CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-018900
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Probable ubiquitin carboxyl-terminal hydrolase FAF-X 
Protein Synonyms/Alias
 Deubiquitinating enzyme FAF-X; Fat facets in mammals; hFAM; Fat facets protein-related, X-linked; Ubiquitin thioesterase FAF-X; Ubiquitin-specific protease 9, X chromosome; Ubiquitin-specific-processing protease FAF-X 
Gene Name
 USP9X 
Gene Synonyms/Alias
 DFFRX; FAM; USP9 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
218SPDPRSPKGWLVDLLubiquitination[1, 2]
315SMIIKSLKNLASRVPubiquitination[1, 2]
329PGQEETVKNLEIFRLubiquitination[1, 2]
424LRFVIKEKALTLQDLubiquitination[1, 2]
486ASKKQREKLLELIRRubiquitination[1, 2]
571KWVIPALKQIREICSubiquitination[1, 2]
794SRAIDLLKEIYTNLGubiquitination[1, 2]
1045DGARVLMKLMPPDSTubiquitination[1, 2]
1153GAYLNALKIAKLLLTubiquitination[1, 2]
1370STARERAKHSGDYFTubiquitination[1, 2, 3]
1435EGHLGVTKELLAFQTubiquitination[4]
1445LAFQTSEKKFHIGCEubiquitination[5]
1446AFQTSEKKFHIGCEKubiquitination[5]
1453KFHIGCEKGGANLIKubiquitination[5, 6]
1627YPQQFEDKPALSKTEubiquitination[1, 2, 4, 5, 6, 7, 8, 9]
1632EDKPALSKTEDRKEYubiquitination[1, 2, 3, 4, 9]
1637LSKTEDRKEYNIGVLubiquitination[1, 2]
1669YVPRGFWKQFRLWGEubiquitination[1, 2]
1712GHPAMLSKVLGGSFAubiquitination[1, 2]
1722GGSFADQKICQGCPHubiquitination[1, 2]
1798PVLAIQLKRFDYDWEubiquitination[1, 2, 6, 8, 9]
1811WERECAIKFNDYFEFubiquitination[1, 2]
1862SETAGSTKYRLVGVLubiquitination[1, 2, 4]
1899GERNRWYKFDDGDVTubiquitination[6, 8]
1935EVFDHMMKRMSYRRQubiquitination[4]
2301SNSEETVKLLRFCCWubiquitination[1, 2, 6]
2360HRIHNALKGIPDDRDubiquitination[1, 2]
Reference
 [1] 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]
 [2] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [3] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
 [4] 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]
 [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] 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]
 [7] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048]
 [8] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [9] 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] 
Functional Description
 Deubiquitinase 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. Regulates chromosome alignment and segregation in mitosis by regulating the localization of BIRC5/survivin to mitotic centromeres. Specifically hydrolyzes both 'Lys-29'- and 'Lys-33'-linked polyubiquitins chains. Specifically deubiquitinates monoubiquitinated SMAD4, opposing the activity of E3 ubiquitin-protein ligase TRIM33. 
Sequence Annotation
 ACT_SITE 1566 1566 Nucleophile (By similarity).
 ACT_SITE 1879 1879 Proton acceptor (By similarity).
 MOD_RES 1600 1600 Phosphoserine.
 MOD_RES 1815 1815 Phosphotyrosine (By similarity).
 MOD_RES 2443 2443 Phosphoserine.
 MOD_RES 2556 2556 Phosphotyrosine.
 MOD_RES 2563 2563 Phosphoserine.
 MOD_RES 2567 2567 Phosphothreonine.  
Keyword
 Alternative splicing; Cell cycle; Cell division; Chromosome partition; Complete proteome; Cytoplasm; Hydrolase; Mitosis; Phosphoprotein; Protease; Reference proteome; Thiol protease; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 2570 AA 
Protein Sequence
MTATTRGSPV GGNDNQGQAP DGQSQPPLQQ NQTSSPDSSN ENSPATPPDE QGQGDAPPQL 60
EDEEPAFPHT DLAKLDDMIN RPRWVVPVLP KGELEVLLEA AIDLSKKGLD VKSEACQRFF 120
RDGLTISFTK ILTDEAVSGW KFEIHRCIIN NTHRLVELCV AKLSQDWFPL LELLAMALNP 180
HCKFHIYNGT RPCESVSSSV QLPEDELFAR SPDPRSPKGW LVDLLNKFGT LNGFQILHDR 240
FINGSALNVQ IIAALIKPFG QCYEFLTLHT VKKYFLPIIE MVPQFLENLT DEELKKEAKN 300
