Human Gene ATG4B (uc002wbv.3) Description and Page Index
  Description: Homo sapiens autophagy related 4B, cysteine peptidase (ATG4B), transcript variant 1, mRNA.
RefSeq Summary (NM_013325): Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr2:242,577,027-242,613,271 Size: 36,245 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr2:242,577,130-242,611,679 Size: 34,550 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:242,577,027-242,613,271)mRNA (may differ from genome)Protein (393 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: ATG4B_HUMAN
DESCRIPTION: 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;
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.
ENZYME REGULATION: Inhibited by N-ethylmaleimide.
INTERACTION: O95166:GABARAP; NbExp=8; IntAct=EBI-712014, EBI-712001; Q9H0R8:GABARAPL1; NbExp=7; IntAct=EBI-712014, EBI-746969; P60520:GABARAPL2; NbExp=5; IntAct=EBI-712014, EBI-720116; Q9GZQ8:MAP1LC3B; NbExp=6; IntAct=EBI-712014, EBI-373144;
SUBCELLULAR LOCATION: Cytoplasm (Probable).
TISSUE SPECIFICITY: Mainly expressed in the skeletal muscle, followed by brain, heart, liver and pancreas.
SIMILARITY: Belongs to the peptidase C54 family.
SEQUENCE CAUTION: Sequence=BAA76787.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAC86110.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 45.71 RPKM in Brain - Cerebellum
Total median expression: 1127.31 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -54.70103-0.531 Picture PostScript Text
3' UTR -710.501592-0.446 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005078 - Peptidase_C54

Pfam Domains:
PF03416 - Peptidase family C54

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2CY7
- X-ray MuPIT

2D1I
- X-ray MuPIT

2Z0D
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2Z0E - X-ray MuPIT 2ZZP - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y4P1
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004175 endopeptidase activity
GO:0004197 cysteine-type endopeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity

Biological Process:
GO:0000045 autophagosome assembly
GO:0000422 mitophagy
GO:0006501 C-terminal protein lipidation
GO:0006508 proteolysis
GO:0006612 protein targeting to membrane
GO:0006914 autophagy
GO:0015031 protein transport
GO:0016236 macroautophagy
GO:0044804 nucleophagy
GO:0045732 positive regulation of protein catabolic process
GO:0051697 protein delipidation

