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PMID: 16211010 Published · ppublish English Journal Article

Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14.

The EMBO journal ·Vol. 24 ·No. 21 ·2005-11-02 ·Pages 3747-56

Hu M, Li P, Song L, Jeffrey PD, Chenova TA, Wilkinson KD, Cohen RE, Shi Y

Abstract

The ubiquitin-specific processing protease (UBP) family of deubiquitinating enzymes plays an essential role in numerous cellular processes. Mammalian USP14 (Ubp6 in yeast) is unique among known UBP enzymes in that it is activated catalytically upon specific association with the 26S proteasome. Here, we report the crystal structures of the 45-kDa catalytic domain of USP14 in isolation and in a complex with ubiquitin aldehyde, which reveal distinct structural features. In the absence of ubiquitin binding, the catalytic cleft leading to the active site of USP14 is blocked by two surface loops. Binding by ubiquitin induces a significant conformational change that translocates the two surface loops thereby allowing access of the ubiquitin C-terminus to the active site. These structural observations, in conjunction with biochemical characterization, identify important regulatory mechanisms for USP14.

MeSH Terms
Amino Acid Sequence Catalytic Domain Crystallography, X-Ray Endopeptidases/chemistry Humans Models, Molecular Molecular Sequence Data Multienzyme Complexes/chemistry,metabolism Proteasome Endopeptidase Complex/chemistry,metabolism Protein Conformation Ubiquitin-Specific Proteases Ubiquitins/metabolism
Chemicals
Multienzyme Complexes Ubiquitins ubiquitin-aldehyde Endopeptidases Ubiquitin-Specific Proteases Proteasome Endopeptidase Complex
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Hu Min
Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA.
Li Pingwei
Song Ling
Jeffrey Philip D
Chenova Tatiana A
Wilkinson Keith D
Cohen Robert E
Shi Yigong
References (40)
40 references, click to expand
  1. Interaction of the Doa4 deubiquitinating enzyme with the yeast 26S proteasome.
    Mol Biol Cell. 1999 Mar;10(3):741-56 PMID: 10069815
  2. The ubiquitin-proteasome pathway and pathogenesis of human diseases.
    Annu Rev Med. 1999;50:57-74 PMID: 10073263
  3. The Ubp6 family of deubiquitinating enzymes contains a ubiquitin-like domain: SUb.
    Protein Sci. 1999 Jun;8(6):1268-75 PMID: 10386876
  4. Structural basis for the specificity of ubiquitin C-terminal hydrolases.
    EMBO J. 1999 Jul 15;18(14):3877-87 PMID: 10406793
  5. The proteasome: a macromolecular assembly designed for controlled proteolysis.
    Philos Trans R Soc Lond B Biol Sci. 1999 Sep 29;354(1389):1501-11 PMID: 10582236
  6. Recognition of the polyubiquitin proteolytic signal.
    EMBO J. 2000 Jan 4;19(1):94-102 PMID: 10619848
  7. Physical association of ubiquitin ligases and the 26S proteasome.
    Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2497-502 PMID: 10688918
  8. Analysis of a gene encoding Rpn10 of the fission yeast proteasome reveals that the polyubiquitin-binding site of this subunit is essential when Rpn12/Mts3 activity is compromised.
    J Biol Chem. 2000 May 19;275(20):15182-92 PMID: 10809753
  9. Basic Medical Research Award. The ubiquitin system.
    Nat Med. 2000 Oct;6(10):1073-81 PMID: 11017125
  10. Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes.
    Mol Biol Cell. 2000 Oct;11(10):3425-39 PMID: 11029046
  11. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14.
    EMBO J. 2001 Sep 17;20(18):5187-96 PMID: 11566882
  12. The role of the ubiquitin-proteasomal pathway in Parkinson's disease and other neurodegenerative disorders.
    Trends Neurosci. 2001 Nov;24(11 Suppl):S7-14 PMID: 11881748
  13. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction.
    Physiol Rev. 2002 Apr;82(2):373-428 PMID: 11917093
  14. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome.
    Science. 2002 Oct 18;298(5593):611-5 PMID: 12183636
  15. A cryptic protease couples deubiquitination and degradation by the proteasome.
