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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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2
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Tundo GR, Sbardella D, Santoro AM, Coletta A, Oddone F, Grasso G, Milardi D, Lacal PM, Marini S, Purrello R, Graziani G, Coletta M. The proteasome as a druggable target with multiple therapeutic potentialities: Cutting and non-cutting edges. Pharmacol Ther 2020; 213:107579. [PMID: 32442437 PMCID: PMC7236745 DOI: 10.1016/j.pharmthera.2020.107579] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 01/10/2023]
Abstract
Ubiquitin Proteasome System (UPS) is an adaptable and finely tuned system that sustains proteostasis network under a large variety of physiopathological conditions. Its dysregulation is often associated with the onset and progression of human diseases; hence, UPS modulation has emerged as a promising new avenue for the development of treatments of several relevant pathologies, such as cancer and neurodegeneration. The clinical interest in proteasome inhibition has considerably increased after the FDA approval in 2003 of bortezomib for relapsed/refractory multiple myeloma, which is now used in the front-line setting. Thereafter, two other proteasome inhibitors (carfilzomib and ixazomib), designed to overcome resistance to bortezomib, have been approved for treatment-experienced patients, and a variety of novel inhibitors are currently under preclinical and clinical investigation not only for haematological malignancies but also for solid tumours. However, since UPS collapse leads to toxic misfolded proteins accumulation, proteasome is attracting even more interest as a target for the care of neurodegenerative diseases, which are sustained by UPS impairment. Thus, conceptually, proteasome activation represents an innovative and largely unexplored target for drug development. According to a multidisciplinary approach, spanning from chemistry, biochemistry, molecular biology to pharmacology, this review will summarize the most recent available literature regarding different aspects of proteasome biology, focusing on structure, function and regulation of proteasome in physiological and pathological processes, mostly cancer and neurodegenerative diseases, connecting biochemical features and clinical studies of proteasome targeting drugs.
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Affiliation(s)
- G R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
| | | | - A M Santoro
- CNR, Institute of Crystallography, Catania, Italy
| | - A Coletta
- Department of Chemistry, University of Aarhus, Aarhus, Denmark
| | - F Oddone
- IRCCS-Fondazione Bietti, Rome, Italy
| | - G Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - D Milardi
- CNR, Institute of Crystallography, Catania, Italy
| | - P M Lacal
- Laboratory of Molecular Oncology, IDI-IRCCS, Rome, Italy
| | - S Marini
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - R Purrello
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - G Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - M Coletta
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
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3
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Suppahia A, Itagi P, Burris A, Kim FMG, Vontz A, Kante A, Kim S, Im W, Deeds EJ, Roelofs J. Cooperativity in Proteasome Core Particle Maturation. iScience 2020; 23:101090. [PMID: 32380419 PMCID: PMC7210456 DOI: 10.1016/j.isci.2020.101090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/07/2020] [Accepted: 04/16/2020] [Indexed: 12/02/2022] Open
Abstract
Proteasomes are multi-subunit protease complexes found in all domains of life. The maturation of the core particle (CP), which harbors the active sites, involves dimerization of two half CPs (HPs) and an autocatalytic cleavage that removes β propeptides. How these steps are regulated remains poorly understood. Here, we used the Rhodococcus erythropolis CP to dissect this process in vitro. Our data show that propeptides regulate the dimerization of HPs through flexible loops we identified. Furthermore, N-terminal truncations of the propeptides accelerated HP dimerization and decelerated CP auto-activation. We identified cooperativity in autocatalysis and found that the propeptide can be partially cleaved by adjacent active sites, potentially aiding an otherwise strictly autocatalytic mechanism. We propose that cross-processing during bacterial CP maturation is the underlying mechanism leading to the observed cooperativity of activation. Our work suggests that the bacterial β propeptide plays an unexpected and complex role in regulating dimerization and autocatalytic activation.
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Affiliation(s)
- Anjana Suppahia
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Pushpa Itagi
- Center for Computational Biology, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 99024, USA
| | - Alicia Burris
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Faith Mi Ge Kim
- Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Alexander Vontz
- Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Anupama Kante
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 99024, USA; Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Seonghoon Kim
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18105, USA
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18105, USA; Department of Bioengineering, Lehigh University, Bethlehem, PA 18105, USA; Department of Chemistry, Lehigh University, Bethlehem, PA 18105, USA
| | - Eric J Deeds
- Center for Computational Biology, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 99024, USA; Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 99024, USA.
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA.
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Mutational Analysis of a Highly Conserved PLSSMXP Sequence in the Small Subunit of Bacillus licheniformis γ-Glutamyltranspeptidase. Biomolecules 2019; 9:biom9090508. [PMID: 31546955 PMCID: PMC6769717 DOI: 10.3390/biom9090508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 01/13/2023] Open
Abstract
A highly conserved 458PLSSMXP464 sequence in the small subunit (S-subunit) of an industrially important Bacillus licheniformis γ-glutamyltranspeptidase (BlGGT) was identified by sequence alignment. Molecular structures of the precursor mimic and the mature form of BlGGT clearly reveal that this peptide sequence is in close spatial proximity to the self-processing and catalytic sites of the enzyme. To probe the role of this conserved sequence, ten mutant enzymes of BlGGT were created through a series of deletion and alanine-scanning mutagenesis. SDS-PAGE and densitometric analyses showed that the intrinsic ability of BlGGT to undergo autocatalytic processing was detrimentally affected by the deletion-associated mutations. However, loss of self-activating capacity was not obviously observed in most of the Ala-replacement mutants. The Ala-replacement mutants had a specific activity comparable to or greater than that of the wild-type enzyme; conversely, all deletion mutants completely lost their enzymatic activity. As compared with BlGGT, S460A and S461S showed greatly enhanced kcat/Km values by 2.73- and 2.67-fold, respectively. The intrinsic tryptophan fluorescence and circular dichroism spectral profiles of Ala-replacement and deletion mutants were typically similar to those of BlGGT. However, heat and guanidine hydrochloride-induced unfolding transitions of the deletion-associated mutant proteins were severely reduced as compared with the wild-type enzyme. The predictive mutant models suggest that the microenvironments required for both self-activation and catalytic reaction of BlGGT can be altered upon mutations.
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Gordo V, Aparicio D, Pérez-Luque R, Benito A, Vilanova M, Usón I, Fita I, Ribó M. Structural Insights into Subunits Assembly and the Oxyester Splicing Mechanism of Neq pol Split Intein. Cell Chem Biol 2018; 25:871-879.e2. [PMID: 29754955 DOI: 10.1016/j.chembiol.2018.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/28/2018] [Accepted: 04/08/2018] [Indexed: 11/28/2022]
Abstract
Split inteins are expressed as two separated subunits (N-intein and C-intein) fused to the corresponding exteins. The specific association of both intein subunits precedes protein splicing, which results in excision of the intein subunits and in ligation, by a peptide bond, of the concomitant exteins. Catalytically active intein precursors are typically too reactive for crystallization or even isolation. Neq pol is the trans-intein of the B-type DNA polymerase I split gene from hyperthermophile Nanoarchaeum equitans. We have determined the crystal structures of both the isolated NeqN and the complex of NeqN and NeqC subunits carrying the wild-type sequences, including the essential catalytic residues Ser1 and Thr+1, in addition to seven and three residues of the N- and C-exteins, respectively. These structures provide detailed information on the unique oxyester chemistry of the splicing mechanism of Neq pol and of the extensive rearrangements that occur in NeqN during the association step.
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Affiliation(s)
- Verónica Gordo
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Rosa Pérez-Luque
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Antoni Benito
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - Maria Vilanova
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain; ICREA Lluís Companys 23, 08003 Barcelona, Spain
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain.
| | - Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain.
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Gebai A, Gorelik A, Li Z, Illes K, Nagar B. Structural basis for the activation of acid ceramidase. Nat Commun 2018; 9:1621. [PMID: 29692406 PMCID: PMC5915598 DOI: 10.1038/s41467-018-03844-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/14/2018] [Indexed: 01/21/2023] Open
Abstract
Acid ceramidase (aCDase, ASAH1) hydrolyzes lysosomal membrane ceramide into sphingosine, the backbone of all sphingolipids, to regulate many cellular processes. Abnormal function of aCDase leads to Farber disease, spinal muscular atrophy with progressive myoclonic epilepsy, and is associated with Alzheimer’s, diabetes, and cancer. Here, we present crystal structures of mammalian aCDases in both proenzyme and autocleaved forms. In the proenzyme, the catalytic center is buried and protected from solvent. Autocleavage triggers a conformational change exposing a hydrophobic channel leading to the active site. Substrate modeling suggests distinct catalytic mechanisms for substrate hydrolysis versus autocleavage. A hydrophobic surface surrounding the substrate binding channel appears to be a site of membrane attachment where the enzyme accepts substrates facilitated by the accessory protein, saposin-D. Structural mapping of disease mutations reveals that most would destabilize the protein fold. These results will inform the rational design of aCDase inhibitors and recombinant aCDase for disease therapeutics. Acid ceramidase (aCDase) hydrolyzes lysosomal membrane ceramide into sphingosine and its dysfunction leads to a variety of disease phenotypes. Here, the authors present structures of aCDase in its proenzyme and autocleaved forms, which provides insight into its mechanism of action.
