CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-000097
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 
Protein Synonyms/Alias
 Deubiquitinating enzyme FAF-Y; Fat facets protein-related, Y-linked; Ubiquitin thioesterase FAF-Y; Ubiquitin-specific protease 9, Y chromosome; Ubiquitin-specific-processing protease FAF-Y 
Gene Name
 USP9Y 
Gene Synonyms/Alias
 DFFRY 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
219SSDPRSPKGWLVDLIubiquitination[1]
667NFLRFLLKDGQLWLCubiquitination[2]
679WLCAPQAKQIWKCLAubiquitination[2]
746KCFERFFKAVNCRERubiquitination[2]
825QSCFDRLKASYDTLCubiquitination[2]
838LCVFDGDKNSINCARubiquitination[2]
871ECDSDYHKERMILPMubiquitination[2]
885MSRAFRGKHLSLIVRubiquitination[2]
957LIGQLNLKDKSLITAubiquitination[2]
959GQLNLKDKSLITAKLubiquitination[2]
965DKSLITAKLTQINFNubiquitination[2]
1046DGARVLMKLMPPDRTubiquitination[2]
1057PDRTAVEKLRAVCLDubiquitination[2]
1067AVCLDHAKLGEGKLSubiquitination[2, 3]
1154GAYLNALKIAKLLLTubiquitination[4]
1372STAREKGKYSGDYFTubiquitination[2]
1417KRIRDNVKNTGETGVubiquitination[2]
1448AFQTSEKKYHFGCEKubiquitination[2]
1634EDKPALSKTEDRKEYubiquitination[5]
1639LSKTEDRKEYNIGVLubiquitination[4]
1671YVPRGFWKQFRLWGEubiquitination[4]
1724GGSFADQKICQGCPHacetylation[3, 6]
1724GGSFADQKICQGCPHubiquitination[4]
1800RVLAIQLKRFDYDWEubiquitination[2]
1813WERECAIKFNDYFEFubiquitination[3, 4]
1901DQTDHWYKFDDGDVTubiquitination[2]
1937EVFDHMMKRMSYRRQubiquitination[1]
2361HRIHNALKGIPDDRDubiquitination[2]
Reference
 [1] 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]
 [2] 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]
 [3] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [4] 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]
 [5] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [6] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377] 
Functional Description
 May function as a ubiquitin-protein or polyubiquitin hydrolase involved both in the processing of ubiquitin precursors and of ubiquitinated proteins. May therefore play an important role regulatory role at the level of protein turnover by preventing degradation of proteins through the removal of conjugated ubiquitin. Essential component of TGF-beta/BMP signaling cascade. Deubiquitinates monoubiquitinated SMAD4, opposing the activity of E3 ubiquitin-protein ligase TRIM33. Monoubiquitination of SMAD4 hampers its ability to form a stable complex with activated SMAD2/3 resulting in inhibition of TGF- beta/BMP signaling cascade. Deubiqitination of SMAD4 by USP9X re- empowers its competence to mediate TGF-beta signaling (By similarity). 
Sequence Annotation
 ACT_SITE 1568 1568 Nucleophile (By similarity).
 ACT_SITE 1881 1881 Proton acceptor (By similarity).  
Keyword
 Alternative splicing; Complete proteome; Cytoplasm; Hydrolase; Polymorphism; Protease; Reference proteome; Thiol protease; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 2555 AA 
Protein Sequence
MTAITHGSPV GGNDSQGQVL DGQSQHLFQQ NQTSSPDSSN ENSVATPPPE EQGQGDAPPQ 60
HEDEEPAFPH TELANLDDMI NRPRWVVPVL PKGELEVLLE AAIDLSVKGL DVKSEACQRF 120
FRDGLTISFT KILMDEAVSG WKFEIHRCII NNTHRLVELC VAKLSQDWFP LLELLAMALN 180
PHCKFHIYNG TRPCELISSN AQLPEDELFA RSSDPRSPKG WLVDLINKFG TLNGFQILHD 240
RFFNGSALNI QIIAALIKPF GQCYEFLSQH TLKKYFIPVI EIVPHLLENL TDEELKKEAK 300
NEAKNDALSM IIKSLKNLAS RISGQDETIK NLEIFRLKMI LRLLQISSFN GKMNALNEIN 360