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK125277 - Homo sapiens cDNA FLJ43287 fis, clone MESAN2006563.
AK302963 - Homo sapiens cDNA FLJ56391 complete cds, highly similar to Cysteine protease ATG4B (EC 3.4.22.-).
AL080168 - Homo sapiens mRNA; cDNA DKFZp434C151 (from clone DKFZp434C151).
LF383627 - JP 2014500723-A/191130: Polycomb-Associated Non-Coding RNAs.
JD080026 - Sequence 61050 from Patent EP1572962.
AK296818 - Homo sapiens cDNA FLJ55223 complete cds, highly similar to Cysteine protease ATG4B (EC 3.4.22.-).
AK298109 - Homo sapiens cDNA FLJ55469 complete cds, highly similar to Cysteine protease ATG4B (EC 3.4.22.-).
AK027763 - Homo sapiens cDNA FLJ14857 fis, clone PLACE1001185.
BX648007 - Homo sapiens mRNA; cDNA DKFZp686G0859 (from clone DKFZp686G0859).
AB023160 - Homo sapiens KIAA0943 mRNA for KIAA0943 protein.
AK027462 - Homo sapiens cDNA FLJ14556 fis, clone NT2RM2001867.
BC000719 - Homo sapiens ATG4 autophagy related 4 homolog B (S. cerevisiae), mRNA (cDNA clone MGC:1353 IMAGE:3504267), complete cds.
AJ504652 - Homo sapiens mRNA for autophagin-1 (AUTL1 gene).
AB384548 - Synthetic construct DNA, clone: pF1KA0943, Homo sapiens ATG4B gene for ATG4 autophagy related 4 homolog B, complete cds, without stop codon, in Flexi system.
AM393751 - Synthetic construct Homo sapiens clone IMAGE:100002509 for hypothetical protein (ATG4B gene).
DQ891869 - Synthetic construct clone IMAGE:100004499; FLH180751.01X; RZPDo839F08134D ATG4 autophagy related 4 homolog B (S. cerevisiae) (ATG4B) gene, encodes complete protein.
AB066215 - Homo sapiens mRNA for Apg4B, complete cds.
AK027332 - Homo sapiens cDNA FLJ14426 fis, clone HEMBA1006108.
LF319127 - JP 2014500723-A/126630: Polycomb-Associated Non-Coding RNAs.
AK316167 - Homo sapiens cDNA, FLJ79066 complete cds, highly similar to Cysteine protease ATG4B (EC 3.4.22.-).
AK123425 - Homo sapiens cDNA FLJ41431 fis, clone BRHIP2005932, highly similar to Cysteine protease ATG4B (EC 3.4.22.-).
AL050288 - Homo sapiens mRNA; cDNA DKFZp586D1822 (from clone DKFZp586D1822).
JD282349 - Sequence 263373 from Patent EP1572962.
JD387752 - Sequence 368776 from Patent EP1572962.
JD248360 - Sequence 229384 from Patent EP1572962.
JD369212 - Sequence 350236 from Patent EP1572962.
JD316243 - Sequence 297267 from Patent EP1572962.
JD180720 - Sequence 161744 from Patent EP1572962.
JD162317 - Sequence 143341 from Patent EP1572962.
JD189109 - Sequence 170133 from Patent EP1572962.
JD218345 - Sequence 199369 from Patent EP1572962.
JD478314 - Sequence 459338 from Patent EP1572962.
JD116122 - Sequence 97146 from Patent EP1572962.
JD197019 - Sequence 178043 from Patent EP1572962.
JD277134 - Sequence 258158 from Patent EP1572962.
JD432681 - Sequence 413705 from Patent EP1572962.
AL133638 - Homo sapiens mRNA; cDNA DKFZp586A1821 (from clone DKFZp586A1821).
JD309135 - Sequence 290159 from Patent EP1572962.
JD211676 - Sequence 192700 from Patent EP1572962.
JD338971 - Sequence 319995 from Patent EP1572962.
JD465538 - Sequence 446562 from Patent EP1572962.
JD403745 - Sequence 384769 from Patent EP1572962.
JD116380 - Sequence 97404 from Patent EP1572962.
JD496532 - Sequence 477556 from Patent EP1572962.
JD335801 - Sequence 316825 from Patent EP1572962.
JD420350 - Sequence 401374 from Patent EP1572962.
JD419341 - Sequence 400365 from Patent EP1572962.
JD423791 - Sequence 404815 from Patent EP1572962.
JD537455 - Sequence 518479 from Patent EP1572962.
LF319136 - JP 2014500723-A/126639: Polycomb-Associated Non-Coding RNAs.
JD474121 - Sequence 455145 from Patent EP1572962.
JD110576 - Sequence 91600 from Patent EP1572962.
JD230789 - Sequence 211813 from Patent EP1572962.
LF319137 - JP 2014500723-A/126640: Polycomb-Associated Non-Coding RNAs.
JD300531 - Sequence 281555 from Patent EP1572962.
MA619204 - JP 2018138019-A/191130: Polycomb-Associated Non-Coding RNAs.
MA554704 - JP 2018138019-A/126630: Polycomb-Associated Non-Coding RNAs.
MA554713 - JP 2018138019-A/126639: Polycomb-Associated Non-Coding RNAs.
MA554714 - JP 2018138019-A/126640: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04140 - Regulation of autophagy

Reactome (by CSHL, EBI, and GO)

Protein Q9Y4P1 (Reactome details) participates in the following event(s):

R-HSA-5681987 LC3 is cleaved by ATG4
R-HSA-5682377 LC3 de-lipidation by ATG4
R-HSA-1632852 Macroautophagy
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: APG4B, ATG4B_HUMAN, AUTL1, B7WNK2, KIAA0943, NM_013325, NP_037457, Q53NU4, Q6ZUV8, Q8WYM9, Q96K07, Q96K96, Q96SZ1, Q9Y2F2, Q9Y4P1, uc002wby.3
UCSC ID: uc002wbv.3
RefSeq Accession: NM_013325
Protein: Q9Y4P1 (aka ATG4B_HUMAN)
CCDS: CCDS46564.1, CCDS46565.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_013325.4
exon count: 13CDS single in 3' UTR: no RNA size: 2892
ORF size: 1182CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2418.00frame shift in genome: no % Coverage: 99.48
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.