revealed C-terminal glycine, is considered to be the phosphatidylethanolamine (PE)-conjugated form, and has the capacity for the binding to autophagosomes. Also mediates the lipid deconjugation required for target recycling. Ref.2 Ref.18
Enzyme regulation	Inhibited by N-ethylmaleimide.
Subcellular location	Cytoplasm Probable.
Tissue specificity	Mainly expressed in the skeletal muscle, followed by brain, heart, liver and pancreas. Ref.1 Ref.2
Sequence similarities	Belongs to the peptidase C54 family.
Sequence caution	The sequence BAA76787.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened. The sequence BAC86110.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Autophagy Protein transport Transport Ubl conjugation pathway
Cellular component	Cytoplasm
Coding sequence diversity	Alternative splicing Polymorphism
Molecular function	Hydrolase Protease Thiol protease
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	autophagic vacuole assembly Inferred from genetic interaction Ref.1. Source: UniProtKB positive regulation of autophagy Inferred from direct assay PubMed 18387192. Source: BHF-UCL protein transport Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from direct assay Ref.2. Source: UniProtKB
Cellular_component	cytoplasm Inferred from sequence or structural similarity Ref.1. Source: UniProtKB
Molecular_function	cysteine-type peptidase activity Inferred from direct assay Ref.2. Source: UniProtKB endopeptidase activity Inferred from direct assay PubMed 18387192. Source: BHF-UCL
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
GABARAP	O95166	8	EBI-712014,EBI-712001
GABARAPL1	Q9H0R8	7	EBI-712014,EBI-746969
GABARAPL2	P60520	6	EBI-712014,EBI-720116
MAP1LC3B	Q9GZQ8	6	EBI-712014,EBI-373144

Alternative products

This entry describes 5 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9Y4P1-1)

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.

Isoform 2 (identifier: Q9Y4P1-2)

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.

Isoform 3 (identifier: Q9Y4P1-3)

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.

Isoform 4 (identifier: Q9Y4P1-4)

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

Isoform 6 (identifier: Q9Y4P1-6)

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

Note: No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 393

393

Cysteine protease ATG4B

PRO_0000215844

Sites

Active site

74

1

Nucleophile

Active site

278

1

Potential

Active site

280

1

Amino acid modifications

Modified residue

1

1

N-acetylmethionine Ref.9

Modified residue

34

1

Phosphoserine By similarity

Modified residue

383

1

Phosphoserine Ref.10 Ref.11 Ref.12 Ref.13 Ref.15

Natural variations

Alternative sequence

1 – 74

74

Missing in isoform 3 and isoform 4.

VSP_013028

Alternative sequence

1

1

M → MAHSVPSDSRTSRRPTTRPH AARGAPRGSRRPGRTPKWRL PRISARAPYRLRRLRRHTYW PPRRPVAASRCWPVGATPLG SVGGRTGKM in isoform 2.

VSP_013029

Alternative sequence

321 – 354

34

FFCKT…ELVEL → KQGRLVRSLIPWAPRPSSWC AAVLGAAVVMCGTP in isoform 3.

VSP_013031

Alternative sequence

355 – 393

39

Missing in isoform 3.

VSP_013032

Alternative sequence

369

1

L → LGESCQVQVGSLG in isoform 4.

VSP_013033

Alternative sequence

370 – 393

24

DSSDV…EILSL → GESCQVQILLM in isoform 2 and isoform 6.

VSP_013034

Natural variant

354

1

L → Q. Ref.1 Ref.2 Ref.3 Ref.6 Ref.8
Corresponds to variant rs7601000 [ dbSNP | Ensembl ].

VAR_021486

Experimental info

Mutagenesis

74

1

C → S: Complete loss of protease activity. Ref.2 Ref.16 Ref.17

Mutagenesis

142

1

W → A: Strongly reduced protease activity. Ref.16

Mutagenesis

229

1

R → A: Strongly reduced protease activity. Ref.16

Mutagenesis

278

1

D → A: Complete loss of protease activity. Ref.16 Ref.17

Mutagenesis

280

1

H → A: Complete loss of protease activity. Ref.16 Ref.17

Sequence conflict

136

1

Missing in BAB83890. Ref.2

Sequence conflict

188

1

P → L in BAB55127. Ref.5

Sequence conflict

247

1

F → Y in BAB55353. Ref.5

Sequence conflict

273

1

E → G in BAB55042. Ref.5

Sequence conflict

312

1

E → N in BAB83890. Ref.2

Secondary structure

1

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393

Helix Strand Turn

Details...