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Affiliation(s)
- Ahmad Gebai
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Alexei Gorelik
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Zixian Li
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Katalin Illes
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Bhushan Nagar
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada.
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7
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Defective immuno- and thymoproteasome assembly causes severe immunodeficiency. Sci Rep 2018; 8:5975. [PMID: 29654304 PMCID: PMC5899138 DOI: 10.1038/s41598-018-24199-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/20/2018] [Indexed: 12/22/2022] Open
Abstract
By N-ethyl-N-nitrosourea (ENU) mutagenesis, we generated the mutant mouse line TUB6 that is characterised by severe combined immunodeficiency (SCID) and systemic sterile autoinflammation in homozygotes, and a selective T cell defect in heterozygotes. The causative missense point mutation results in the single amino acid exchange G170W in multicatalytic endopeptidase complex subunit-1 (MECL-1), the β2i-subunit of the immuno- and thymoproteasome. Yeast mutagenesis and crystallographic data suggest that the severe TUB6-phenotype compared to the MECL-1 knockout mouse is caused by structural changes in the C-terminal appendage of β2i that prevent the biogenesis of immuno- and thymoproteasomes. Proteasomes are essential for cell survival, and defective proteasome assembly causes selective death of cells expressing the mutant MECL-1, leading to the severe immunological phenotype. In contrast to the immunosubunits β1i (LMP2) and β5i (LMP7), mutations in the gene encoding MECL-1 have not yet been assigned to human disorders. The TUB6 mutant mouse line exemplifies the involvement of MECL-1 in immunopathogenesis and provides the first mouse model for primary immuno- and thymoproteasome-associated immunodeficiency that may also be relevant in humans.
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On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral β-Subunit Protein Anbu. J Mol Biol 2018; 430:628-640. [DOI: 10.1016/j.jmb.2018.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 12/30/2017] [Accepted: 01/04/2018] [Indexed: 11/20/2022]
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Chand D, Avinash VS, Yadav Y, Pundle AV, Suresh CG, Ramasamy S. Molecular features of bile salt hydrolases and relevance in human health. Biochim Biophys Acta Gen Subj 2017; 1861:2981-2991. [DOI: 10.1016/j.bbagen.2016.09.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/20/2016] [Accepted: 09/23/2016] [Indexed: 01/18/2023]
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Yedidi RS, Fatehi AK, Enenkel C. Proteasome dynamics between proliferation and quiescence stages of Saccharomyces cerevisiae. Crit Rev Biochem Mol Biol 2016; 51:497-512. [PMID: 27677933 DOI: 10.1080/10409238.2016.1230087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The ubiquitin-proteasome system (UPS) plays a critical role in cellular protein homeostasis and is required for the turnover of short-lived and unwanted proteins, which are targeted by poly-ubiquitination for degradation. Proteasome is the key protease of UPS and consists of multiple subunits, which are organized into a catalytic core particle (CP) and a regulatory particle (RP). In Saccharomyces cerevisiae, proteasome holo-enzymes are engaged in degrading poly-ubiquitinated substrates and are mostly localized in the nucleus during cell proliferation. While in quiescence, the RP and CP are sequestered into motile and reversible storage granules in the cytoplasm, called proteasome storage granules (PSGs). The reversible nature of PSGs allows the proteasomes to be transported back into the nucleus upon exit from quiescence. Nuclear import of RP and CP through nuclear pores occurs via the canonical pathway that includes the importin-αβ heterodimer and takes advantage of the Ran-GTP gradient across the nuclear membrane. Dependent on the growth stage, either inactive precursor complexes or mature holo-enzymes are imported into the nucleus. The present review discusses the dynamics of proteasomes including their assembly, nucleo-cytoplasmic transport during proliferation and the sequestration of proteasomes into PSGs during quiescence. [Formula: see text].
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Affiliation(s)
| | | | - Cordula Enenkel
- a Department of Biochemistry , University of Toronto , Toronto , Canada
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11
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A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome. Nat Commun 2016; 7:10900. [PMID: 26964885 PMCID: PMC4792962 DOI: 10.1038/ncomms10900] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/31/2016] [Indexed: 11/28/2022] Open
Abstract
Biogenesis of the 20S proteasome is tightly regulated. The N-terminal propeptides protecting the active-site threonines are autocatalytically released only on completion of assembly. However, the trigger for the self-activation and the reason for the strict conservation of threonine as the active site nucleophile remain enigmatic. Here we use mutagenesis, X-ray crystallography and biochemical assays to suggest that Lys33 initiates nucleophilic attack of the propeptide by deprotonating the Thr1 hydroxyl group and that both residues together with Asp17 are part of a catalytic triad. Substitution of Thr1 by Cys disrupts the interaction with Lys33 and inactivates the proteasome. Although a Thr1Ser mutant is active, it is less efficient compared with wild type because of the unfavourable orientation of Ser1 towards incoming substrates. This work provides insights into the basic mechanism of proteolysis and propeptide autolysis, as well as the evolutionary pressures that drove the proteasome to become a threonine protease. The proteasome, an essential molecular machine, is a threonine protease, but the evolution and the components of its proteolytic centre are unclear. Here, the authors use structural biology and biochemistry to investigate the role of proteasome active site residues on maturation and activity.
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12
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Li X, Li Y, Arendt CS, Hochstrasser M. Distinct Elements in the Proteasomal β5 Subunit Propeptide Required for Autocatalytic Processing and Proteasome Assembly. J Biol Chem 2015; 291:1991-2003. [PMID: 26627836 DOI: 10.1074/jbc.m115.677047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Indexed: 01/02/2023] Open
Abstract
Eukaryotic 20S proteasome assembly remains poorly understood. The subunits stack into four heteroheptameric rings; three inner-ring subunits (β1, β2, and β5) bear the protease catalytic residues and are synthesized with N-terminal propeptides. These propeptides are removed autocatalytically late in assembly. In Saccharomyces cerevisiae, β5 (Doa3/Pre2) has a 75-residue propeptide, β5pro, that is essential for proteasome assembly and can work in trans. We show that deletion of the poorly conserved N-terminal half of the β5 propeptide nonetheless causes substantial defects in proteasome maturation. Sequences closer to the cleavage site have critical but redundant roles in both assembly and self-cleavage. A conserved histidine two residues upstream of the autocleavage site strongly promotes processing. Surprisingly, although β5pro is functionally linked to the Ump1 assembly factor, trans-expressed β5pro associates only weakly with Ump1-containing precursors. Several genes were identified as dosage suppressors of trans-expressed β5pro mutants; the strongest encoded the β7 proteasome subunit. Previous data suggested that β7 and β5pro have overlapping roles in bringing together two half-proteasomes, but the timing of β7 addition relative to half-mer joining was unclear. Here we report conditions where dimerization lags behind β7 incorporation into the half-mer. Our results suggest that β7 insertion precedes half-mer dimerization, and the β7 tail and β5 propeptide have unequal roles in half-mer joining.
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Affiliation(s)
- Xia Li
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Yanjie Li
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Cassandra S Arendt
- the Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Mark Hochstrasser
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and.
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Pica A, Chi MC, Chen YY, d'Ischia M, Lin LL, Merlino A. The maturation mechanism of γ-glutamyl transpeptidases: Insights from the crystal structure of a precursor mimic of the enzyme from Bacillus licheniformis and from site-directed mutagenesis studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:195-203. [PMID: 26536828 DOI: 10.1016/j.bbapap.2015.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 01/20/2023]
Abstract
γ-Glutamyl transpeptidases (γ-GTs) are members of N-terminal nucleophile hydrolase superfamily. They are synthetized as single-chain precursors, which are then cleaved to form mature enzymes. Basic aspects of autocatalytic processing of these pro-enzymes are still unknown. Here we describe the X-ray structure of the precursor mimic of Bacillus licheniformis γ-GT (BlGT), obtained by mutating catalytically important threonine to alanine (T399A-BlGT), and report results of autoprocessing of mutants of His401, Thr415, Thr417, Glu419 and Arg571. Data suggest that Thr417 is in a competent position to activate the catalytic threonine (Thr399) for nucleophilic attack of the scissile peptide bond and that Thr415 plays a major role in assisting the process. On the basis of these new structural results, a possible mechanism of autoprocessing is proposed. This mechanism, which guesses the existence of a six-membered transition state involving one carbonyl and two hydroxyl groups, is in agreement with all the available experimental data collected on γ-GTs from different species and with our new Ala-scanning mutagenesis data.
