CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-000278
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Apoptotic protease-activating factor 1 
Protein Synonyms/Alias
 APAF-1 
Gene Name
 APAF1 
Gene Synonyms/Alias
 KIAA0413 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
198DKSGLLMKLQNLCTRubiquitination[1]
224PLNIEEAKDRLRILMubiquitination[1, 2]
267ILLTTRDKSVTDSVMubiquitination[1]
277TDSVMGPKYVVPVESubiquitination[1]
288PVESSLGKEKGLEILubiquitination[2]
290ESSLGKEKGLEILSLubiquitination[1]
380EMLREDIKDYYTDLSubiquitination[1]
643DKTLQVFKAETGEKLubiquitination[1]
733KLWDLNQKECRNTMFubiquitination[1]
756CRFSPDDKLLASCSAubiquitination[1]
768CSADGTLKLWDATSAubiquitination[1]
820IMVAAKNKIFLFDIHubiquitination[3]
916WETKKVCKNSAVMLKubiquitination[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]
 [3] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473] 
Functional Description
 Oligomeric Apaf-1 mediates the cytochrome c-dependent autocatalytic activation of pro-caspase-9 (Apaf-3), leading to the activation of caspase-3 and apoptosis. This activation requires ATP. Isoform 6 is less effective in inducing apoptosis. 
Sequence Annotation
 DOMAIN 1 90 CARD.
 DOMAIN 104 415 NB-ARC.
 REPEAT 613 652 WD 1-1.
 REPEAT 655 694 WD 1-2.
 REPEAT 697 738 WD 1-3.
 REPEAT 741 780 WD 1-4.
 REPEAT 796 836 WD 1-5.
 REPEAT 838 877 WD 1-6.
 REPEAT 880 910 WD 1-7.
 REPEAT 922 958 WD 2-1.
 REPEAT 959 998 WD 2-2.
 REPEAT 1001 1040 WD 2-3.
 REPEAT 1042 1080 WD 2-4.
 REPEAT 1083 1122 WD 2-5.
 REPEAT 1125 1164 WD 2-6.
 REPEAT 1175 1212 WD 2-7.
 REPEAT 1213 1248 WD 2-8.
 NP_BIND 154 161 ATP (Potential).
 REGION 910 921 Interpropeller linker (By similarity).
 BINDING 265 265 ATP (By similarity).  
Keyword
 3D-structure; Alternative splicing; Apoptosis; ATP-binding; Calcium; Complete proteome; Cytoplasm; Direct protein sequencing; Nucleotide-binding; Reference proteome; Repeat; WD repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1248 AA 
Protein Sequence
MDAKARNCLL QHREALEKDI KTSYIMDHMI SDGFLTISEE EKVRNEPTQQ QRAAMLIKMI 60
LKKDNDSYVS FYNALLHEGY KDLAALLHDG IPVVSSSSGK DSVSGITSYV RTVLCEGGVP 120
QRPVVFVTRK KLVNAIQQKL SKLKGEPGWV TIHGMAGCGK SVLAAEAVRD HSLLEGCFPG 180
GVHWVSVGKQ DKSGLLMKLQ NLCTRLDQDE SFSQRLPLNI EEAKDRLRIL MLRKHPRSLL 240
ILDDVWDSWV LKAFDSQCQI LLTTRDKSVT DSVMGPKYVV PVESSLGKEK GLEILSLFVN 300
MKKADLPEQA HSIIKECKGS PLVVSLIGAL LRDFPNRWEY YLKQLQNKQF KRIRKSSSYD 360
