CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-024397
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DENN domain-containing protein 3 
Protein Synonyms/Alias
  
Gene Name
 DENND3 
Gene Synonyms/Alias
 KIAA0870 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
10SLRKKREKPRPEQWKubiquitination[1]
341LLSSTDLKEGRAHRRubiquitination[1]
374VSIFRDVKNHLNYEHubiquitination[1]
391FNSEEFLKTRAPGDHubiquitination[1, 2, 3, 4]
415YMFHSFLKARLNRRMubiquitination[1]
511AVLNVTPKSPYTFKIubiquitination[1, 4, 5]
517PKSPYTFKIPEIHFPubiquitination[1, 5]
597IFPTDLVKRTVESMSubiquitination[1, 4, 5]
627LISEILDKPHEASKLubiquitination[1, 3]
633DKPHEASKLDDHVKKubiquitination[3]
646KKFKLPKKHMQLGDFubiquitination[1]
655MQLGDFMKRVQESGIubiquitination[1]
664VQESGIVKDASIIHRacetylation[6]
664VQESGIVKDASIIHRubiquitination[1]
730CKLSSSVKTNLGVGKubiquitination[1, 5]
737KTNLGVGKIAMTQKRubiquitination[1]
816KEMWAGKKLADDHKDubiquitination[1]
861SKLSYFDKMSNEMPMubiquitination[1]
Reference
 [1] 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]
 [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] 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]
 [4] 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]
 [5] 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]
 [6] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786
Functional Description
 Guanine nucleotide exchange factor (GEF) activating RAB12. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB12 into its active GTP-bound form. Thereby, may play a role in protein transport from recycling endosomes to lysosomes regulating, for instance, the degradation of the transferrin receptor. 
Sequence Annotation
 DOMAIN 6 83 UDENN.
 DOMAIN 105 291 DENN.
 DOMAIN 354 417 dDENN.
 REPEAT 984 1026 WD 1.
 REPEAT 1073 1113 WD 2.
 REPEAT 1165 1198 WD 3.  
Keyword
 Alternative splicing; Complete proteome; Guanine-nucleotide releasing factor; Polymorphism; Reference proteome; Repeat; WD repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1198 AA 
Protein Sequence
MRSLRKKREK PRPEQWKGLP GPPRAPEPED VAVPGGVDLL TLPQLCFPGG VCVATEPKED 60
CVHFLVLTDV CGNRTYGVVA QYYRPLHDEY CFYNGKTHRE CPGCFVPFAV CVVSRFPYYN 120
SLKDCLSCLL ALLKPCKDFE VDSHIKDFAA KLSLIPSPPP GPLHLVFNMK SLQIVLPARA 180
DPESPILDLD LHLPLLCFRP EKVLQILTCI LTEQRIVFFS SDWALLTLVT ECFMAYLYPL 240
QWQHPFVPIL SDQMLDFVMA PTSFLMGCHL DHFEEVSKEA DGLVLINIDH GSITYSKSTD 300
DNVDIPDVPL LAAQTFIQRV QSLQLHHELH AAHLLSSTDL KEGRAHRRSW QQKLNCQIQQ 360
TTLQLLVSIF RDVKNHLNYE HRVFNSEEFL KTRAPGDHQF YKQVLDTYMF HSFLKARLNR 420
RMDAFAQMDL DTQSEEDRIN GMLLSPRRPT VEKRASRKSS HLHVTHRRMV VSMPNLQDIA 480
MPELAPRNSS LRLTDTAGCR GSSAVLNVTP KSPYTFKIPE IHFPLESKCV QAYHAHFVSM 540
LSEAMCFLAP DNSLLLARYL YLRGLVYLMQ GQLLNALLDF QNLYKTDIRI FPTDLVKRTV 600
ESMSAPEWEG AEQAPELMRL ISEILDKPHE ASKLDDHVKK FKLPKKHMQL GDFMKRVQES 660
GIVKDASIIH RLFEALTVGQ EKQIDPETFK DFYNCWKETE AEAQEVSLPW LVMEHLDKNE 720
CVCKLSSSVK TNLGVGKIAM TQKRLFLLTE GRPGYLEIST FRNIEEVRRT TTTFLLRRIP 780
TLKIRVASKK EVFEANLKTE CDLWHLMVKE MWAGKKLADD HKDPHYVQQA LTNVLLMDAV 840
VGTLQSPGAI YAASKLSYFD KMSNEMPMTL PETTLETLKH KINPSAGEAF PQAVDVLLYT 900
PGHLDPAEKV EDAHPKLWCA LSEGKVTVFN ASSWTIHQHS FKVGTAKVNC MVMADQNQVW 960
VGSEDSVIYI INVHSMSCNK QLTAHCSSVT DLIVQDGQEA PSNVYSCSMD GMVLVWNVST 1020
LQVTSRFQLP RGGLTSIRLH GGRLWCCTGN SIMVMKMNGS LHQELKIEEN FKDTSTSFLA 1080
FQLLPEEEQL WAACAGRSEV YIWSLKDLAQ PPQRVPLEDC SEINCMIRVK KQVWVGSRGL 1140
GQGTPKGKIY VIDAERKTVE KELVAHMDTV RTLCSAEDRY VLSGSGREEG KVAIWKGE 1198 
Gene Ontology
 GO:0017112; F:Rab guanyl-nucleotide exchange factor activity; IDA:UniProtKB.
 GO:0044257; P:cellular protein catabolic process; ISS:UniProtKB.
 GO:0008333; P:endosome to lysosome transport; ISS:UniProtKB. 
Interpro
 IPR005112; dDENN_dom.
 IPR001194; DENN_dom.
 IPR005113; uDENN_dom.
 IPR015943; WD40/YVTN_repeat-like_dom.
 IPR001680; WD40_repeat.
 IPR019775; WD40_repeat_CS.
 IPR017986; WD40_repeat_dom. 
Pfam
 PF03455; dDENN
 PF02141; DENN
 PF03456; uDENN
 PF00400; WD40 
SMART
 SM00801; dDENN
 SM00799; DENN
 SM00320; WD40 
PROSITE
 PS50947; DDENN
 PS50211; DENN
 PS50946; UDENN
 PS00678; WD_REPEATS_1
 PS50082; WD_REPEATS_2
 PS50294; WD_REPEATS_REGION 
PRINTS