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Affiliation(s)
- Andrea Pica
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Naples I-80126, Italy; Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, Naples 80133, Italy
| | - Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - Yi-Yu Chen
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - Marco d'Ischia
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Naples I-80126, Italy
| | - Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Naples I-80126, Italy; Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, Naples 80133, Italy.
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14
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Bastiaansen KC, van Ulsen P, Wijtmans M, Bitter W, Llamas MA. Self-cleavage of the Pseudomonas aeruginosa Cell-surface Signaling Anti-sigma Factor FoxR Occurs through an N-O Acyl Rearrangement. J Biol Chem 2015; 290:12237-46. [PMID: 25809487 DOI: 10.1074/jbc.m115.643098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/06/2022] Open
Abstract
The Fox system of Pseudomonas aeruginosa is a cell-surface signaling (CSS) pathway employed by the bacterium to sense and respond to the presence of the heterologous siderophore ferrioxamine in the environment. This regulatory pathway controls the transcription of the foxA ferrioxamine receptor gene through the extracytoplasmic function sigma factor σ(FoxI). In the absence of ferrioxamine, the activity of σ(FoxI) is inhibited by the transmembrane anti-sigma factor FoxR. Upon binding of ferrioxamine by the FoxA receptor, FoxR is processed by a complex proteolytic cascade leading to the release and activation of σ(FoxI). Interestingly, we have recently shown that FoxR undergoes self-cleavage between the periplasmic Gly-191 and Thr-192 residues independent of the perception of ferrioxamine. This autoproteolytic event, which is widespread among CSS anti-sigma factors, produces two distinct domains that interact and function together to transduce the presence of the signal. In this work, we provide evidence that the self-cleavage of FoxR is not an enzyme-dependent process but is induced by an N-O acyl rearrangement. Mutation analysis showed that the nucleophilic side chain of the Thr-192 residue at +1 of the cleavage site is required for an attack on the preceding Gly-191, after which the resulting ester bond is likely hydrolyzed. Because the cleavage site is well preserved and the hydrolysis of periplasmic CSS anti-sigma factors is widely observed, we hypothesize that cleavage via an N-O acyl rearrangement is a conserved feature of these proteins.
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Affiliation(s)
- Karlijn C Bastiaansen
- From the Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada E-18008, Spain and Section of Molecular Microbiology, Department of Molecular Cell Biology and
| | - Peter van Ulsen
- Section of Molecular Microbiology, Department of Molecular Cell Biology and
| | - Maikel Wijtmans
- Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Wilbert Bitter
- Section of Molecular Microbiology, Department of Molecular Cell Biology and
| | - María A Llamas
- From the Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada E-18008, Spain and
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15
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The amazing ubiquitin-proteasome system: structural components and implication in aging. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 314:171-237. [PMID: 25619718 DOI: 10.1016/bs.ircmb.2014.09.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteome quality control (PQC) is critical for the maintenance of cellular functionality and it is assured by the curating activity of the proteostasis network (PN). PN is constituted of several complex protein machines that under conditions of proteome instability aim to, firstly identify, and then, either rescue or degrade nonnative polypeptides. Central to the PN functionality is the ubiquitin-proteasome system (UPS) which is composed from the ubiquitin-conjugating enzymes and the proteasome; the latter is a sophisticated multi-subunit molecular machine that functions in a bimodal way as it degrades both short-lived ubiquitinated normal proteins and nonfunctional polypeptides. UPS is also involved in PQC of the nucleus, the endoplasmic reticulum and the mitochondria and it also interacts with the other main cellular degradation axis, namely the autophagy-lysosome system. UPS functionality is optimum in the young organism but it is gradually compromised during aging resulting in increasing proteotoxic stress; these effects correlate not only with aging but also with most age-related diseases. Herein, we present a synopsis of the UPS components and of their functional alterations during cellular senescence or in vivo aging. We propose that mild UPS activation in the young organism will, likely, promote antiaging effects and/or suppress age-related diseases.
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16
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Buller AR, Freeman MF, Schildbach JF, Townsend CA. Exploring the role of conformational heterogeneity in cis-autoproteolytic activation of ThnT. Biochemistry 2014; 53:4273-81. [PMID: 24933323 PMCID: PMC4095933 DOI: 10.1021/bi500385d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
the past decade, there have been major achievements in understanding
the relationship between enzyme catalysis and protein structural plasticity.
In autoprocessing systems, however, there is a sparsity of direct
evidence of the role of conformational dynamics, which are complicated
by their intrinsic chemical reactivity. ThnT is an autoproteolytically
activated enzyme involved in the biosynthesis of the β-lactam
antibiotic thienamycin. Conservative mutation of ThnT results in multiple
conformational states that can be observed via X-ray crystallography,
establishing ThnT as a representative and revealing system for studing
how conformational dynamics control autoactivation at a molecular
level. Removal of the nucleophile by mutation to Ala disrupts the
population of a reactive state and causes widespread structural changes
from a conformation that promotes autoproteolysis to one associated
with substrate catalysis. Finer probing of the active site polysterism
was achieved by EtHg derivatization of the nucleophile, which indicates
the active site and a neighboring loop have coupled dynamics. Disruption
of these interactions by mutagenesis precludes the ability to observe
a reactive state through X-ray crystallography, and application of
this insight to other autoproteolytically activated enzymes offers
an explanation for the widespread crystallization of inactive states.
We suggest that the N → O(S) acyl shift in cis-autoproteolysis might occur through a si-face attack,
thereby unifying the fundamental chemistry of these enzymes through
a common mechanism.
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Affiliation(s)
- Andrew R Buller
- Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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17
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Volkmann G, Mootz HD. Recent progress in intein research: from mechanism to directed evolution and applications. Cell Mol Life Sci 2013; 70:1185-206. [PMID: 22926412 PMCID: PMC11113529 DOI: 10.1007/s00018-012-1120-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 07/23/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022]
Abstract
Inteins catalyze a post-translational modification known as protein splicing, where the intein removes itself from a precursor protein and concomitantly ligates the flanking protein sequences with a peptide bond. Over the past two decades, inteins have risen from a peculiarity to a rich source of applications in biotechnology, biomedicine, and protein chemistry. In this review, we focus on developments of intein-related research spanning the last 5 years, including the three different splicing mechanisms and their molecular underpinnings, the directed evolution of inteins towards improved splicing in exogenous protein contexts, as well as novel applications of inteins for cell biology and protein engineering, which were made possible by a clearer understanding of the protein splicing mechanism.
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Affiliation(s)
- Gerrit Volkmann
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Henning D. Mootz
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
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18
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Chi MC, Chen YY, Lo HF, Lin LL. Experimental evidence for the involvement of amino acid residue Glu398 in the autocatalytic processing of Bacillus licheniformis γ-glutamyltranspeptidase. FEBS Open Bio 2012; 2:298-304. [PMID: 23772362 PMCID: PMC3678132 DOI: 10.1016/j.fob.2012.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 09/25/2012] [Accepted: 09/25/2012] [Indexed: 11/18/2022] Open
Abstract
The role of glutamate 398 in the autocatalytic processing of Bacillus licheniformis γ-glutamyltranspeptidase (BlGGT) was explored by site-directed mutagenesis. This glutamate was substituted by either alanine, aspartate, arginine or glutamine and the expressed mutant enzymes were purified to apparent homogeneity with metal-affinity chromatography. SDS–PAGE analysis showed that E398A, E398D and E398K were unable to process themselves into a large and a small subunit. However, E398Q was not only able to process itself, but also had a catalytic activity comparable to that of BlGGT. As compared with the wild-type enzyme, no significant change in circular dichroism spectra was observed for the mutant proteins. Thermal unfolding of BlGGT, E398A, E398D, E398K and E398Q followed the two-state unfolding process with a transition point (Tm) of 47.7–69.4 °C. Tryptophan fluorescence spectra of the mutant enzymes were different from the wild-type protein in terms of fluorescence intensity. Native BlGGT started to unfold beyond ∼1.92 M guanidine hydrochloride (GdnHCl) and reached an unfolded intermediate, [GdnHCl]0.5, N–U, at 3.07 M equivalent to free energy change (ΔGN−UH2O) of 14.53 kcal/mol for the N → U process, whereas the denaturation midpoints for the mutant enzymes were 1.31–2.99 M equivalent to ΔGN−UH2O of 3.29–12.05 kcal/mol. Taken together, these results strongly suggest that the explored glutamate residue is indeed important for the autocatalytic processing of BlGGT.