EAKNDALSMI IKSLKNLASR VPGQEETVKN LEIFRLKMIL RLLQISSFNG KMNALNEVNK 360
VISSVSYYTH RHGNPEEEEW LTAERMAEWI QQNNILSIVL RDSLHQPQYV EKLEKILRFV 420
IKEKALTLQD LDNIWAAQAG KHEAIVKNVH DLLAKLAWDF SPEQLDHLFD CFKASWTNAS 480
KKQREKLLEL IRRLAEDDKD GVMAHKVLNL LWNLAHSDDV PVDIMDLALS AHIKILDYSC 540
SQDRDTQKIQ WIDRFIEELR TNDKWVIPAL KQIREICSLF GEAPQNLSQT QRSPHVFYRH 600
DLINQLQHNH ALVTLVAENL ATYMESMRLY ARDHEDYDPQ TVRLGSRYSH VQEVQERLNF 660
LRFLLKDGQL WLCAPQAKQI WKCLAENAVY LCDREACFKW YSKLMGDEPD LDPDINKDFF 720
ESNVLQLDPS LLTENGMKCF ERFFKAVNCR EGKLVAKRRA YMMDDLELIG LDYLWRVVIQ 780
SNDDIASRAI DLLKEIYTNL GPRLQVNQVV IHEDFIQSCF DRLKASYDTL CVLDGDKDSV 840
NCARQEAVRM VRVLTVLREY INECDSDYHE ERTILPMSRA FRGKHLSFVV RFPNQGRQVD 900
DLEVWSHTND TIGSVRRCIL NRIKANVAHT KIELFVGGEL IDPADDRKLI GQLNLKDKSL 960
ITAKLTQISS NMPSSPDSSS DSSTGSPGNH GNHYSDGPNP EVESCLPGVI MSLHPRYISF 1020
LWQVADLGSS LNMPPLRDGA RVLMKLMPPD STTIEKLRAI CLDHAKLGES SLSPSLDSLF 1080
FGPSASQVLY LTEVVYALLM PAGAPLADDS SDFQFHFLKS GGLPLVLSML TRNNFLPNAD 1140
METRRGAYLN ALKIAKLLLT AIGYGHVRAV AEACQPGVEG VNPMTQINQV THDQAVVLQS 1200
ALQSIPNPSS ECMLRNVSVR LAQQISDEAS RYMPDICVIR AIQKIIWASG CGSLQLVFSP 1260
NEEITKIYEK TNAGNEPDLE DEQVCCEALE VMTLCFALIP TALDALSKEK AWQTFIIDLL 1320
LHCHSKTVRQ VAQEQFFLMC TRCCMGHRPL LFFITLLFTV LGSTARERAK HSGDYFTLLR 1380
HLLNYAYNSN INVPNAEVLL NNEIDWLKRI RDDVKRTGET GIEETILEGH LGVTKELLAF 1440
QTSEKKFHIG CEKGGANLIK ELIDDFIFPA SNVYLQYMRN GELPAEQAIP VCGSPPTINA 1500
GFELLVALAV GCVRNLKQIV DSLTEMYYIG TAITTCEALT EWEYLPPVGP RPPKGFVGLK 1560
NAGATCYMNS VIQQLYMIPS IRNGILAIEG TGSDVDDDMS GDEKQDNESN VDPRDDVFGY 1620
PQQFEDKPAL SKTEDRKEYN IGVLRHLQVI FGHLAASRLQ YYVPRGFWKQ FRLWGEPVNL 1680
REQHDALEFF NSLVDSLDEA LKALGHPAML SKVLGGSFAD QKICQGCPHR YECEESFTTL 1740
NVDIRNHQNL LDSLEQYVKG DLLEGANAYH CEKCNKKVDT VKRLLIKKLP PVLAIQLKRF 1800
DYDWERECAI KFNDYFEFPR ELDMEPYTVA GVAKLEGDNV NPESQLIQQS EQSESETAGS 1860
TKYRLVGVLV HSGQASGGHY YSYIIQRNGG DGERNRWYKF DDGDVTECKM DDDEEMKNQC 1920
FGGEYMGEVF DHMMKRMSYR RQKRWWNAYI LFYERMDTID QDDELIRYIS ELAITTRPHQ 1980
IIMPSAIERS VRKQNVQFMH NRMQYSMEYF QFMKKLLTCN GVYLNPPPGQ DHLLPEAEEI 2040
TMISIQLAAR FLFTTGFHTK KVVRGSASDW YDALCILLRH SKNVRFWFAH NVLFNVSNRF 2100
SEYLLECPSA EVRGAFAKLI VFIAHFSLQD GPCPSPFASP GPSSQAYDNL SLSDHLLRAV 2160
LNLLRREVSE HGRHLQQYFN LFVMYANLGV AEKTQLLKLS VPATFMLVSL DEGPGPPIKY 2220
QYAELGKLYS VVSQLIRCCN VSSRMQSSIN GNPPLPNPFG DPNLSQPIMP IQQNVADILF 2280
VRTSYVKKII EDCSNSEETV KLLRFCCWEN PQFSSTVLSE LLWQVAYSYT YELRPYLDLL 2340
LQILLIEDSW QTHRIHNALK GIPDDRDGLF DTIQRSKNHY QKRAYQCIKC MVALFSNCPV 2400
AYQILQGNGD LKRKWTWAVE WLGDELERRP YTGNPQYTYN NWSPPVQSNE TSNGYFLERS 2460
HSARMTLAKA CELCPEEVKK ATSVQQIEME ESKEPDDQDA PDEHESPPPE DAPLYPHSPG 2520
SQYQQNNHVH GQPYTGPAAH HMNNPQRTGQ RAQENYEGSE EVSPPQTKDQ 2570 
Gene Ontology
 GO:0045177; C:apical part of cell; IEA:Compara.
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0004197; F:cysteine-type endopeptidase activity; TAS:ProtInc.
 GO:0004221; F:ubiquitin thiolesterase activity; TAS:Reactome.
 GO:0030509; P:BMP signaling pathway; IDA:UniProtKB.
 GO:0051301; P:cell division; IEA:UniProtKB-KW.
 GO:0007059; P:chromosome segregation; IEA:UniProtKB-KW.
 GO:0007292; P:female gamete generation; TAS:ProtInc.
 GO:0007067; P:mitosis; IEA:UniProtKB-KW.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; TAS:Reactome.
 GO:0016579; P:protein deubiquitination; IDA:UniProtKB.
 GO:0006367; P:transcription initiation from RNA polymerase II promoter; TAS:Reactome.
 GO:0007179; P:transforming growth factor beta receptor signaling pathway; IMP: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