CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-005955
UniProt Accession
Genbank Protein ID
 X79353; X79354; X79355; X79356; X79357; X79358; X79359; X79360; X79364; X79361; X79362; X79363; D45021; L44140; AF400433; AB101741; AB101742; AB101743; AB101744; AB101745; AB101746; AB101747; AB101748; AB101749; AB101750; AB101751; AB101752; AB101753; AB101754; AB101755; AB101756; AB101757; AB101758; AB101759; AB101760; AB101771; AB101772; AB101773; AB101774; AB101775; AB101776; AB101777; AB101778; AB101779; AB101780; AB101781; AB101782; AB101783; AB101784; AB101785; AB101786; AB101787; AB101788; AB101789; AB101790; AB101801; AB101802; AB101803; AB101804; AB101805; AB101806; AB101807; AB101808; AB101809; AB101810; AB101811; AB101812; AB101813; AB101814; AB101815; AB101816; AB101817; AB101818; AB101819; AB101820; AB101831; AB101832; AB101833; AB101834; AB101835; AB101836; AB101837; AB101838; AB101839; AB101840; AB101841; AB101842; AB101843; AB101844; AB101845; AB101846; AB101847; AB101848; AB101849; AB101850; AB102647; CR542258; CR542276; BT019884; BX936385; CH471172; BC000317; BC012201; U14623; L05086 
Genbank Nucleotide ID
 CAA55908.1; CAA55909.1; CAA55909.1; CAA55909.1; CAA55909.1; CAA55909.1; CAA55909.1; CAA55909.1; CAA55909.1; CAA55909.1; CAA55909.1; CAA55909.1; BAA08078.1; AAA92648.1; AAK92482.1; BAC80330.1; BAC80331.1; BAC80332.1; BAC80333.1; BAC80334.1; BAC80335.1; BAC80336.1; BAC80337.1; BAC80338.1; BAC80339.1; BAC80340.1; BAC80341.1; BAC80342.1; BAC80343.1; BAC80344.1; BAC80345.1; BAC80346.1; BAC80347.1; BAC80348.1; BAC80349.1; BAC80360.1; BAC80361.1; BAC80362.1; BAC80363.1; BAC80364.1; BAC80365.1; BAC80366.1; BAC80367.1; BAC80368.1; BAC80369.1; BAC80370.1; BAC80371.1; BAC80372.1; BAC80373.1; BAC80374.1; BAC80375.1; BAC80376.1; BAC80377.1; BAC80378.1; BAC80379.1; BAC80390.1; BAC80391.1; BAC80392.1; BAC80393.1; BAC80394.1; BAC80395.1; BAC80396.1; BAC80397.1; BAC80398.1; BAC80399.1; BAC80400.1; BAC80401.1; BAC80402.1; BAC80403.1; BAC80404.1; BAC80405.1; BAC80406.1; BAC80407.1; BAC80408.1; BAC80409.1; BAC80420.1; BAC80421.1; BAC80422.1; BAC80423.1; BAC80424.1; BAC80425.1; BAC80426.1; BAC80427.1; BAC80428.1; BAC80429.1; BAC80430.1; BAC80431.1; BAC80432.1; BAC80433.1; BAC80434.1; BAC80435.1; BAC80436.1; BAC80437.1; BAC80438.1; BAC80439.1; BAC81116.1; CAG47054.1; CAG47072.1; AAV38687.1; CAI95780.1; EAW72710.1; AAH00317.1; AAH12201.1; AAA21558.1; AAC15851.1 
Protein Name
 Rab GDP dissociation inhibitor alpha 
Protein Synonyms/Alias
 Rab GDI alpha; Guanosine diphosphate dissociation inhibitor 1; GDI-1; Oligophrenin-2; Protein XAP-4 
Gene Name
 GDI1 
Gene Synonyms/Alias
 GDIL; OPHN2; RABGDIA; XAP4 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
54TPLEELYKRFQLLEGubiquitination[1, 2, 3, 4]
79WNVDLIPKFLMANGQubiquitination[3]
112VEGSFVYKGGKIYKVubiquitination[2]
115SFVYKGGKIYKVPSTubiquitination[3]