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Affiliation(s)
- Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, Taiwan
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19
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Buller AR, Labonte JW, Freeman MF, Wright NT, Schildbach JF, Townsend CA. Autoproteolytic activation of ThnT results in structural reorganization necessary for substrate binding and catalysis. J Mol Biol 2012; 422:508-18. [PMID: 22706025 PMCID: PMC3428426 DOI: 10.1016/j.jmb.2012.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 06/02/2012] [Accepted: 06/08/2012] [Indexed: 11/01/2022]
Abstract
cis-Autoproteolysis is a post-translational modification necessary for the function of ThnT, an enzyme involved in the biosynthesis of the β-lactam antibiotic thienamycin. This modification generates an N-terminal threonine nucleophile that is used to hydrolyze the pantetheinyl moiety of its natural substrate. We determined the crystal structure of autoactivated ThnT to 1.8Å through X-ray crystallography. Comparison to a mutationally inactivated precursor structure revealed several large conformational rearrangements near the active site. To probe the relevance of these transitions, we designed a pantetheine-like chloromethyl ketone inactivator and co-crystallized it with ThnT. Although this class of inhibitor has been in use for several decades, the mode of inactivation had not been determined for an enzyme that uses an N-terminal nucleophile. The co-crystal structure revealed the chloromethyl ketone bound to the N-terminal nucleophile of ThnT through an ether linkage, and analysis suggests inactivation through a direct displacement mechanism. More importantly, this inactivated complex shows that three regions of ThnT that are critical to the formation of the substrate binding pocket undergo rearrangement upon autoproteolysis. Comparison of ThnT with other autoproteolytic enzymes of disparate evolutionary lineage revealed a high degree of similarity within the proenzyme active site, reflecting shared chemical constraints. However, after autoproteolysis, many enzymes, like ThnT, are observed to rearrange in order to accommodate their specific substrate. We propose that this is a general phenomenon, whereby autoprocessing systems with shared chemistry may possess similar structural features that dissipate upon rearrangement into a mature state.
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Affiliation(s)
- Andrew R Buller
- Department of Biophysics, The Johns Hopkins University, Baltimore, MD 21218, USA
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20
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Insights into cis-autoproteolysis reveal a reactive state formed through conformational rearrangement. Proc Natl Acad Sci U S A 2012; 109:2308-13. [PMID: 22308359 DOI: 10.1073/pnas.1113633109] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ThnT is a pantetheine hydrolase from the DmpA/OAT superfamily involved in the biosynthesis of the β-lactam antibiotic thienamycin. We performed a structural and mechanistic investigation into the cis-autoproteolytic activation of ThnT, a process that has not previously been subject to analysis within this superfamily of enzymes. Removal of the γ-methyl of the threonine nucleophile resulted in a rate deceleration that we attribute to a reduction in the population of the reactive rotamer. This phenomenon is broadly applicable and constitutes a rationale for the evolutionary selection of threonine nucleophiles in autoproteolytic systems. Conservative substitution of the nucleophile (T282C) allowed determination of a 1.6-Å proenzyme ThnT crystal structure, which revealed a level of structural flexibility not previously observed within an autoprocessing active site. We assigned the major conformer as a nonreactive state that is unable to populate a reactive rotamer. Our analysis shows the system is activated by a structural rearrangement that places the scissile amide into an oxyanion hole and forces the nucleophilic residue into a forbidden region of Ramachandran space. We propose that conformational strain may drive autoprocessing through the destabilization of nonproductive states. Comparison of our data with previous reports uncovered evidence that many inactivated structures display nonreactive conformations. For penicillin and cephalosporin acylases, this discrepancy between structure and function may be resolved by invoking the presence of a hidden conformational state, similar to that reported here for ThnT.
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21
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Dembek M, Reynolds CB, Fairweather NF. Clostridium difficile cell wall protein CwpV undergoes enzyme-independent intramolecular autoproteolysis. J Biol Chem 2011; 287:1538-44. [PMID: 22128177 PMCID: PMC3256870 DOI: 10.1074/jbc.m111.302463] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Clostridium difficile infection is a leading cause of antibiotic-associated diarrhea, placing considerable economic pressure on healthcare systems and resulting in significant morbidity and mortality. The pathogen produces a proteinaceous array on its cell surface known as the S-layer, consisting primarily of the major S-layer protein SlpA and a family of SlpA homologs. CwpV is the largest member of this family and is expressed in a phase-variable manner. The protein is post-translationally processed into two fragments that form a noncovalent, heterodimeric complex. To date, no specific proteases capable of cleaving CwpV have been identified. Using site-directed mutagenesis we show that CwpV undergoes intramolecular autoproteolysis, most likely facilitated by a N-O acyl shift, with Thr-413 acting as the source of a nucleophile driving this rearrangement. We demonstrate that neighboring residues are also important for correct processing of CwpV. Based on protein structural predictions and analogy to the glycosylasparaginase family of proteins, it appears likely that these residues play key roles in determining the correct protein fold and interact directly with Thr-413 to promote nucleophilic attack. Furthermore, using a cell-free protein synthesis assay we show that CwpV maturation requires neither cofactors nor auxiliary enzymes.
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Affiliation(s)
- Marcin Dembek
- Division of Cell and Molecular Biology, Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
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22
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Ruschak AM, Slassi M, Kay LE, Schimmer AD. Novel proteasome inhibitors to overcome bortezomib resistance. J Natl Cancer Inst 2011; 103:1007-17. [PMID: 21606441 DOI: 10.1093/jnci/djr160] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The proteasome is an intracellular enzyme complex that degrades ubiquitin-tagged proteins and thereby regulates protein levels within the cell. Given this important role in maintaining cellular homeostasis, it is perhaps somewhat surprising that proteasome inhibitors have a therapeutic window. Proteasome inhibitors have demonstrated clinical efficacy in the treatment of multiple myeloma and mantle cell lymphoma and are under evaluation for the treatment of other malignancies. Bortezomib is the first and only Food and Drug Administration-approved proteasome inhibitor that inhibits this enzyme complex in a reversible fashion. Although bortezomib improves clinical outcomes when used as a single agent, most patients do not respond to this drug and those who do respond almost uniformly relapse. As such, efforts are underway to develop proteasome inhibitors that act through mechanisms distinct from that of bortezomib. Specifically, inhibitors that bind the active site of the proteasome and inhibit the complex irreversibly have been developed and are in advanced clinical trials. Inhibitors that act on sites of the proteasome outside of the catalytic center have also been identified and are in preclinical development. In this review, we discuss the structure and function of the proteasome. We then focus on the molecular biology, chemistry, and the preclinical and clinical efficacy of novel proteasome inhibitors as strategies to inhibit this target and overcome some forms of bortezomib resistance.
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Affiliation(s)
- Amy M Ruschak
- Department of Molecular Genetics, The University of Toronto, Toronto, ON, Canada
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23
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Chang HP, Liang WC, Lyu RC, Chi MC, Wang TF, Su KL, Hung HC, Lin LL. Effects of C-terminal truncation on autocatalytic processing of Bacillus licheniformis gamma-glutamyl transpeptidase. BIOCHEMISTRY (MOSCOW) 2010; 75:919-29. [PMID: 20673217 DOI: 10.1134/s0006297910070151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The role of the C-terminal region of Bacillus licheniformis gamma-glutamyl transpeptidase (BlGGT) was investigated by deletion analysis. Seven C-terminally truncated BlGGTs lacking 581-585, 577-585, 576-585, 566-585, 558-585, 523-585, and 479-585 amino acids, respectively, were generated by site-directed mutagenesis. Deletion of the last nine amino acids had no appreciable effect on the autocatalytic processing of the enzyme, and the engineered protein was active towards the synthetic substrate L-gamma-glutamyl-p-nitroanilide. However, a further deletion to Val576 impaired the autocatalytic processing. In vitro maturation experiments showed that the truncated BlGGT precursors, pro-Delta(576-585), pro-Delta(566-585), and pro-Delta(558-585), could partially precede a time-dependent autocatalytic process to generate the L- and S-subunits, and these proteins showed a dramatic decrease in catalytic activity with respect to the wild-type enzyme. The parental enzyme (BlGGT-4aa) and BlGGT were unfolded biphasically by guanidine hydrochloride (GdnCl), but Delta(577-585), Delta(576-585), Delta(566-585), Delta(558-585), Delta(523-585), and Delta(479-585) followed a monophasic unfolding process and showed a sequential reduction in the GdnCl concentration corresponding to half effect and DeltaG(0) for the unfolding. BlGGT-4aa and BlGGT sedimented at ~4.85 S and had a heterodimeric structure of approximately 65.23 kDa in solution, and this structure was conserved in all of the truncated proteins. The frictional ratio (f/f(o)) of BlGGT-4aa, BlGGT, Delta(581-585), and Delta(577-585) was 1.58, 1.57, 1.46, and 1.39, respectively, whereas the remaining enzymes existed exclusively as precursor form with a ratio of less than 1.18. Taken together, these results provide direct evidence for the functional role of the C-terminal region in the autocatalytic processing of BlGGT.
