PDBsum entry 5a5b

Hydrolase

PDB id: 5a5b

Contents

Protein chains

205 a.a.

223 a.a.

204 a.a.

198 a.a.

212 a.a.

222 a.a.

233 a.a.

368 a.a.

76 a.a.

243 a.a.

250 a.a.

245 a.a.

242 a.a.

243 a.a.

233 a.a.

245 a.a.

359 a.a.

362 a.a.

373 a.a.

381 a.a.

361 a.a.

367 a.a.

849 a.a.

387 a.a.

415 a.a.

431 a.a.

400 a.a.

353 a.a.

272 a.a.

255 a.a.

247 a.a.

197 a.a.

127 a.a.

19 a.a.

813 a.a.

PDB id:

5a5b

Name:

Hydrolase

Title:

Structure of the 26s proteasome-ubp6 complex

Structure:

Proteasome component pre3. Chain: 1. Synonym: 20s proteasome beta subunit 1, macropain subunit pre3, multicatalytic endopeptidase complex subunit pre3, proteinase ysce subunit pre3. Proteasome component pup1. Chain: 2. Synonym: 20s proteasome beta subunit 2 macropain subunit pup1, multicatalytic endopeptidase complex subunit pup1, proteinase ysce

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: yfr010w. Homo sapiens. Human. Organism_taxid: 9606. Organism_taxid: 4932

Authors:

A.Aufderheide,F.Beck,F.Stengel,M.Hartwig,A.Schweitzer,G.Pfeifer, A.L.Goldberg,E.Sakata,W.Baumeister,F.Foerster

Key ref:

A.Aufderheide et al. (2015). Structural characterization of the interaction of Ubp6 with the 26S proteasome. Proc Natl Acad Sci U S A, 112, 8626-8631. PubMed id: 26130806 DOI: 10.1073/pnas.1510449112

Date:

17-Jun-15 Release date: 22-Jul-15

Protein chain

P38624  (PSB1_YEAST) -  Proteasome subunit beta type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 205 a.a.

Protein chain

P25043  (PSB2_YEAST) -  Proteasome subunit beta type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 261 a.a.

Struc: 223 a.a.

Protein chain

P25451  (PSB3_YEAST) -  Proteasome subunit beta type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 205 a.a.

Struc: 204 a.a.

Protein chain

P22141  (PSB4_YEAST) -  Proteasome subunit beta type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 198 a.a.

Struc: 198 a.a.

Protein chain

P30656  (PSB5_YEAST) -  Proteasome subunit beta type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 287 a.a.

Struc: 212 a.a.*

Protein chain

P23724  (PSB6_YEAST) -  Proteasome subunit beta type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 241 a.a.

Struc: 222 a.a.

Protein chain

P30657  (PSB7_YEAST) -  Proteasome subunit beta type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 266 a.a.

Struc: 233 a.a.

Protein chain

P43593  (UBP6_YEAST) -  Ubiquitin carboxyl-terminal hydrolase 6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 499 a.a.

Struc: 368 a.a.*

Protein chain

P62987  (RL40_HUMAN) -  Ubiquitin-ribosomal protein eL40 fusion protein from Homo sapiens

Seq: 128 a.a.

Struc: 76 a.a.*

Protein chain

P21243  (PSA1_YEAST) -  Proteasome subunit alpha type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 252 a.a.

Struc: 243 a.a.

Protein chain

P23639  (PSA2_YEAST) -  Proteasome subunit alpha type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 250 a.a.

Struc: 250 a.a.

Protein chain

P23638  (PSA3_YEAST) -  Proteasome subunit alpha type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 258 a.a.

Struc: 245 a.a.

Protein chain

P40303  (PSA4_YEAST) -  Proteasome subunit alpha type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 254 a.a.

Struc: 242 a.a.

Protein chain

P32379  (PSA5_YEAST) -  Proteasome subunit alpha type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 260 a.a.

Struc: 243 a.a.

Protein chain

P40302  (PSA6_YEAST) -  Proteasome subunit alpha type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 234 a.a.

Struc: 233 a.a.

Protein chain

P21242  (PSA7_YEAST) -  Probable proteasome subunit alpha type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 288 a.a.

Struc: 245 a.a.

Protein chain

P33299  (PRS7_YEAST) -  26S proteasome regulatory subunit 7 homolog from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 467 a.a.

Struc: 359 a.a.

Protein chain

P40327  (PRS4_YEAST) -  26S proteasome regulatory subunit 4 homolog from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 437 a.a.

Struc: 362 a.a.

Protein chain

Q01939  (PRS8_YEAST) -  26S proteasome regulatory subunit 8 homolog from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 405 a.a.

Struc: 373 a.a.

