CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-023015
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Rab5 GDP/GTP exchange factor 
Protein Synonyms/Alias
 RAP1; Rabaptin-5-associated exchange factor for Rab5; Rabex-5 
Gene Name
 RABGEF1 
Gene Synonyms/Alias
 RABEX5 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
263AQSLTFSKFEEKKTNubiquitination[1, 2, 3, 4, 5, 6]
268FSKFEEKKTNEKTRKubiquitination[5]
281RKVTTVKKFFSASSRubiquitination[1, 2, 3, 4, 5, 6]
299KKEIQEAKAPSPSINubiquitination[3, 5]
318IETDRVSKEFIEFLKubiquitination[2, 4, 5, 6]
325KEFIEFLKTFHKTGQubiquitination[2, 5, 6]
329EFLKTFHKTGQEIYKacetylation[7]
329EFLKTFHKTGQEIYKubiquitination[2, 5, 6]
336KTGQEIYKQTKLFLEubiquitination[5]
348FLEGMHYKRDLSIEEacetylation[7]
348FLEGMHYKRDLSIEEubiquitination[2, 5, 6]
423VPPERVEKIMDQIEKubiquitination[2, 6]
520KHIFNAIKITKNEPAubiquitination[2, 4, 5, 6]
629LGVKQMYKNLDLLSQubiquitination[2, 5, 6]
650RIMNEAKKLEKDLIDubiquitination[5]
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] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861] 
Functional Description
 Rab effector protein acting as linker between gamma- adaptin, RAB4A or RAB5A. Involved in endocytic membrane fusion and membrane trafficking of recycling endosomes. Stimulates nucleotide exchange on RAB5A. Can act as a ubiquitin ligase (By similarity). 
Sequence Annotation
 DOMAIN 449 592 VPS9.
 ZN_FING 151 185 A20-type.
 REGION 139 252 Interaction with ubiquitinated proteins.  
Keyword
 3D-structure; Alternative splicing; Coiled coil; Complete proteome; Cytoplasm; Endocytosis; Endosome; Metal-binding; Protein transport; Reference proteome; Transport; Ubl conjugation; Ubl conjugation pathway; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 708 AA 
Protein Sequence
MVVVTGREPD SRRQDGAMSS SDAEDDFLEP ATPTATQAGH ALPLLPQERC AEFPALRGPP 60
TQGACSSCVQ RGPVLCHRAP PGAAGEHAAT EGREGAPSVS GTHALLQRPL GADCGDRPAA 120
CGPAEGPLCQ AQVVSRKKMS LKSERRGIHV DQSDLLCKKG CGYYGNPAWQ GFCSKCWREE 180
YHKARQKQIQ EDWELAERVL LCCPGWSAMV QFQLTATSAS WAQVILLLQP PKWLGLQKLQ 240
REEEEAFASS QSSQGAQSLT FSKFEEKKTN EKTRKVTTVK KFFSASSRVG SKKEIQEAKA 300
PSPSINRQTS IETDRVSKEF IEFLKTFHKT GQEIYKQTKL FLEGMHYKRD LSIEEQSECA 360
QDFYHNVAER MQTRGKERRF HHVGQAGLEL LTSGDPPASA SQSAGNTGVE PPHPAVPPER 420
VEKIMDQIEK YIMTRLYKYV FCPETTDDEK KDLAIQKRIR ALRWVTPQML CVPVNEDIPE 480
VSDMVVKAIT DIIEMDSKRV PRDKLACITK CSKHIFNAIK ITKNEPASAD DFLPTLIYIV 540
LKGNPPRLQS NIQYITRFCN PSRLMTGEDG YYFTNLCCAV AFIEKLDAQS LNLSQEDFDR 600
YMSGQTSPRK QEAESWSPDA CLGVKQMYKN LDLLSQLNER QERIMNEAKK LEKDLIDWTD 660
GIAREVQDIV EKYPLEIKPP NQPLAAIDSE NVENDKLPPP LQPQVYAG 708 
Gene Ontology
 GO:0005769; C:early endosome; IEA:UniProtKB-SubCell.
 GO:0055037; C:recycling endosome; IEA:UniProtKB-SubCell.
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0017112; F:Rab guanyl-nucleotide exchange factor activity; IDA:UniProtKB.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0006897; P:endocytosis; IEA:UniProtKB-KW.
 GO:0015031; P:protein transport; IEA:UniProtKB-KW. 
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