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Affiliation(s)
- Hui-Ping Chang
- Department of Applied Chemistry, National Chiayi University, Taiwan
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24
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Wang Y, Guo HC. Crystallographic snapshot of glycosylasparaginase precursor poised for autoprocessing. J Mol Biol 2010; 403:120-130. [PMID: 20800597 DOI: 10.1016/j.jmb.2010.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 08/19/2010] [Accepted: 08/19/2010] [Indexed: 10/19/2022]
Abstract
Glycosylasparaginase belongs to a family of N-terminal nucleophile hydrolases that autoproteolytically generate their mature enzymes from single-chain protein precursors. Previously, based on a precursor structure paused at pre-autoproteolysis stage by a reversible inhibitor (glycine), we proposed a mechanism of intramolecular autoproteolysis. A key structural feature, a highly strained conformation at the scissile peptide bond, had been identified and was hypothesized to be critical for driving autoproteolysis through an N-O acyl shift. To examine this "twist-and-break" hypothesis, we report here a 1. 9-Å-resolution structure of an autoproteolysis-active precursor (a T152C mutant) that is free of inhibitor or ligand and is poised to undergo autoproteolysis. The current crystallographic study has provided direct evidence for the natural conformation of the glycosylasparaginase autocatalytic site without influence from any inhibitor or ligand. This finding has confirmed our previous proposal that conformational strain is an intrinsic feature of an active precursor.
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Affiliation(s)
- Yeming Wang
- Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118-2526, USA
| | - Hwai-Chen Guo
- Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118-2526, USA.
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25
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Bokhove M, Yoshida H, Hensgens CMH, van der Laan JM, Sutherland JD, Dijkstra BW. Structures of an isopenicillin N converting Ntn-hydrolase reveal different catalytic roles for the active site residues of precursor and mature enzyme. Structure 2010; 18:301-8. [PMID: 20223213 DOI: 10.1016/j.str.2010.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 01/06/2010] [Accepted: 01/18/2010] [Indexed: 10/19/2022]
Abstract
Penicillium chrysogenum Acyl coenzyme A:isopenicillin N acyltransferase (AT) performs the last step in the biosynthesis of hydrophobic penicillins, exchanging the hydrophilic side chain of a precursor for various hydrophobic side chains. Like other N-terminal nucleophile hydrolases AT is produced as an inactive precursor that matures upon posttranslational cleavage. The structure of a Cys103Ala precursor mutant shows that maturation is autoproteolytic, initiated by Cys103 cleaving its preceding peptide bond. The crystal structure of the mature enzyme shows that after autoproteolysis residues 92-102 fold outwards, exposing a buried pocket. This pocket is structurally and chemically flexible and can accommodate substrates of different size and polarity. Modeling of a substrate-bound state indicates the residues important for catalysis. Comparison of the proposed autoproteolytic and substrate hydrolysis mechanisms shows that in both events the same catalytic residues are used, but that they perform different roles in catalysis.
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Affiliation(s)
- Marcel Bokhove
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, Groningen, Netherlands
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26
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Gallastegui N, Groll M. The 26S proteasome: assembly and function of a destructive machine. Trends Biochem Sci 2010; 35:634-42. [PMID: 20541423 DOI: 10.1016/j.tibs.2010.05.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 05/06/2010] [Accepted: 05/11/2010] [Indexed: 11/29/2022]
Abstract
The heart of the ubiquitin-mediated degradation pathway, the 26S proteasome, endoproteolytically cleaves most intracellular proteins, thereby maintaining biological homeostasis and regulating many crucial processes in the cell. This hydrolyzing machine comprises more than 30 different subunits, which perform different functions including the recognition, unfolding, translocating and cleavage of protein substrates. Thus, careful assemblage and regulation of the 26S proteasome is essential to ensure correct positioning and function of each subunit, thereby preserving the delicate cellular balance between protein synthesis and degradation. Here, we review the most current research on the 26S proteasome assembly pathway, and describe the mechanism used by the cell to manage the complex structure and functions of the proteasome.
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Affiliation(s)
- Nerea Gallastegui
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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27
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Cho KJ, Kim JK, Lee JH, Shin HJ, Park SS, Kim KH. Structural features of cephalosporin acylase reveal the basis of autocatalytic activation. Biochem Biophys Res Commun 2009; 390:342-8. [PMID: 19800869 DOI: 10.1016/j.bbrc.2009.09.134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 09/30/2009] [Indexed: 10/20/2022]
Abstract
Cephalosporin acylase (CA), a member of the N-terminal nucleophile hydrolase family, is activated through two steps of intramolecular autoproteolysis, the first mediated by a serine residue, and the second by a glutamate, which releases the pro-segment and produces an active enzyme. In this study, we have determined the crystal structures of mutants which could affect primary or secondary auto-cleavage and of sequential intermediates of a slow-processing mutant at 2.0-2.5A resolutions. The pro-segments of the mutants undergo dynamic conformational changes during activation and adopt surprisingly different loop conformations from one another. However, the autoproteolytic site was found to form a catalytically competent conformation with a solvent water molecule, which was essentially conserved in the CA mutants.
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Affiliation(s)
- Ki Joon Cho
- Department of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea
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28
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Marques AJ, Palanimurugan R, Matias AC, Ramos PC, Dohmen RJ. Catalytic mechanism and assembly of the proteasome. Chem Rev 2009; 109:1509-36. [PMID: 19265443 DOI: 10.1021/cr8004857] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- António J Marques
- Institute for Genetics, University of Cologne, Zulpicher Strasse 47, D-50674 Cologne, Germany
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29
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Cuccioloni M, Montecchia F, Amici M, Mozzicafreddo M, Eleuteri AM, Angeletti M. Co-chaperonin GroES as a modulator of proteasomal activity. J Mol Recognit 2009; 22:46-54. [PMID: 19006106 DOI: 10.1002/jmr.929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The proteasome has a crucial part in the degradation of normal, damaged, mutant or misfolded proteins within both the ubiquitin ATP-dependent and the ubiquitin ATP-independent pathways. Proteasome-mediated proteolysis is modulated by diverse factors, and in this regard, chaperonins have been attracting great interest. The investigation on the role of a co-chaperonin, namely GroES, in the modulation of proteasomal activity was the focus of this work. Our study reports on an analytical approach based on combined fluorimetric, chromatographic (applied to the enzymatic activity evaluation), surface plasmon resonance techniques and molecular modelling, addressed to the assessment and characterization of the interaction. Globally, we described a high affinity interaction between GroES and two different 20 S (immuno- and constitutive) proteasomes, uncovering new scenarios on their possible physio-pathological role, specifically on the ability of proteasomes to interact both with unfolding and folding- assisting macromolecules.
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Affiliation(s)
- Massimiliano Cuccioloni
- Department of Molecular, Cellular and Animal Biology, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy.
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30
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Jung T, Grune T. The proteasome and its role in the degradation of oxidized proteins. IUBMB Life 2009; 60:743-52. [PMID: 18636510 DOI: 10.1002/iub.114] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The generation of free radicals and the resulting oxidative modification of cell structures are omnipresent in mammalian cells. This includes the permanent oxidation of proteins leading to the disruption of the protein structure and an impaired functionality. In consequence, these oxidized proteins have to be removed in order to prevent serious metabolic disturbances. The most important cellular proteolytic system responsible for the removal of oxidized proteins is the proteasomal system. For normal functioning, the proteasomal system needs the coordinated interaction of numerous components. This review describes the fundamental functions of the 20S "core" proteasome, its regulators, and the roles of the proteasomal system beyond the removal of oxidized proteins in mammalian cells.