Helix

5 – 7

3

Helix

10 – 13

4

Helix

14 – 18

5

Beta strand

22 – 24

3

Beta strand

26 – 28

3

Beta strand

31 – 33

3

Turn

35 – 37

3

Helix

39 – 48

10

Beta strand

54 – 57

4

Turn

61 – 64

4

Turn

70 – 72

3

Helix

74 – 91

18

Beta strand

100 – 102

3

Helix

106 – 113

8

Beta strand

116 – 118

3

Helix

125 – 133

9

Turn

134 – 136

3

Helix

145 – 156

12

Turn

160 – 162

3

Beta strand

165 – 168

4

Beta strand

173 – 175

3

Helix

176 – 183

8

Beta strand

184 – 186

3

Beta strand

222 – 229

8

Beta strand

232 – 234

3

Helix

237 – 239

3

Helix

240 – 246

7

Beta strand

252 – 257

6

Beta strand

264 – 270

7

Beta strand

273 – 277

5

Beta strand

281 – 284

4

Beta strand

290 – 292

3

Helix

297 – 299

3

Beta strand

306 – 309

4

Helix

310 – 312

3

Beta strand

315 – 325

11

Helix

326 – 341

16

Beta strand

349 – 353

5

Helix

371 – 376

6

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 18, 2010. Version 2. Checksum: F4ADB3192176E0E5	FASTA	393	44,294
	10 20 30 40 50 60 MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EILSDVASRL WFTYRKNFPA 70 80 90 100 110 120 IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ RKRQPDSYFS VLNAFIDRKD 130 140 150 160 170 180 SYYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ VLKKLAVFDT WSSLAVHIAM DNTVVMEEIR 190 200 210 220 230 240 RLCRTSVPCA GATAFPADSD RHCNGFPAGA EVTNRPSPWR PLVLLIPLRL GLTDINEAYV 250 260 270 280 290 300 ETLKHCFMMP QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVEPTD GCFIPDESFH 310 320 330 340 350 360 CQHPPCRMSI AELDPSIAVG FFCKTEDDFN DWCQQVKKLS LLGGALPMFE LVELQPSHLA 370 380 390 CPDVLNLSLD SSDVERLERF FDSEDEDFEI LSL
	Isoform 2 [UniParc]. Checksum: F9731E7C406960D6	FASTA	468	52,529
	10 20 30 40 50 60 MAHSVPSDSR TSRRPTTRPH AARGAPRGSR RPGRTPKWRL PRISARAPYR LRRLRRHTYW 70 80 90 100 110 120 PPRRPVAASR CWPVGATPLG SVGGRTGKMD AATLTYDTLR FAEFEDFPET SEPVWILGRK 130 140 150 160 170 180 YSIFTEKDEI LSDVASRLWF TYRKNFPAIG GTGPTSDTGW GCMLRCGQMI FAQALVCRHL 190 200 210 220 230 240 GRDWRWTQRK RQPDSYFSVL NAFIDRKDSY YSIHQIAQMG VGEGKSIGQW YGPNTVAQVL 250 260 270 280 290 300 KKLAVFDTWS SLAVHIAMDN TVVMEEIRRL CRTSVPCAGA TAFPADSDRH CNGFPAGAEV 310 320 330 340 350 360 TNRPSPWRPL VLLIPLRLGL TDINEAYVET LKHCFMMPQS LGVIGGKPNS AHYFIGYVGE 370 380 390 400 410 420 ELIYLDPHTT QPAVEPTDGC FIPDESFHCQ HPPCRMSIAE LDPSIAVGFF CKTEDDFNDW 430 440 450 460 CQQVKKLSLL GGALPMFELV ELQPSHLACP DVLNLSLGES CQVQILLM
	Isoform 3 [UniParc]. Checksum: 0904A795A1B596B3	FASTA	280	31,042
	10 20 30 40 50 60 MLRCGQMIFA QALVCRHLGR DWRWTQRKRQ PDSYFSVLNA FIDRKDSYYS IHQIAQMGVG 70 80 90 100 110 120 EGKSIGQWYG PNTVAQVLKK LAVFDTWSSL AVHIAMDNTV VMEEIRRLCR TSVPCAGATA 130 140 150 160 170 180 FPADSDRHCN GFPAGAEVTN RPSPWRPLVL LIPLRLGLTD INEAYVETLK HCFMMPQSLG 190 200 210 220 230 240 VIGGKPNSAH YFIGYVGEEL IYLDPHTTQP AVEPTDGCFI PDESFHCQHP PCRMSIAELD 250 260 270 280 PSIAVGKQGR LVRSLIPWAP RPSSWCAAVL GAAVVMCGTP
	Isoform 4 [UniParc]. Checksum: 97592E25838601B2	FASTA	331	37,037
	10 20 30 40 50 60 MLRCGQMIFA QALVCRHLGR DWRWTQRKRQ PDSYFSVLNA FIDRKDSYYS IHQIAQMGVG 70 80 90 100 110 120 EGKSIGQWYG PNTVAQVLKK LAVFDTWSSL AVHIAMDNTV VMEEIRRLCR TSVPCAGATA 130 140 150 160 170 180 FPADSDRHCN GFPAGAEVTN RPSPWRPLVL LIPLRLGLTD INEAYVETLK HCFMMPQSLG 190 200 210 220 230 240 VIGGKPNSAH YFIGYVGEEL IYLDPHTTQP AVEPTDGCFI PDESFHCQHP PCRMSIAELD 250 260 270 280 290 300 PSIAVGFFCK TEDDFNDWCQ QVKKLSLLGG ALPMFELVEL QPSHLACPDV LNLSLGESCQ 310 320 330 VQVGSLGDSS DVERLERFFD SEDEDFEILS L
	Isoform 6 [UniParc]. Checksum: 48140873BCE7533D	FASTA	380	42,622
	10 20 30 40 50 60 MDAATLTYDT LRFAEFEDFP ETSEPVWILG RKYSIFTEKD EILSDVASRL WFTYRKNFPA 70 80 90 100 110 120 IGGTGPTSDT GWGCMLRCGQ MIFAQALVCR HLGRDWRWTQ RKRQPDSYFS VLNAFIDRKD 130 140 150 160 170 180 SYYSIHQIAQ MGVGEGKSIG QWYGPNTVAQ VLKKLAVFDT WSSLAVHIAM DNTVVMEEIR 190 200 210 220 230 240 RLCRTSVPCA GATAFPADSD RHCNGFPAGA EVTNRPSPWR PLVLLIPLRL GLTDINEAYV 250 260 270 280 290 300 ETLKHCFMMP QSLGVIGGKP NSAHYFIGYV GEELIYLDPH TTQPAVEPTD GCFIPDESFH 310 320 330 340 350 360 CQHPPCRMSI AELDPSIAVG FFCKTEDDFN DWCQQVKKLS LLGGALPMFE LVELQPSHLA 370 380 CPDVLNLSLG ESCQVQILLM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"The full-ORF clone resource of the German cDNA consortium." 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. BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract] 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, MASS SPECTROMETRY. Tissue: Ovarian carcinoma.
[10]	"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, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[11]	"Large-scale proteomics analysis of the human kinome." Oppermann F.S., Gnad F., Olsen J.V., Hornberger R., Greff Z., Keri G., Mann M., Daub H. Mol. Cell. Proteomics 8:1751-1764(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383, MASS SPECTROMETRY.
[12]	"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, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[13]	"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, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[14]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]	"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, MASS SPECTROMETRY.
[16]	"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.
[17]	"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.
[18]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00554649.
IPI00647200.
IPI00746254.
IPI00941681.
IPI01018366.

