A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system.
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.
van Wijk
Sjoerd J L
SJ
Division of Biomedical Genetics, Department of Physiological Chemistry, University Medical Center Utrecht, Utrecht, The Netherlands.
de Vries
Sjoerd J
SJ
Kemmeren
Patrick
P
Huang
Anding
A
Boelens
Rolf
R
Bonvin
Alexandre M J J
AM
Timmers
H Th Marc
HT
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*
D011506:Proteins; D025801:Ubiquitin; D044763:Ubiquitin-Conjugating Enzymes; D005982:Glutathione Transferase; D046988:Proteasome Endopeptidase Complex
Mol Cell. 2006 Mar 17;21(6):873-80
16543155
J Struct Biol. 2008 May;162(2):205-18
18276160
Curr Protoc Mol Biol. 2001 May;Chapter 20:Unit 20.1
18265190
Annu Rev Biochem. 2001;70:503-33
11395416
Nat Cell Biol. 2006 Oct;8(10):1064-73
16964248
EMBO J. 1990 Feb;9(2):543-50
2154373
Gene. 1993 Mar 30;125(2):205-9
8462875
Mol Cell Biol. 1994 Aug;14(8):5501-9
8035826
Nature. 2005 Oct 20;437(7062):1173-8
16189514
Nat Cell Biol. 2009 Mar;11(3):295-302
19182791
EMBO J. 1992 Aug;11(8):3091-8
1639076
J Neurosci. 2003 Oct 15;23(28):9385-94
14561866
Gene. 2006 Jun 7;374:112-20
16549277
BMC Struct Biol. 2008 May 16;8:26
18485199
Nature. 2000 Nov 16;408(6810):381-6
11099048
EMBO J. 2007 Jan 10;26(1):90-101
17170710
Science. 2004 Jan 23;303(5657):540-3
14704431
Cell. 2000 Aug 18;102(4):533-9
10966114
Nat Struct Mol Biol. 2007 Oct;14(10):941-8
17873885
Curr Opin Immunol. 2007 Dec;19(6):665-73
18036806
PLoS One. 2008 Jan 23;3(1):e1487
18213395
Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11364-9
10500182
Mol Cell. 2009 Feb 27;33(4):483-95
19250909
Science. 2002 May 3;296(5569):910-3
11988575
Nature. 2007 Jun 28;447(7148):1135-8
17597759
Genome Biol. 2006;7(7):R63
16859555
Biochemistry. 1997 Aug 26;36(34):10526-37
9265633
Biochemistry. 1996 Feb 6;35(5):1664-71
8634298
Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18890-5
16365295
Biochim Biophys Acta. 2004 Nov 29;1695(1-3):235-47
15571819
Structure. 2004 Apr;12(4):633-44
15062086
Immunity. 2003 Apr;18(4):535-47
12705856
Nucleic Acids Res. 1998 Aug 1;26(15):3453-9
9671804
Annu Rev Cell Dev Biol. 2006;22:159-80
16753028
Cell Cycle. 2006 Jul;5(14):1481-6
16861894
Cell. 1992 Jun 26;69(7):1237-45
1535557
Cell. 2001 Jun 15;105(6):711-20
11440714
EMBO J. 2002 Apr 15;21(8):2009-18
11953320
Science. 1999 Oct 8;286(5438):309-12
10514377
Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):341-6
16407162
Annu Rev Biophys Biomol Struct. 2007;36:131-50
17477837
Science. 1999 Nov 12;286(5443):1321-6
10558980
Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5
17145710
Mol Cell. 2008 Aug 22;31(4):544-556
18722180
Mol Cell. 2002 May;9(5):945-56
12049732
Essays Biochem. 2005;41:15-30
16250895
Genomics. 1999 Apr 1;57(1):94-101
10191088
Methods Enzymol. 2002;350:87-96
12073338
Biochem Biophys Res Commun. 2003 Mar 21;302(4):635-45
12646216
J Neurosci. 2007 Mar 7;27(10):2472-82
17344385
J Mol Biol. 2004 Mar 12;337(1):157-65
15001359
Mol Cell Biol. 2000 Dec;20(24):9391-8
11094089
Nature. 2001 May 3;411(6833):41-2
11333967
J Biol Chem. 1982 Mar 10;257(5):2543-8
6277905
J Biol Chem. 2004 Oct 1;279(40):42169-81
15280377
Cell. 2000 Oct 13;103(2):351-61
11057907
J Natl Cancer Inst. 1994 Sep 7;86(17):1297-302
8064888
Yeast. 2000 Jun 30;16(9):857-60
10861908
Nat Genet. 2000 Jul;25(3):302-5
10888878
Cancer Cell. 2008 Jul 8;14(1):10-21
18598940