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Affiliation(s)
- Tobias Jung
- Institute for Biological Chemistry and Nutrition, Biofunctionality and Food Safety (140f), University of Hohenheim, Stuttgart, Germany
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31
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Ekici OD, Paetzel M, Dalbey RE. Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration. Protein Sci 2008; 17:2023-37. [PMID: 18824507 DOI: 10.1110/ps.035436.108] [Citation(s) in RCA: 217] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Serine proteases comprise nearly one-third of all known proteases identified to date and play crucial roles in a wide variety of cellular as well as extracellular functions, including the process of blood clotting, protein digestion, cell signaling, inflammation, and protein processing. Their hallmark is that they contain the so-called "classical" catalytic Ser/His/Asp triad. Although the classical serine proteases are the most widespread in nature, there exist a variety of "nonclassical" serine proteases where variations to the catalytic triad are observed. Such variations include the triads Ser/His/Glu, Ser/His/His, and Ser/Glu/Asp, and include the dyads Ser/Lys and Ser/His. Other variations are seen with certain serine and threonine peptidases of the Ntn hydrolase superfamily that carry out catalysis with a single active site residue. This work discusses the structure and function of these novel serine proteases and threonine proteases and how their catalytic machinery differs from the prototypic serine protease class.
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Affiliation(s)
- Ozlem Doğan Ekici
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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32
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PACemakers of Proteasome Core Particle Assembly. Structure 2008; 16:1296-304. [DOI: 10.1016/j.str.2008.07.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 06/30/2008] [Accepted: 07/01/2008] [Indexed: 01/08/2023]
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33
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Michalska K, Hernandez-Santoyo A, Jaskolski M. The Mechanism of Autocatalytic Activation of Plant-type L-Asparaginases. J Biol Chem 2008; 283:13388-97. [DOI: 10.1074/jbc.m800746200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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34
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Sun Y, Guo HC. Structural constraints on autoprocessing of the human nucleoporin Nup98. Protein Sci 2008; 17:494-505. [PMID: 18287282 DOI: 10.1110/ps.073311808] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Nucleoporin Nup98, a 98-kDa protein component of the nuclear pore complex, plays an important role in both protein and RNA transport. During its maturation process, Nup98 undergoes post-translational autoproteolysis, which is critical for targeting to the NPC. Here we present high-resolution crystal structures of the C-terminal autoproteolytic domains of Nup98 (2.3 A for the wild type and 1.9 A for the S864A precursor), and propose a detailed autoproteolysis mechanism through an N-O acyl shift. Structural constraints are found at the autocleavage site, and could thus provide a driving force for autocleavage at the scissile peptide bond. Such structural constraints appear to be generated, at least in part, by anchoring a conserved phenylalanine side chain into a highly conserved hydrophobic pocket at the catalytic site. Our high-resolution crystal structures also reveal that three highly conserved residues, Tyr866, Gly867, and Leu868, provide most of the interactions between the autoproteolytic domain and the C-terminal tail. These results suggest that Nup98 may represent a new subtype of protein that utilizes autoprocessing to control biogenesis pathways and intracellular translocation.
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Affiliation(s)
- Yixin Sun
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118-2526, USA
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35
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Sandberg A, Johansson DG, Macao B, Härd T. SEA Domain Autoproteolysis Accelerated by Conformational Strain: Energetic Aspects. J Mol Biol 2008; 377:1117-29. [DOI: 10.1016/j.jmb.2008.01.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 12/28/2007] [Accepted: 01/18/2008] [Indexed: 11/25/2022]
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36
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Johansson DGA, Macao B, Sandberg A, Härd T. SEA domain autoproteolysis accelerated by conformational strain: mechanistic aspects. J Mol Biol 2008; 377:1130-43. [PMID: 18314133 DOI: 10.1016/j.jmb.2008.01.050] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 12/28/2007] [Accepted: 01/18/2008] [Indexed: 11/29/2022]
Abstract
A subclass of SEA (sea urchin sperm protein, enterokinase, and agrin) domain proteins undergoes autoproteolysis between glycine and serine in a conserved G(-1)S+1VVV motif to generate stable heterodimers. Autoproteolysis has been suggested to involve only the intramolecular catalytic action of the conserved serine hydroxyl in combination with conformational strain of the glycine-serine peptide bond. We conducted a number of experiments and simulations on the SEA domain from the MUC1 mucin to test this mechanism. Alanine-scanning mutagenesis of polar residues in the vicinity of the cleavage site demonstrates that only the nucleophile at position +1 is required for efficient proteolysis. Molecular modeling shows that an uncleaved trans peptide is incompatible with the native heterodimeric structure, resulting in disruption of secondary structure elements and distortion of the scissile peptide bond. Insertion of glycine residues (to obtain G(n)G(-1)S+1VVV motifs) appears to relieve strain, and autoproteolysis is 100 times slower in a 1G (n=1) mutant and not measurable in 2G and 4G mutants. Removal of the catalytic serine hydroxyl hampers cleavage considerably, but measurable autoproteolysis of this S1098A mutant still proceeds in the presence of strain alone. The uncleaved SEA precursor populates interconverting partially folded conformations, and autoproteolysis coincides with adoption of proper beta-sheet secondary structure and completed folding. Molecular dynamics simulations of the precursor show that the serine hydroxyl and the preceding glycine carbonyl carbon can be in van der Waals contact at the same time as the scissile peptide bond becomes strained. These observations are all consistent with autoproteolysis accelerated by N-->O acyl shift and conformational strain imposed upon protein folding in a reaction for which the free-energy barrier is decreased by substrate destabilization rather than by transition-state stabilization. The energetics of this coupled folding and autoproteolysis mechanism is accounted for in an accompanying article.
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Affiliation(s)
- Denny G A Johansson
- Department of Medical Biochemistry, Göteborg University, PO Box 440, SE-405 30 Göteborg, Sweden
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37
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Rho SH, Park HH, Kang GB, Im YJ, Kang MS, Lim BK, Seong IS, Seol J, Chung CH, Wang J, Eom SH. Crystal structure ofBacillus subtilis CodW, a noncanonical HslV-like peptidase with an impaired catalytic apparatus. Proteins 2008; 71:1020-6. [DOI: 10.1002/prot.21758] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Abstract
The majority of cellular proteins are degraded by proteasomes within the ubiquitin-proteasome ATP-dependent degradation pathway. Products of proteasomal activity are short peptides that are further hydrolysed by proteases to single amino acids. However, some peptides can escape this degradation, being selected and taken up by major histocompatibility complex (MHC) class I molecules for presentation to the immune system on the cell surface. MHC class I molecules are highly selective and specific in terms of ligand binding. Variability of peptides produced in living cells arises in a variety of ways, ensuring fast and efficient immune responses. Substitution of constitutive proteasomal subunits with immunosubunits leads to conformational changes in the substrate binding channels, resulting in a modified protein cleavage pattern and consequently in the generation of new antigenic peptides. The recently discovered event of proteasomal peptide splicing opens new horizons in the understanding of additional functions that proteasomes apparently possess. Whether peptide splicing is an occasional side product of proteasomal activity still needs to be clarified. Both gamma-interferon-induced immunoproteasomes and peptide splicing represent two significant events providing increased diversity of antigenic peptides for flexible and fine-tuned immune response.
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Affiliation(s)
- Ljudmila Borissenko
- Charité (CCM), Institut für Biochemie, AG Strukturforschung, Monbijoustrasse 2, D-10117 Berlin, Germany
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39
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Ong PL, Yao YF, Weng YM, Hsu WH, Lin LL. Residues Arg114 and Arg337 are critical for the proper function of Escherichia coli gamma-glutamyltranspeptidase. Biochem Biophys Res Commun 2007; 366:294-300. [PMID: 18036555 DOI: 10.1016/j.bbrc.2007.11.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Accepted: 11/08/2007] [Indexed: 11/16/2022]
Abstract
To evaluate the importance of conserved Arg114 and Arg337 residues of Escherichia coli gamma-glutamyltranspeptidase (EcGGT), Lys, Leu, or Asp-substituted mutants were constructed by site-directed mutagenesis. The wild-type and mutant enzymes were overexpressed in the recombinant E. coli M15 and purified by nickel-chelate chromatography to near homogeneity. With the exception of R114K, all the other mutants significantly lost GGT activity, confirming the importance of these two residues in EcGGT. Kinetic analysis of R114L, R114D, R337K, and R337L revealed a significant increase in K(m) with a minor change in k(cat), leading to more than an 8-fold decrease in k(cat)/K(m) values. Mutations of Arg337 impaired the capability of autocatalytic processing of the enzyme. In vitro maturation experiments revealed that EcGGT precursor mutants, pro-R337K and pro-R337L, could precede a time-dependent autocatalytic process to generate the small and large subunits, while no autocatalytic processing was observed in pro-R337D. Computer modeling showed that the critical bonding distance of Gln390 O-Thr391 HG1 and Gln390 C-Thr391 OG1 are significantly increased in Arg337 replacements, implying that these distance changes might be responsible for the lack of enzyme maturation.