Protein chain

P33298  (PRS6B_YEAST) -  26S proteasome regulatory subunit 6B homolog from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 428 a.a.

Struc: 381 a.a.

Protein chain

P53549  (PRS10_YEAST) -  26S proteasome subunit RPT4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 437 a.a.

Struc: 361 a.a.

Protein chain

P33297  (PRS6A_YEAST) -  26S proteasome regulatory subunit 6A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 434 a.a.

Struc: 367 a.a.

Protein chain

P32565  (RPN2_YEAST) -  26S proteasome regulatory subunit RPN2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 945 a.a.

Struc: 849 a.a.

Protein chain

Q04062  (RPN9_YEAST) -  26S proteasome regulatory subunit RPN9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 393 a.a.

Struc: 387 a.a.

Protein chain

Q12250  (RPN5_YEAST) -  26S proteasome regulatory subunit RPN5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 445 a.a.

Struc: 415 a.a.

Protein chain

Q12377  (RPN6_YEAST) -  26S proteasome regulatory subunit RPN6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 434 a.a.

Struc: 431 a.a.

Protein chain

Q06103  (RPN7_YEAST) -  26S proteasome regulatory subunit RPN7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 429 a.a.

Struc: 400 a.a.

Protein chain

P40016  (RPN3_YEAST) -  26S proteasome regulatory subunit RPN3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 523 a.a.

Struc: 353 a.a.

Protein chain

P32496  (RPN12_YEAST) -  26S proteasome regulatory subunit RPN12 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 274 a.a.

Struc: 272 a.a.

Protein chain

Q08723  (RPN8_YEAST) -  26S proteasome regulatory subunit RPN8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 338 a.a.

Struc: 255 a.a.

Protein chain

P43588  (RPN11_YEAST) -  Ubiquitin carboxyl-terminal hydrolase RPN11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 306 a.a.

Struc: 247 a.a.

Protein chain

P38886  (RPN10_YEAST) -  26S proteasome regulatory subunit RPN10 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 268 a.a.

Struc: 197 a.a.

Protein chain

O13563  (RPN13_YEAST) -  26S proteasome regulatory subunit RPN13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 156 a.a.

Struc: 127 a.a.

Protein chain

O94742  (SEM1_YEAST) -  26S proteasome complex subunit SEM1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 89 a.a.

Struc: 19 a.a.

Protein chain

P38764  (RPN1_YEAST) -  26S proteasome regulatory subunit RPN1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 993 a.a.

Struc: 813 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains 1, 2, 3, 4, 5, 6, 7, A, B, C, D, E, F, G: E.C.3.4.25.1 - proteasome endopeptidase complex.
• Reaction: Cleavage at peptide bonds with very broad specificity.
• Enzyme class 2: Chains 8, V: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1073/pnas.1510449112

Proc Natl Acad Sci U S A 112:8626-8631 (2015)

PubMed id: 26130806

Structural characterization of the interaction of Ubp6 with the 26S proteasome.

A.Aufderheide, F.Beck, F.Stengel, M.Hartwig, A.Schweitzer, G.Pfeifer, A.L.Goldberg, E.Sakata, W.Baumeister, F.Förster.

ABSTRACT

In eukaryotic cells, the 26S proteasome is responsible for the regulated degradation of intracellular proteins. Several cofactors interact transiently with this large macromolecular machine and modulate its function. The deubiquitylating enzyme ubiquitin C-terminal hydrolase 6 [Ubp6; ubiquitin-specific protease (USP) 14 in mammals] is the most abundant proteasome-interacting protein and has multiple roles in regulating proteasome function. Here, we investigate the structural basis of the interaction between Ubp6 and the 26S proteasome in the presence and absence of the inhibitor ubiquitin aldehyde. To this end we have used single-particle electron cryomicroscopy in combination with cross-linking and mass spectrometry. Ubp6 binds to the regulatory particle non-ATPase (Rpn) 1 via its N-terminal ubiquitin-like domain, whereas its catalytic USP domain is positioned variably. Addition of ubiquitin aldehyde stabilizes the binding of the USP domain in a position where it bridges the proteasome subunits Rpn1 and the regulatory particle triple-A ATPase (Rpt) 1. The USP domain binds to Rpt1 in the immediate vicinity of the Ubp6 active site, which may effect its activation. The catalytic triad is positioned in proximity to the mouth of the ATPase module and to the deubiquitylating enzyme Rpn11, strongly implying their functional linkage. On the proteasome side, binding of Ubp6 favors conformational switching of the 26S proteasome into an intermediate-energy conformational state, in particular upon the addition of ubiquitin aldehyde. This modulation of the conformational space of the 26S proteasome by Ubp6 explains the effects of Ubp6 on the kinetics of proteasomal degradation.