PIR

T12492.

RefSeq

NP_037457.3. NM_013325.4.
NP_847896.1. NM_178326.2.

UniGene

Hs.283610.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2CY7	X-ray	1.90	A	1-393	[»]
2D1I	X-ray	2.00	A/B	1-393	[»]
2Z0D	X-ray	1.90	A	1-353	[»]
2Z0E	X-ray	1.90	A	1-353	[»]
2ZZP	X-ray	2.05	A	1-353	[»]

ProteinModelPortal

Q9Y4P1.

SMR

Q9Y4P1. Positions 10-373.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9Y4P1. 17 interactions.

MINT

MINT-1414043.

STRING

9606.ENSP00000384259.

Protein family/group databases

MEROPS

C54.003.

PTM databases

PhosphoSite

Q9Y4P1.

Polymorphism databases

DMDM

296434400.

Proteomic databases

PaxDb

Q9Y4P1.

PRIDE

Q9Y4P1.

Protocols and materials databases

DNASU

23192.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000402096; ENSP00000384661; ENSG00000168397.
ENST00000404914; ENSP00000384259; ENSG00000168397.
ENST00000405546; ENSP00000383964; ENSG00000168397.

GeneID

23192.

KEGG

hsa:23192.

UCSC

uc002wbu.3. human.
uc002wbv.3. human.
uc002wbw.3. human.

Organism-specific databases

CTD

23192.

GeneCards

GC02P242578.

H-InvDB

HIX0180188.

HGNC

HGNC:20790. ATG4B.

HPA

CAB037195.

MIM

611338. gene.

neXtProt

NX_Q9Y4P1.

PharmGKB

PA134898340.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG239662.

HOVERGEN

HBG050536.

KO

K08342.

Gene expression databases

ArrayExpress

Q9Y4P1.

Bgee

Q9Y4P1.

CleanEx

HS_ATG4B.

Genevestigator

Q9Y4P1.

GermOnline

ENSG00000168397. Homo sapiens.

Family and domain databases

InterPro

IPR005078. Peptidase_C54.
[Graphical view]

PANTHER

PTHR22624. PTHR22624. 1 hit.

Pfam

PF03416. Peptidase_C54. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

Q9Y4P1.

ChEMBL

CHEMBL1741221.

ChiTaRS

ATG4B. human.

EvolutionaryTrace

Q9Y4P1.

GenomeRNAi

23192.

NextBio

44679.

SOURCE

Search...

Entry information

Entry name

ATG4B_HUMAN

Accession

Primary (citable) accession number: Q9Y4P1
Secondary accession number(s): B7WNK2 , Q53NU4, Q6ZUV8, Q8WYM9, Q96K07, Q96K96, Q96SZ1, Q9Y2F2

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2005
Last sequence update:	May 18, 2010
Last modified:	May 1, 2013
This is version 117 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.