title: A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system.
abstract: Covalent attachment of ubiquitin to substrates is crucial to protein degradation, transcription regulation and cell signalling. Highly specific interactions between ubiquitin-conjugating enzymes (E2) and ubiquitin protein E3 ligases fulfil essential roles in this process. We performed a global yeast-two hybrid screen to study the specificity of interactions between catalytic domains of the 35 human E2s with 250 RING-type E3s. Our analysis showed over 300 high-quality interactions, uncovering a large fraction of new E2-E3 pairs. Both within the E2 and the E3 cohorts, several members were identified that are more versatile in their interaction behaviour than others. We also found that the physical interactions of our screen compare well with reported functional E2-E3 pairs in in vitro ubiquitination experiments. For validation we confirmed the interaction of several versatile E2s with E3s in in vitro protein interaction assays and we used mutagenesis to alter the E3 interactions of the E2 specific for K63 linkages, UBE2N(Ubc13), towards the K48-specific UBE2D2(UbcH5B). Our data provide a detailed, genome-wide overview of binary E2-E3 interactions of the human ubiquitination system.
authors.affiliation: Division of Biomedical Genetics, Department of Physiological Chemistry, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Sjoerd J L
authors.initials: SJ
authors.lastname: van Wijk
authors.forename: Sjoerd J
authors.initials: SJ
authors.lastname: de Vries
authors.forename: Patrick
authors.initials: P
authors.lastname: Kemmeren
authors.forename: Anding
authors.initials: A
authors.lastname: Huang
authors.forename: Rolf
authors.initials: R
authors.lastname: Boelens
authors.forename: Alexandre M J J
authors.initials: AM
authors.lastname: Bonvin
authors.forename: H Th Marc
authors.initials: HT
authors.lastname: Timmers
mesh_terms: D020134:Catalytic Domain; D045744:Cell Line, Tumor; D004926:Escherichia coli / Q000378:metabolism; D016678:Genome; D016681:Genome, Fungal; D005982:Glutathione Transferase / Q000378:metabolism; D006801:Humans; D016296:Mutagenesis; D009154:Mutation; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry*; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry; D020798:Two-Hybrid System Techniques; D025801:Ubiquitin / Q000737:chemistry*; D044763:Ubiquitin-Conjugating Enzymes / Q000737:chemistry*
chemical_list: D011506:Proteins; D025801:Ubiquitin; D044763:Ubiquitin-Conjugating Enzymes; D005982:Glutathione Transferase; D046988:Proteasome Endopeptidase Complex
references.citation: Mol Cell. 2006 Mar 17;21(6):873-80
references.pmid: 16543155
references.citation: J Struct Biol. 2008 May;162(2):205-18
references.pmid: 18276160
references.citation: Curr Protoc Mol Biol. 2001 May;Chapter 20:Unit 20.1
references.pmid: 18265190
references.citation: Annu Rev Biochem. 2001;70:503-33
references.pmid: 11395416
references.citation: Nat Cell Biol. 2006 Oct;8(10):1064-73
references.pmid: 16964248
references.citation: EMBO J. 1990 Feb;9(2):543-50
references.pmid: 2154373
references.citation: Gene. 1993 Mar 30;125(2):205-9
references.pmid: 8462875
references.citation: Mol Cell Biol. 1994 Aug;14(8):5501-9
references.pmid: 8035826
references.citation: Nature. 2005 Oct 20;437(7062):1173-8
references.pmid: 16189514
references.citation: Nat Cell Biol. 2009 Mar;11(3):295-302
references.pmid: 19182791
references.citation: EMBO J. 1992 Aug;11(8):3091-8
references.pmid: 1639076
references.citation: J Neurosci. 2003 Oct 15;23(28):9385-94
references.pmid: 14561866
references.citation: Gene. 2006 Jun 7;374:112-20
references.pmid: 16549277
references.citation: BMC Struct Biol. 2008 May 16;8:26
references.pmid: 18485199
references.citation: Nature. 2000 Nov 16;408(6810):381-6
references.pmid: 11099048
