CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-031440
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Rab5 GDP/GTP exchange factor 
Protein Synonyms/Alias
 cDNA FLJ55772, highly similar to Rab5 GDP/GTP exchange factor 
Gene Name
 RABGEF1 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
99AQSLTFSKFEEKKTNubiquitination[1, 2, 3, 4, 5, 6, 7, 8, 9]
103TFSKFEEKKTNEKTRubiquitination[3, 8]
104FSKFEEKKTNEKTRKubiquitination[7]
116TRKVTTVKKFFSASSubiquitination[3]
117RKVTTVKKFFSASSRubiquitination[1, 2, 4, 6, 7, 8, 9]
135KKEIQEAKAPSPSINubiquitination[3, 4, 6, 7, 8, 9]
154IETDRVSKEFIEFLKubiquitination[2, 3, 7, 9]
161KEFIEFLKTFHKTGQubiquitination[2, 7]
165EFLKTFHKTGQEIYKubiquitination[2, 7, 8, 9]
172KTGQEIYKQTKLFLEubiquitination[7, 8]
175QEIYKQTKLFLEGMHubiquitination[3]
184FLEGMHYKRDLSIEEubiquitination[2, 3, 7]
220VPPERVEKIMDQIEKubiquitination[2]
254KKDLAIQKRIRALRWubiquitination[3]
317KHIFNAIKITKNEPAubiquitination[2, 3, 4, 7, 9]
422PDACLGVKQMYKNLDubiquitination[4]
426LGVKQMYKNLDLLSQubiquitination[2, 3, 7]
447RIMNEAKKLEKDLIDubiquitination[7]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [5] 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]
 [6] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [7] 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]
 [8] 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]
 [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
  
Sequence Annotation
  
Keyword
 Complete proteome; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 505 AA 
Protein Sequence
MMASSYHEVV SRKKMSLKSE RRGIHVDQSD LLCKKGCGYY GNPAWQGFCS KCWREEYHKA 60
RQKQIQEDWE LAERLQREEE EAFASSQSSQ GAQSLTFSKF EEKKTNEKTR KVTTVKKFFS 120
ASSRVGSKKE IQEAKAPSPS INRQTSIETD RVSKEFIEFL KTFHKTGQEI YKQTKLFLEG 180
MHYKRDLSIE EQSECAQDFY HNVAERMQTR GKVPPERVEK IMDQIEKYIM TRLYKYVFCP 240
ETTDDEKKDL AIQKRIRALR WVTPQMLCVP VNEDIPEVSD MVVKAITDII EMDSKRVPRD 300
KLACITKCSK HIFNAIKITK NEPASADDFL PTLIYIVLKG NPPRLQSNIQ YITRFCNPSR 360
LMTGEDGYYF TNLCCAVAFI EKLDAQSLNL SQEDFDRYMS GQTSPRKQEA ESWSPDACLG 420
VKQMYKNLDL LSQLNERQER IMNEAKKLEK DLIDWTDGIA REVQDIVEKY PLEIKPPNQP 480
LAAIDSENVE NDKLPPPLQP QVYAG 505 
Gene Ontology
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0008270; F:zinc ion binding; IEA:InterPro. 
Interpro
 IPR003123; VPS9.
 IPR013995; VPS9_subgr.
 IPR002653; Znf_A20. 
Pfam
 PF02204; VPS9
 PF01754; zf-A20 
SMART
 SM00167; VPS9
 SM00259; ZnF_A20 
PROSITE
 PS51205; VPS9
 PS51036; ZF_A20 
PRINTS