Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.
Degradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of one ubiquitin subunit (the "proximal" one) is covalently bonded to G76 of the other (the "distal" subunit). We demonstrate that S5a's UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains.
Zhang
Naixia
N
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, 55455, USA.
Wang
Qinghua
Q
Ehlinger
Aaron
A
Randles
Leah
L
Lary
Jeffrey W
JW
Kang
Yang
Y
Haririnia
Aydin
A
Storaska
Andrew J
AJ
Cole
James L
JL
Fushman
David
D
Walters
Kylie J
KJ
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D008562:Membrane Glycoproteins / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D016601:RNA-Binding Proteins; D025801:Ubiquitin / Q000737:chemistry / Q000378:metabolism*; D054875:Ubiquitination; D014461:Ultracentrifugation
C500781:ADRM1 protein, human; D047908:Intracellular Signaling Peptides and Proteins; D008562:Membrane Glycoproteins; C498506:PSMD4 protein, human; D021122:Protein Subunits; D016601:RNA-Binding Proteins; D025801:Ubiquitin; D046988:Proteasome Endopeptidase Complex
Mol Cell. 2002 Sep;10(3):495-507
12408819
Cell. 1984 May;37(1):57-66
6327060
J Mol Biol. 2007 May 4;368(3):753-66
17368669
Nature. 1997 Feb 20;385(6618):737-40
9034192
J Biol Chem. 2000 May 19;275(20):15182-92
10809753
BMC Biochem. 2002 Sep 20;3:28
12370088
J Mol Biol. 2005 May 6;348(3):727-39
15826667
Science. 2002 Oct 18;298(5593):611-5
12183636
J Biol Chem. 1994 Mar 11;269(10):7059-61
8125911
Cell. 1984 May;37(1):43-55
6327059
J Cell Sci. 2003 Mar 15;116(Pt 6):1023-33
12584246
EMBO J. 2006 Dec 13;25(24):5742-53
17139257
J Biol Chem. 1999 Sep 24;274(39):28019-25
10488153
Anal Biochem. 2003 Sep 1;320(1):104-24
12895474
J Biol Chem. 2001 Jul 27;276(30):27936-43
11369780
Nat Cell Biol. 2002 Sep;4(9):725-30
12198498
J Biol Chem. 2003 Mar 14;278(11):8951-9
12643283
Cell. 1994 Oct 7;79(1):13-21
7923371
EMBO J. 2006 Oct 4;25(19):4524-36
16990800
Cell. 2004 Jul 9;118(1):99-110
15242647
Nature. 2002 Sep 26;419(6905):403-7
12353037
Biochemistry. 2003 Nov 25;42(46):13529-35
14621999
Nat Cell Biol. 2001 Oct;3(10):939-43
11584278
Mol Cell. 2005 Jun 10;18(6):687-98
15949443
Nat Cell Biol. 2006 Sep;8(9):994-1002
16906146
J Mol Biol. 2007 May 25;369(1):168-76
17408689
Nature. 2008 May 22;453(7194):548-52
18497827
Nat Struct Biol. 2001 May;8(5):417-22
11323716
Mol Cell. 2008 Nov 7;32(3):415-25
18995839
Nature. 2008 May 22;453(7194):481-8
18497817
Annu Rev Immunol. 1999;17:739-79
10358773
J Biol Chem. 2003 Sep 19;278(38):36621-7
12832454
Biochemistry. 2002 Feb 12;41(6):1767-77
11827521
Mol Cell Biol. 2007 Oct;27(19):6629-38
17646385
EMBO J. 2000 Jan 4;19(1):94-102
10619848
Mol Cell Biol. 1996 Nov;16(11):6020-8
8887631