YEALDEAMSI SVEMLREDIK DYYTDLSILQ KDVKVPTKVL CILWDMETEE VEDILQEFVN 420
KSLLFCDRNG KSFRYYLHDL QVDFLTEKNC SQLQDLHKKI ITQFQRYHQP HTLSPDQEDC 480
MYWYNFLAYH MASAKMHKEL CALMFSLDWI KAKTELVGPA HLIHEFVEYR HILDEKDCAV 540
SENFQEFLSL NGHLLGRQPF PNIVQLGLCE PETSEVYQQA KLQAKQEVDN GMLYLEWINK 600
KNITNLSRLV VRPHTDAVYH ACFSEDGQRI ASCGADKTLQ VFKAETGEKL LEIKAHEDEV 660
LCCAFSTDDR FIATCSVDKK VKIWNSMTGE LVHTYDEHSE QVNCCHFTNS SHHLLLATGS 720
SDCFLKLWDL NQKECRNTMF GHTNSVNHCR FSPDDKLLAS CSADGTLKLW DATSANERKS 780
INVKQFFLNL EDPQEDMEVI VKCCSWSADG ARIMVAAKNK IFLFDIHTSG LLGEIHTGHH 840
STIQYCDFSP QNHLAVVALS QYCVELWNTD SRSKVADCRG HLSWVHGVMF SPDGSSFLTS 900
SDDQTIRLWE TKKVCKNSAV MLKQEVDVVF QENEVMVLAV DHIRRLQLIN GRTGQIDYLT 960
EAQVSCCCLS PHLQYIAFGD ENGAIEILEL VNNRIFQSRF QHKKTVWHIQ FTADEKTLIS 1020
SSDDAEIQVW NWQLDKCIFL RGHQETVKDF RLLKNSRLLS WSFDGTVKVW NIITGNKEKD 1080
FVCHQGTVLS CDISHDATKF SSTSADKTAK IWSFDLLLPL HELRGHNGCV RCSAFSVDST 1140
LLATGDDNGE IRIWNVSNGE LLHLCAPLSE EGAATHGGWV TDLCFSPDGK MLISAGGYIK 1200
WWNVVTGESS QTFYTNGTNL KKIHVSPDFK TYVTVDNLGI LYILQTLE 1248 
Gene Ontology
 GO:0043293; C:apoptosome; IDA:UniProtKB.
 GO:0005794; C:Golgi apparatus; IDA:HPA.
 GO:0005634; C:nucleus; IDA:HPA.
 GO:0043531; F:ADP binding; IEA:InterPro.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0008656; F:cysteine-type endopeptidase activator activity involved in apoptotic process; NAS:UniProtKB.
 GO:0000166; F:nucleotide binding; TAS:UniProtKB.
 GO:0008635; P:activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c; IDA:UniProtKB.
 GO:0006309; P:apoptotic DNA fragmentation; IEA:Compara.
 GO:0006952; P:defense response; IEA:InterPro.
 GO:0030900; P:forebrain development; IEA:Compara.
 GO:0097193; P:intrinsic apoptotic signaling pathway; TAS:UniProtKB.
 GO:0007399; P:nervous system development; TAS:ProtInc.
 GO:0001843; P:neural tube closure; IEA:Compara.
 GO:0051402; P:neuron apoptotic process; IEA:Compara. 
Interpro
 IPR017251; Apoptotic_pept-activating_1.
 IPR001315; CARD.
 IPR011029; DEATH-like_dom.
 IPR000767; Disease_R.
 IPR020472; G-protein_beta_WD-40_rep.
 IPR002182; NB-ARC.
 IPR027417; P-loop_NTPase.
 IPR015943; WD40/YVTN_repeat-like_dom.
 IPR001680; WD40_repeat.
 IPR019775; WD40_repeat_CS.
 IPR017986; WD40_repeat_dom. 
Pfam
 PF00619; CARD
 PF00931; NB-ARC
 PF00400; WD40 
SMART
 SM00320; WD40 
PROSITE
 PS50209; CARD
 PS00678; WD_REPEATS_1
 PS50082; WD_REPEATS_2
 PS50294; WD_REPEATS_REGION 
PRINTS
 PR00364; DISEASERSIST.
 PR00320; GPROTEINBRPT.