CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-016180
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Cysteine protease ATG4D 
Protein Synonyms/Alias
 AUT-like 4 cysteine endopeptidase; Autophagin-4; Autophagy-related cysteine endopeptidase 4; Autophagy-related protein 4 homolog D 
Gene Name
 ATG4D 
Gene Synonyms/Alias
 APG4D; AUTL4 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
64SEPDEVDKFKAKFLTubiquitination[1]
66PDEVDKFKAKFLTAWubiquitination[1]
68EVDKFKAKFLTAWNNubiquitination[1]
241ELGQSSGKKAGDWYGubiquitination[1, 2]
258LVAHILRKAVESCSDubiquitination[1]
298PDPTAEWKSVVILVPubiquitination[1]
322PVYVPCVKELLRCELubiquitination[1]
388PRKMAFAKMDPSCTVubiquitination[1]
464TGRLLRAKRPSSEDFubiquitination[1]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983] 
Functional Description
 Cysteine protease required for autophagy, which cleaves the C-terminal part of either MAP1LC3, GABARAPL2 or 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. 
Sequence Annotation
 ACT_SITE 144 144 Nucleophile (By similarity).
 ACT_SITE 356 356 Potential.
 ACT_SITE 358 358 By similarity.  
Keyword
 Autophagy; Complete proteome; Cytoplasm; Hydrolase; Protease; Protein transport; Reference proteome; Thiol protease; Transport; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 474 AA 
Protein Sequence
MNSVSPAAAQ YRSSSPEDAR RRPEARRPRG PRGPDPNGLG PSGASGPALG SPGAGPSEPD 60
EVDKFKAKFL TAWNNVKYGW VVKSRTSFSK ISSIHLCGRR YRFEGEGDIQ RFQRDFVSRL 120
WLTYRRDFPP LPGGCLTSDC GWGCMLRSGQ MMLAQGLLLH FLPRDWTWAE GMGLGPPELS 180
GSASPSRYHG PARWMPPRWA QGAPELEQER RHRQIVSWFA DHPRAPFGLH RLVELGQSSG 240
KKAGDWYGPS LVAHILRKAV ESCSDVTRLV VYVSQDCTVY KADVARLVAR PDPTAEWKSV 300
VILVPVRLGG ETLNPVYVPC VKELLRCELC LGIMGGKPRH SLYFIGYQDD FLLYLDPHYC 360
QPTVDVSQAD FPLESFHCTS PRKMAFAKMD PSCTVGFYAG DRKEFETLCS ELTRVLSSSS 420
ATERYPMFTL AEGHAQDHSL DDLCSQLAQP TLRLPRTGRL LRAKRPSSED FVFL 474 
Gene Ontology
 GO:0005737; C:cytoplasm; ISS:UniProtKB.
 GO:0004197; F:cysteine-type endopeptidase activity; ISS:UniProtKB.
 GO:0006914; P:autophagy; IEA:UniProtKB-KW.
 GO:0015031; P:protein transport; IEA:UniProtKB-KW.
 GO:0006508; P:proteolysis; IEA:UniProtKB-KW. 
Interpro
 IPR005078; Peptidase_C54. 
Pfam
 PF03416; Peptidase_C54 
SMART
  
PROSITE
  
PRINTS