    Nature. 2002 Sep 26;419(6905):403-7 PMID: 12353037
  16. Synaptic defects in ataxia mice result from a mutation in Usp14, encoding a ubiquitin-specific protease.
    Nat Genet. 2002 Nov;32(3):420-5 PMID: 12368914
  17. Multiple associated proteins regulate proteasome structure and function.
    Mol Cell. 2002 Sep;10(3):495-507 PMID: 12408819
  18. Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde.
    Cell. 2002 Dec 27;111(7):1041-54 PMID: 12507430
  19. Deubiquitinating enzymes--the importance of driving in reverse along the ubiquitin-proteasome pathway.
    Int J Biochem Cell Biol. 2003 May;35(5):590-605 PMID: 12672452
  20. Deubiquitinating enzymes as cellular regulators.
    J Biochem. 2003 Jul;134(1):9-18 PMID: 12944365
  21. Pleiotropic effects of Ubp6 loss on drug sensitivities and yeast prion are due to depletion of the free ubiquitin pool.
    J Biol Chem. 2003 Dec 26;278(52):52102-15 PMID: 14559899
  22. Complementary roles for Rpn11 and Ubp6 in deubiquitination and proteolysis by the proteasome.
    J Biol Chem. 2004 Jan 16;279(3):1729-38 PMID: 14581483
  23. Ubiquitin depletion as a key mediator of toxicity by translational inhibitors.
    Mol Cell Biol. 2003 Dec;23(24):9251-61 PMID: 14645527
  24. Back to the future with ubiquitin.
    Cell. 2004 Jan 23;116(2):181-90 PMID: 14744430
  25. Proteasomes and their kin: proteases in the machine age.
    Nat Rev Mol Cell Biol. 2004 Mar;5(3):177-87 PMID: 14990998
  26. Deubiquitinating enzymes are IN/(trinsic to proteasome function).
    Curr Protein Pept Sci. 2004 Jun;5(3):201-11 PMID: 15188770
  27. The finger domain of the human deubiquitinating enzyme HAUSP is a zinc ribbon.
    Cell Cycle. 2004 Aug;3(8):1046-9 PMID: 15254399
  28. The CCP4 suite: programs for protein crystallography.
    Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3 PMID: 15299374
  29. Correlated phasing of multiple isomorphous replacement data.
    Acta Crystallogr D Biol Crystallogr. 1996 Jul 1;52(Pt 4):749-57 PMID: 15299639
  30. Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate.
    J Biol Chem. 2005 Jan 14;280(2):1512-20 PMID: 15531586
  31. Mechanism and function of deubiquitinating enzymes.
    Biochim Biophys Acta. 2004 Nov 29;1695(1-3):189-207 PMID: 15571815
  32. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.
    Proteins. 1991;11(4):281-96 PMID: 1758883
  33. Improved methods for building protein models in electron density maps and the location of errors in these models.
    Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9 PMID: 2025413
  34. Processing of X-ray diffraction data collected in oscillation mode.
    Methods Enzymol. 1997;276:307-26 PMID: 27754618
  35. Ubiquitin carboxyl-terminal hydrolase acts on ubiquitin carboxyl-terminal amides.
    J Biol Chem. 1985 Jul 5;260(13):7903-10 PMID: 2989266
  36. Ubiquitin-aldehyde: a general inhibitor of ubiquitin-recycling processes.
    Proc Natl Acad Sci U S A. 1987 Apr;84(7):1829-33 PMID: 3031653
  37. The yeast DOA4 gene encodes a deubiquitinating enzyme related to a product of the human tre-2 oncogene.
    Nature. 1993 Nov 25;366(6453):313-9 PMID: 8247125
  38. Editing of ubiquitin conjugates by an isopeptidase in the 26S proteasome.
    Nature. 1997 Feb 20;385(6618):737-40 PMID: 9034192
  39. Crystallography & NMR system: A new software suite for macromolecular structure determination.
    Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21 PMID: 9757107
  40. Deubiquitinating enzymes: a new class of biological regulators.
    Crit Rev Biochem Mol Biol. 1998;33(5):337-52 PMID: 9827704
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
DOI
10.1038/sj.emboj.7600832
Published
2005-11-02
Epub
2005-00-06
Pages
3747-56
Language
English
Region
England
NLM ID
8208664
PMCID
PMC1276716
Subset
IM
Databases
PDB
2AYN, 2AYO
External Links
PubMed source DOI: 10.1038/sj.emboj.7600832 PMC Full Text View journal details
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