KVISSVSYYT HRHSNPEEEE WLTAERMAEW IQQNNILSIV LQDSLHQPQY VEKLEKILRF 420
VIKEKALTLQ DLDNIWAAQA GKHEAIVKNV HDLLAKLAWD FSPGQLDHLF DCFKASWTNA 480
SKKQREKLLE LIRRLAEDDK DGVMAHKVLN LLWNLAQSDD VPVDIMDLAL SAHIKILDYS 540
CSQDRDAQKI QWIDHFIEEL RTNDKWVIPA LKQIREICSL FGEASQNLSQ TQRSPHIFYR 600
HDLINQLQQN HALVTLVAEN LATYMNSIRL YAGDHEDYDP QTVRLGSRYS HVQEVQERLN 660
FLRFLLKDGQ LWLCAPQAKQ IWKCLAENAV YLCDREACFK WYSKLMGDEP DLDPDINKDF 720
FESNVLQLDP SLLTENGMKC FERFFKAVNC RERKLIAKRR SYMMDDLELI GLDYLWRVVI 780
QSSDEIANRA IDLLKEIYTN LGPRLKANQV VIHEDFIQSC FDRLKASYDT LCVFDGDKNS 840
INCARQEAIR MVRVLTVIKE YINECDSDYH KERMILPMSR AFRGKHLSLI VRFPNQGRQV 900
DELDIWSHTN DTIGSVRRCI VNRIKANVAH KKIELFVGGE LIDSEDDRKL IGQLNLKDKS 960
LITAKLTQIN FNMPSSPDSS SDSSTASPGN HRNHYNDGPN LEVESCLPGV IMSVHPRYIS 1020
FLWQVADLGS NLNMPPLRDG ARVLMKLMPP DRTAVEKLRA VCLDHAKLGE GKLSPPLDSL 1080
FFGPSASQVL YLTEVVYALL MPAGVPLTDG SSDFQVHFLK SGGLPLVLSM LIRNNFLPNT 1140
DMETRRGAYL NALKIAKLLL TAIGYGHVRA VAEACQPVVD GTDPITQINQ VTHDQAVVLQ 1200
SALQSIPNPS SECVLRNESI LLAQEISNEA SRYMPDICVI RAIQKIIWAS ACGALGLVFS 1260
PNEEITKIYQ MTTNGSNKLE VEDEQVCCEA LEVMTLCFAL LPTALDALSK EKAWQTFIID 1320
LLLHCPSKTV RQLAQEQFFL MCTRCCMGHR PLLFFITLLF TILGSTAREK GKYSGDYFTL 1380
LRHLLNYAYN GNINIPNAEV LLVSEIDWLK RIRDNVKNTG ETGVEEPILE GHLGVTKELL 1440
AFQTSEKKYH FGCEKGGANL IKELIDDFIF PASKVYLQYL RSGELPAEQA IPVCSSPVTI 1500
NAGFELLVAL AIGCVRNLKQ IVDCLTEMYY MGTAITTCEA LTEWEYLPPV GPRPPKGFVG 1560
LKNAGATCYM NSVIQQLYMI PSIRNSILAI EGTGSDLHDD MFGDEKQDSE SNVDPRDDVF 1620
GYPHQFEDKP ALSKTEDRKE YNIGVLRHLQ VIFGHLAASQ LQYYVPRGFW KQFRLWGEPV 1680
NLREQHDALE FFNSLVDSLD EALKALGHPA ILSKVLGGSF ADQKICQGCP HRYECEESFT 1740
TLNVDIRNHQ NLLDSLEQYI KGDLLEGANA YHCEKCDKKV DTVKRLLIKK LPRVLAIQLK 1800
RFDYDWEREC AIKFNDYFEF PRELDMGPYT VAGVANLERD NVNSENELIE QKEQSDNETA 1860
GGTKYRLVGV LVHSGQASGG HYYSYIIQRN GKDDQTDHWY KFDDGDVTEC KMDDDEEMKN 1920
QCFGGEYMGE VFDHMMKRMS YRRQKRWWNA YILFYEQMDM IDEDDEMIRY ISELTIARPH 1980
QIIMSPAIER SVRKQNVKFM HNRLQYSLEY FQFVKKLLTC NGVYLNPAPG QDYLLPEAEE 2040
ITMISIQLAA RFLFTTGFHT KKIVRGPASD WYDALCVLLR HSKNVRFWFT HNVLFNVSNR 2100
FSEYLLECPS AEVRGAFAKL IVFIAHFSLQ DGSCPSPFAS PGPSSQACDN LSLSDHLLRA 2160
TLNLLRREVS EHGHHLQQYF NLFVMYANLG VAEKTQLLKL NVPATFMLVS LDEGPGPPIK 2220
YQYAELGKLY SVVSQLIRCC NVSSTMQSSI NGNPPLPNPF GDLNLSQPIM PIQQNVLDIL 2280
FVRTSYVKKI IEDCSNSEDT IKLLRFCSWE NPQFSSTVLS ELLWQVAYSY TYELRPYLDL 2340
LFQILLIEDS WQTHRIHNAL KGIPDDRDGL FDTIQRSKNH YQKRAYQCIK CMVALFSSCP 2400
VAYQILQGNG DLKRKWTWAV EWLGDELERR PYTGNPQYSY NNWSPPVQSN ETANGYFLER 2460
SHSARMTLAK ACELCPEEEP DDQDAPDEHE PSPSEDAPLY PHSPASQYQQ NNHVHGQPYT 2520
GPAAHHLNNP QKTGQRTQEN YEGNEEVSSP QMKDQ 2555 
Gene Ontology
 GO:0005737; C:cytoplasm; ISS:UniProtKB.
 GO:0070410; F:co-SMAD binding; ISS:BHF-UCL.
 GO:0004221; F:ubiquitin thiolesterase activity; IEA:InterPro.
 GO:0004843; F:ubiquitin-specific protease activity; TAS:ProtInc.
 GO:0030509; P:BMP signaling pathway; ISS:UniProtKB.
 GO:0016579; P:protein deubiquitination; ISS:UniProtKB.
 GO:0007283; P:spermatogenesis; TAS:ProtInc.
 GO:0007179; P:transforming growth factor beta receptor signaling pathway; ISS:UniProtKB.
 GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro. 
Interpro
 IPR018200; Pept_C19ubi-hydrolase_C_CS.
 IPR001394; Peptidase_C19. 
Pfam
 PF00443; UCH 
SMART
  
PROSITE
 PS00972; UCH_2_1
 PS00973; UCH_2_2
 PS50235; UCH_2_3 
PRINTS