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Affiliation(s)
- Ping-Lin Ong
- Department of Biochemical Science and Technology, National Chiayi University, 300 University Road, Chiayi, Taiwan
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40
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Towards the control of intracellular protein turnover: mitochondrial Lon protease inhibitors versus proteasome inhibitors. Biochimie 2007; 90:260-9. [PMID: 18021745 DOI: 10.1016/j.biochi.2007.10.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 10/19/2007] [Indexed: 01/21/2023]
Abstract
Cellular protein homeostasis results from the combination of protein biogenesis processes and protein quality control mechanisms, which contribute to the functional state of cells under normal and stress conditions. Proteolysis constitutes the final step by which short-lived, misfolded and damaged intracellular proteins are eliminated. Protein turnover and oxidatively modified protein degradation are mainly achieved by the proteasome in the cytosol and nucleus of eukaryotic cells while several ATP-dependent proteases including the matrix protease Lon take part in the mitochondrial protein degradation. Moreover, Lon protease seems to play a major role in the elimination of oxidatively modified proteins in the mitochondrial matrix. Specific inhibitors are commonly used to assess cellular functions of proteolytic systems as well as to identify their protein substrates. Here, we present and discuss known proteasome and Lon protease inhibitors. To date, very few inhibitors of Lon have been described and no specific inhibitors of this protease are available. The current knowledge on both catalytic mechanisms and inhibitors of these two proteases is first described and attempts to define specific non-peptidic inhibitors of the human Lon protease are presented.
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41
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Borissenko L, Groll M. 20S proteasome and its inhibitors: crystallographic knowledge for drug development. Chem Rev 2007; 107:687-717. [PMID: 17316053 DOI: 10.1021/cr0502504] [Citation(s) in RCA: 332] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ljudmila Borissenko
- Charité (CCM), Institut für Biochemie, AG Strukturforschung, Monbijoustrasse 2, 10117 Berlin, Germany
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42
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Okada T, Suzuki H, Wada K, Kumagai H, Fukuyama K. Crystal structure of the gamma-glutamyltranspeptidase precursor protein from Escherichia coli. Structural changes upon autocatalytic processing and implications for the maturation mechanism. J Biol Chem 2006; 282:2433-9. [PMID: 17135273 DOI: 10.1074/jbc.m607490200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gamma-glutamyltranspeptidase (GGT) is an extracellular enzyme that plays a key role in glutathione metabolism. The mature GGT is a heterodimer consisting of L- and S-subunits that is generated by posttranslational cleavage of the peptide bond between Gln-390 and Thr-391 in the precursor protein. Thr-391, which becomes the N-terminal residue of the S-subunit, acts as the active residue in the catalytic reaction. The crystal structure of a mutant GGT, T391A, that is unable to undergo autocatalytic processing, has been determined at 2.55-A resolution. Structural comparison of the precursor protein and mature GGT demonstrates that the structures of the core regions in the two proteins are unchanged, but marked differences are found near the active site. In particular, in the precursor, the segment corresponding to the C-terminal region of the L-subunit occupies the site where the loop (residues 438-449) forms the lid of the gamma-glutamyl group-binding pocket in the mature GGT. This result demonstrates that, upon cleavage of the N-terminal peptide bond of Thr-391, the newly produced C terminus (residues 375-390) flips out, allowing the 438-449 segment to form the gamma-glutamyl group-binding pocket. The electron density map for the T391A protein also identified a water molecule near the carbonyl carbon atom of Gln-390. The spatial arrangement around the water and Thr-391 relative to the scissile peptide bond appears suitable for the initiation of autocatalytic processing, as in other members of the N-terminal nucleophile hydrolase superfamily.
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Affiliation(s)
- Toshihiro Okada
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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43
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Witt S, Kwon YD, Sharon M, Felderer K, Beuttler M, Robinson CV, Baumeister W, Jap BK. Proteasome Assembly Triggers a Switch Required for Active-Site Maturation. Structure 2006; 14:1179-88. [PMID: 16843899 DOI: 10.1016/j.str.2006.05.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 04/20/2006] [Accepted: 05/02/2006] [Indexed: 11/15/2022]
Abstract
The processing of propeptides and the maturation of 20S proteasomes require the association of beta rings from two half proteasomes. We propose an assembly-dependent activation model in which interactions between helix (H3 and H4) residues of the opposing half proteasomes are prerequisite for appropriate positioning of the S2-S3 loop; such positioning enables correct coordination of the active-site residue needed for propeptide cleavage. Mutations of H3 or H4 residues that participate in the association of two half proteasomes inhibit activation and prevent, in nearly all cases, the formation of full proteasomes. In contrast, mutations affecting interactions with residues of the S2-S3 loop allow the assembly of full, but activity impacted, proteasomes. The crystal structure of the inactive H3 mutant, Phe145Ala, shows that the S2-S3 loop is displaced from the position observed in wild-type proteasomes. These data support the proposed assembly-dependent activation model in which the S2-S3 loop acts as an activation switch.
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Affiliation(s)
- Susanne Witt
- Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Martinsried 82152, Germany
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44
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Lin LL, Chou PR, Hua YW, Hsu WH. Overexpression, one-step purification, and biochemical characterization of a recombinant gamma-glutamyltranspeptidase from Bacillus licheniformis. Appl Microbiol Biotechnol 2006; 73:103-12. [PMID: 16850301 DOI: 10.1007/s00253-006-0440-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Revised: 03/18/2006] [Accepted: 03/23/2006] [Indexed: 10/24/2022]
Abstract
A truncated gene from Bacillus lichenifromis ATCC 27811 encoding a recombinant gamma-glutamyltranspeptidase (BLrGGT) was cloned into pQE-30 to generate pQE-BLGGT, and the overexpressed enzyme was purified from the crude extract of IPTG-induced E. coli M15 (pQE-BLGGT) to homogeneity by nickel-chelate chromatography. This protocol yielded over 25 mg of purified BLrGGT per liter of growth culture under optimum conditions. The molecular masses of the subunits of the purified enzyme were determined to be 41 and 22 kDa, respectively, by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The optimum pH and temperature for the recombinant enzyme were 6-8 and 40 degrees C, respectively. The chloride salt of metal ions Mg(2+), K(+), and Na(+) can activate BLrGGT, whereas that of Pb(2+) dramatically inhibited it. The substrate specificity study showed that L-gamma-glutamyl-p-nitroanilide (L-gamma-Glu-p-NA) is a preference for the enzyme. Steady-state kinetic study revealed that BLrGGT has a k (cat) of 105 s(-1) and a K (m) of 21 microM when using L-gamma-Glu-p-NA as the substrate. With this overexpression and purification system, BLrGGT can now be obtained in quantities necessary for structural characterization and synthesis of commercially important gamma-glutamyl compounds.
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Affiliation(s)
- Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, 300 University Road, Chiayi, Taiwan, 60083, Republic of China.
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45
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Hu G, Lin G, Wang M, Dick L, Xu RM, Nathan C, Li H. Structure of the Mycobacterium tuberculosis proteasome and mechanism of inhibition by a peptidyl boronate. Mol Microbiol 2006; 59:1417-28. [PMID: 16468986 DOI: 10.1111/j.1365-2958.2005.05036.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has the remarkable ability to resist killing by human macrophages. The 750 kDa proteasome, not available in most eubacteria except Actinomycetes, appears to contribute to Mtb's resistance. The crystal structure of the Mtb proteasome at 3.0 A resolution reveals a substrate-binding pocket with composite features of the distinct beta1, beta2 and beta5 substrate binding sites of eukaryotic proteasomes, accounting for the broad specificity of the Mtb proteasome towards oligopeptides described in the companion article [Lin et al. (2006), Mol Microbiol doi:10.1111/j.1365-2958.2005.05035.x]. The substrate entrance at the end of the cylindrical proteasome appears open in the crystal structure due to partial disorder of the alpha-subunit N-terminal residues. However, cryo-electron microscopy of the core particle reveals a closed end, compatible with the density observed in negative-staining electron microscopy that depended on the presence of the N-terminal octapetides of the alpha-subunits in the companion article, suggesting that the Mtb proteasome has a gated structure. We determine for the first time the proteasomal inhibition mechanism of the dipeptidyl boronate N-(4-morpholine)carbonyl-beta-(1-naphthyl)-L-alanine-L-leucine boronic acid (MLN-273), an analogue of the antimyeloma drug bortezomib. The structure improves prospects for designing Mtb-specific proteasomal inhibitors as a novel approach to chemotherapy of tuberculosis.