137NLMGMFEKRRFRKFLubiquitination[2]
174SMRDVYRKFDLGQDVubiquitination[3, 4, 5]
210LETVNRIKLYSESLAubiquitination[2, 3, 5]
221ESLARYGKSPYLYPLubiquitination[2, 3, 4, 5]
253GGTYMLNKPVDDIIMubiquitination[2, 3]
269NGKVVGVKSEGEVARacetylation[6]
269NGKVVGVKSEGEVARubiquitination[2, 3, 7]
278EGEVARCKQLICDPSubiquitination[3, 8]
309CILSHPIKNTNDANSubiquitination[3]
435AFDFENMKRKQNDVFubiquitination[2, 3, 4, 5, 9]
437DFENMKRKQNDVFGEubiquitination[2, 3, 7]
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] 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] 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]
 [4] 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]
 [5] 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]
 [6] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [7] 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]
 [8] 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]
 [9] 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] 
Functional Description
 Regulates the GDP/GTP exchange reaction of most Rab proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them. 
Sequence Annotation
 MOD_RES 339 339 Phosphotyrosine (By similarity).  
Keyword
 Complete proteome; Cytoplasm; Direct protein sequencing; Disease mutation; GTPase activation; Mental retardation; Phosphoprotein; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 447 AA 
Protein Sequence
MDEEYDVIVL GTGLTECILS GIMSVNGKKV LHMDRNPYYG GESSSITPLE ELYKRFQLLE 60
GPPESMGRGR DWNVDLIPKF LMANGQLVKM LLYTEVTRYL DFKVVEGSFV YKGGKIYKVP 120
STETEALASN LMGMFEKRRF RKFLVFVANF DENDPKTFEG VDPQTTSMRD VYRKFDLGQD 180
VIDFTGHALA LYRTDDYLDQ PCLETVNRIK LYSESLARYG KSPYLYPLYG LGELPQGFAR 240
LSAIYGGTYM LNKPVDDIIM ENGKVVGVKS EGEVARCKQL ICDPSYIPDR VRKAGQVIRI 300
ICILSHPIKN TNDANSCQII IPQNQVNRKS DIYVCMISYA HNVAAQGKYI AIASTTVETT 360
DPEKEVEPAL ELLEPIDQKF VAISDLYEPI DDGCESQVFC SCSYDATTHF ETTCNDIKDI 420
YKRMAGTAFD FENMKRKQND VFGEAEQ 447 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0030496; C:midbody; IDA:UniProtKB.
 GO:0043005; C:neuron projection; IEA:Compara.
 GO:0043234; C:protein complex; IEA:Compara.
 GO:0005092; F:GDP-dissociation inhibitor activity; TAS:ProtInc.
 GO:0005096; F:GTPase activator activity; IEA:UniProtKB-KW.
 GO:0005093; F:Rab GDP-dissociation inhibitor activity; IEA:Compara.
 GO:0050771; P:negative regulation of axonogenesis; ISS:UniProtKB.
 GO:0043547; P:positive regulation of GTPase activity; IEA:GOC.
 GO:0015031; P:protein transport; IEA:InterPro.
 GO:0051056; P:regulation of small GTPase mediated signal transduction; TAS:Reactome.
 GO:0051592; P:response to calcium ion; IEA:Compara.
 GO:0007264; P:small GTPase mediated signal transduction; TAS:Reactome. 
Interpro
 IPR018203; GDP_dissociation_inhibitor.
 IPR000806; RabGDI. 
Pfam
 PF00996; GDI 
SMART
  
PROSITE
  
PRINTS
 PR00892; RABGDI.
 PR00891; RABGDIREP.