references.citation: EMBO J. 2007 Jan 10;26(1):90-101
references.pmid: 17170710
references.citation: Science. 2004 Jan 23;303(5657):540-3
references.pmid: 14704431
references.citation: Cell. 2000 Aug 18;102(4):533-9
references.pmid: 10966114
references.citation: Nat Struct Mol Biol. 2007 Oct;14(10):941-8
references.pmid: 17873885
references.citation: Curr Opin Immunol. 2007 Dec;19(6):665-73
references.pmid: 18036806
references.citation: PLoS One. 2008 Jan 23;3(1):e1487
references.pmid: 18213395
references.citation: Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11364-9
references.pmid: 10500182
references.citation: Mol Cell. 2009 Feb 27;33(4):483-95
references.pmid: 19250909
references.citation: Science. 2002 May 3;296(5569):910-3
references.pmid: 11988575
references.citation: Nature. 2007 Jun 28;447(7148):1135-8
references.pmid: 17597759
references.citation: Genome Biol. 2006;7(7):R63
references.pmid: 16859555
references.citation: Biochemistry. 1997 Aug 26;36(34):10526-37
references.pmid: 9265633
references.citation: Biochemistry. 1996 Feb 6;35(5):1664-71
references.pmid: 8634298
references.citation: Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18890-5
references.pmid: 16365295
references.citation: Biochim Biophys Acta. 2004 Nov 29;1695(1-3):235-47
references.pmid: 15571819
references.citation: Structure. 2004 Apr;12(4):633-44
references.pmid: 15062086
references.citation: Immunity. 2003 Apr;18(4):535-47
references.pmid: 12705856
references.citation: Nucleic Acids Res. 1998 Aug 1;26(15):3453-9
references.pmid: 9671804
references.citation: Annu Rev Cell Dev Biol. 2006;22:159-80
references.pmid: 16753028
references.citation: Cell Cycle. 2006 Jul;5(14):1481-6
references.pmid: 16861894
references.citation: Cell. 1992 Jun 26;69(7):1237-45
references.pmid: 1535557
references.citation: Cell. 2001 Jun 15;105(6):711-20
references.pmid: 11440714
references.citation: EMBO J. 2002 Apr 15;21(8):2009-18
references.pmid: 11953320
references.citation: Science. 1999 Oct 8;286(5438):309-12
references.pmid: 10514377
references.citation: Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):341-6
references.pmid: 16407162
references.citation: Annu Rev Biophys Biomol Struct. 2007;36:131-50
references.pmid: 17477837
references.citation: Science. 1999 Nov 12;286(5443):1321-6
references.pmid: 10558980
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5
references.pmid: 17145710
references.citation: Mol Cell. 2008 Aug 22;31(4):544-556
references.pmid: 18722180
references.citation: Mol Cell. 2002 May;9(5):945-56
references.pmid: 12049732
references.citation: Essays Biochem. 2005;41:15-30
references.pmid: 16250895
references.citation: Genomics. 1999 Apr 1;57(1):94-101
references.pmid: 10191088
references.citation: Methods Enzymol. 2002;350:87-96
references.pmid: 12073338
references.citation: Biochem Biophys Res Commun. 2003 Mar 21;302(4):635-45
references.pmid: 12646216
references.citation: J Neurosci. 2007 Mar 7;27(10):2472-82
references.pmid: 17344385
references.citation: J Mol Biol. 2004 Mar 12;337(1):157-65
references.pmid: 15001359
references.citation: Mol Cell Biol. 2000 Dec;20(24):9391-8
references.pmid: 11094089
references.citation: Nature. 2001 May 3;411(6833):41-2
references.pmid: 11333967
references.citation: J Biol Chem. 1982 Mar 10;257(5):2543-8
references.pmid: 6277905
references.citation: J Biol Chem. 2004 Oct 1;279(40):42169-81
references.pmid: 15280377
references.citation: Cell. 2000 Oct 13;103(2):351-61
references.pmid: 11057907
references.citation: J Natl Cancer Inst. 1994 Sep 7;86(17):1297-302
references.pmid: 8064888
references.citation: Yeast. 2000 Jun 30;16(9):857-60
references.pmid: 10861908
references.citation: Nat Genet. 2000 Jul;25(3):302-5
references.pmid: 10888878
references.citation: Cancer Cell. 2008 Jul 8;14(1):10-21
references.pmid: 18598940