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Affiliation(s)
- Guiqing Hu
- Biology Department, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973, USA
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46
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Groll M, Huber R, Potts BCM. Crystal Structures of Salinosporamide A (NPI-0052) and B (NPI-0047) in Complex with the 20S Proteasome Reveal Important Consequences of β-Lactone Ring Opening and a Mechanism for Irreversible Binding. J Am Chem Soc 2006; 128:5136-41. [PMID: 16608349 DOI: 10.1021/ja058320b] [Citation(s) in RCA: 232] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structures of the yeast 20S proteasome core particle (CP) in complex with Salinosporamides A (NPI-0052; 1) and B (4) were solved at <3 angstroms resolution. Each ligand is covalently bound to Thr1O(gamma) via an ester linkage to the carbonyl derived from the beta-lactone ring of the inhibitor. In the case of 1, nucleophilic addition to the beta-lactone ring is followed by addition of C-3O to the chloroethyl group, giving rise to a cyclic ether. The crystal structures were compared to that of the omuralide/CP structure solved previously, and the collective data provide new insights into the mechanism of inhibition and irreversible binding of 1. Upon opening of the beta-lactone ring, C-3O assumes the position occupied by a water molecule in the unligated enzyme and hinders deacylation of the enzyme-ligand complex. Furthermore, the resulting protonation state of Thr1NH2 deactivates the catalytic N-terminus.
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Affiliation(s)
- Michael Groll
- Ludwig-Maximilians-University of Munich, Butenandtstr. 5, Building B, 81377 Munich, Germany.
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47
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Groll M, Larionov OV, Huber R, de Meijere A. Inhibitor-binding mode of homobelactosin C to proteasomes: new insights into class I MHC ligand generation. Proc Natl Acad Sci U S A 2006; 103:4576-9. [PMID: 16537370 PMCID: PMC1450213 DOI: 10.1073/pnas.0600647103] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most class I MHC ligands are generated from the vast majority of cellular proteins by proteolysis within the ubiquitin-proteasome pathway and are presented on the cell surface by MHC class I molecules. Here, we present the crystallographic analysis of yeast 20S proteasome in complex with the inhibitor homobelactosin C. The structure reveals a unique inhibitor-binding mode and provides information about the composition of proteasomal primed substrate-binding sites. IFN-gamma inducible substitution of proteasomal constitutive subunits by immunosubunits modulates characteristics of generated peptides, thus producing fragments with higher preference for binding to MHC class I molecules. The structural data for the proteasome:homobelactosin C complex provide an explanation for involvement of immunosubunits in antigen generation and open perspectives for rational design of ligands, inhibiting exclusively constitutive proteasomes or immunoproteasomes.
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Affiliation(s)
- Michael Groll
- *Ludwig Maximilians Universität, Adolf Butenandt Institut, Butenandtstrasse 5, Gebäude B, D-81377 Munich, Germany
| | - Oleg V. Larionov
- Institut für Organische und Biomolekulare Chemie, Tammannstrasse 2, D-37077 Göttingen, Germany
| | - Robert Huber
- Max Planck Institut für Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany; and
- Technische Universität München, D-85747 Garching, Germany
| | - Armin de Meijere
- Institut für Organische und Biomolekulare Chemie, Tammannstrasse 2, D-37077 Göttingen, Germany
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48
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Kim JK, Yang IS, Shin HJ, Cho KJ, Ryu EK, Kim SH, Park SS, Kim KH. Insight into autoproteolytic activation from the structure of cephalosporin acylase: a protein with two proteolytic chemistries. Proc Natl Acad Sci U S A 2006; 103:1732-7. [PMID: 16446446 PMCID: PMC1413634 DOI: 10.1073/pnas.0507862103] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Indexed: 11/18/2022] Open
Abstract
Cephalosporin acylase (CA), a member of the N-terminal nucleophile hydrolase family, is activated through sequential primary and secondary autoproteolytic reactions with the release of a pro segment. We have determined crystal structures of four CA mutants. Two mutants are trapped after the primary cleavage, and the other two undergo secondary cleavage slowly. These structures provide a look at pro-segment conformation during activation in N-terminal nucleophile hydrolases. The highly strained helical pro segment of precursor is transformed into a relaxed loop in the intermediates, suggesting that the relaxation of structural constraints drives the primary cleavage reaction. The secondary autoproteolytic step has been proposed to be intermolecular. However, our analysis provides evidence that CA is processed in two sequential steps of intramolecular autoproteolysis involving two distinct residues in the active site, the first a serine and the second a glutamate.
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Affiliation(s)
- Jin Kwang Kim
- *Department of Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, and
| | - In Seok Yang
- *Department of Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, and
| | - Hye Jeong Shin
- Department of Bio-Microsystem Technology, Korea University, Seoul 136-701, Korea; and
| | - Ki Joon Cho
- *Department of Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, and
| | - Eui Kyung Ryu
- *Department of Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, and
| | - Sun Hwa Kim
- *Department of Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, and
| | - Sung Soo Park
- *Department of Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, and
| | - Kyung Hyun Kim
- Department of Bio-Microsystem Technology, Korea University, Seoul 136-701, Korea; and
- Department of Biotechnology, College of Science and Technology, Korea University, Jochiwon 339-700, Korea
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49
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Groll M, Bochtler M, Brandstetter H, Clausen T, Huber R. Molecular machines for protein degradation. Chembiochem 2005; 6:222-56. [PMID: 15678420 DOI: 10.1002/cbic.200400313] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
One of the most precisely regulated processes in living cells is intracellular protein degradation. The main component of the degradation machinery is the 20S proteasome present in both eukaryotes and prokaryotes. In addition, there exist other proteasome-related protein-degradation machineries, like HslVU in eubacteria. Peptides generated by proteasomes and related systems can be used by the cell, for example, for antigen presentation. However, most of the peptides must be degraded to single amino acids, which are further used in cell metabolism and for the synthesis of new proteins. Tricorn protease and its interacting factors are working downstream of the proteasome and process the peptides into amino acids. Here, we summarise the current state of knowledge about protein-degradation systems, focusing in particular on the proteasome, HslVU, Tricorn protease and its interacting factors and DegP. The structural information about these protein complexes opens new possibilities for identifying, characterising and elucidating the mode of action of natural and synthetic inhibitors, which affects their function. Some of these compounds may find therapeutic applications in contemporary medicine.
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Affiliation(s)
- Michael Groll
- Adolf-Butenandt-Institut Physiological Chemistry, LMU München, Butenandtstrasse 5, Gebäude B, 81377 München, Germany.
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50
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Groll M, Huber R. Inhibitors of the eukaryotic 20S proteasome core particle: a structural approach. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1695:33-44. [PMID: 15571807 DOI: 10.1016/j.bbamcr.2004.09.025] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The ubiquitin-proteasome pathway is particularly important for the regulated degradation of various proteins which control a vast array of biological processes. Therefore, proteasome inhibitors are promising candidates for anti-tumoral or anti-inflammatory drugs. N-Acetyl-Leu-Leu-Norleucinal (Ac-LLN-al, also termed calpain inhibitor I) was one of the first proteasome inhibitors discovered and has been widely used to study the 20S proteasome core particle (CP) function in vivo, despite its lack of specificity. Vinyl sulfones, like Ac-PRLN-vs, show covalent binding of the beta-carbon atom of the vinyl sulfone group to the Thr1Ogamma only of subunit beta2. However, vinyl sulfones have similar limitations as peptide aldehydes as they have been reported also to bind and block intracellular cysteine proteases. A more specific proteasome inhibitor is the natural product lactacystin, which can be isolated from Streptomyces. It was found that this compound forms an ester bond only to the Thr1Ogamma of the chymotrypsin-like active subunit beta5 due to specific P1 interactions. In contrast to most other proteasome inhibitors, the natural alpha',beta'-epoxyketone peptide epoxomicin binds specifically to the small class of N-terminal nucleophilic (Ntn) hydrolases (CPs belong to this protease family) with the formation of a morpholino adduct. All previously described proteasome inhibitors bind covalently to the proteolytic active sites. However, as the proteasome is involved in a variety of biological important functions, it is of particular interest to block the CP only for limited time in order to reduce cytotoxic effects. Recently, the binding mode of the natural specific proteasome inhibitor TMC-95 obtained from Apiospora montagnei was investigated. The crystal structure revealed that the TMC-95 blocks the active sites of the CP noncovalently in the low nanomolar range. This review summarizes the current structural knowledge of inhibitory compounds bound to the CP, showing the proteasome as a potential target for drug development in medical research.
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Affiliation(s)
- Michael Groll
- Abteilung für Physiologische Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 München, Germany.
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