title: Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.
abstract: 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.
authors.affiliation: Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, 55455, USA.
authors.forename: Naixia
authors.initials: N
authors.lastname: Zhang
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Wang
authors.forename: Aaron
authors.initials: A
authors.lastname: Ehlinger
authors.forename: Leah
authors.initials: L
authors.lastname: Randles
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Lary
authors.forename: Yang
authors.initials: Y
authors.lastname: Kang
authors.forename: Aydin
authors.initials: A
authors.lastname: Haririnia
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Storaska
authors.forename: James L
authors.initials: JL
authors.lastname: Cole
authors.forename: David
authors.initials: D
authors.lastname: Fushman
authors.forename: Kylie J
authors.initials: KJ
authors.lastname: Walters
mesh_terms: 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
chemical_list: 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
references.citation: Mol Cell. 2002 Sep;10(3):495-507
references.pmid: 12408819
references.citation: Cell. 1984 May;37(1):57-66
references.pmid: 6327060
references.citation: J Mol Biol. 2007 May 4;368(3):753-66
references.pmid: 17368669
references.citation: Nature. 1997 Feb 20;385(6618):737-40
references.pmid: 9034192
references.citation: J Biol Chem. 2000 May 19;275(20):15182-92
references.pmid: 10809753
references.citation: BMC Biochem. 2002 Sep 20;3:28
references.pmid: 12370088
references.citation: J Mol Biol. 2005 May 6;348(3):727-39
references.pmid: 15826667
references.citation: Science. 2002 Oct 18;298(5593):611-5
references.pmid: 12183636
references.citation: J Biol Chem. 1994 Mar 11;269(10):7059-61
references.pmid: 8125911
references.citation: Cell. 1984 May;37(1):43-55
references.pmid: 6327059
references.citation: J Cell Sci. 2003 Mar 15;116(Pt 6):1023-33
references.pmid: 12584246
references.citation: EMBO J. 2006 Dec 13;25(24):5742-53
references.pmid: 17139257
references.citation: J Biol Chem. 1999 Sep 24;274(39):28019-25
references.pmid: 10488153
references.citation: Anal Biochem. 2003 Sep 1;320(1):104-24
references.pmid: 12895474
references.citation: J Biol Chem. 2001 Jul 27;276(30):27936-43
references.pmid: 11369780
references.citation: Nat Cell Biol. 2002 Sep;4(9):725-30
references.pmid: 12198498
references.citation: J Biol Chem. 2003 Mar 14;278(11):8951-9
references.pmid: 12643283
references.citation: Cell. 1994 Oct 7;79(1):13-21
references.pmid: 7923371
references.citation: EMBO J. 2006 Oct 4;25(19):4524-36
references.pmid: 16990800
references.citation: Cell. 2004 Jul 9;118(1):99-110
references.pmid: 15242647
references.citation: Nature. 2002 Sep 26;419(6905):403-7
references.pmid: 12353037
references.citation: Biochemistry. 2003 Nov 25;42(46):13529-35
references.pmid: 14621999
references.citation: Nat Cell Biol. 2001 Oct;3(10):939-43
references.pmid: 11584278
references.citation: Mol Cell. 2005 Jun 10;18(6):687-98
references.pmid: 15949443
references.citation: Nat Cell Biol. 2006 Sep;8(9):994-1002
references.pmid: 16906146
references.citation: J Mol Biol. 2007 May 25;369(1):168-76
references.pmid: 17408689
references.citation: Nature. 2008 May 22;453(7194):548-52
references.pmid: 18497827
references.citation: Nat Struct Biol. 2001 May;8(5):417-22
references.pmid: 11323716
references.citation: Mol Cell. 2008 Nov 7;32(3):415-25
references.pmid: 18995839
references.citation: Nature. 2008 May 22;453(7194):481-8
references.pmid: 18497817
references.citation: Annu Rev Immunol. 1999;17:739-79
references.pmid: 10358773
references.citation: J Biol Chem. 2003 Sep 19;278(38):36621-7
references.pmid: 12832454
references.citation: Biochemistry. 2002 Feb 12;41(6):1767-77
references.pmid: 11827521
references.citation: Mol Cell Biol. 2007 Oct;27(19):6629-38
references.pmid: 17646385
references.citation: EMBO J. 2000 Jan 4;19(1):94-102
references.pmid: 10619848
references.citation: Mol Cell Biol. 1996 Nov;16(11):6020-8
references.pmid: 8887631