Architecture and Assembly of the 19S Proteasome Regulatory Particle
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The Proteasome: a Proteolytic Nanomachine of Cell Regulation and Waste Disposal
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1695 (2004) 19–31 http://www.elsevier.com/locate/bba Review The proteasome: a proteolytic nanomachine of cell regulation and waste disposal Dieter H. Wolf *, Wolfgang Hilt Institut fu¨r Biochemie, Universita¨t Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany Available online 26 October 2004 Abstract The final destination of the majority of proteins that have to be selectively degraded in eukaryotic cells is the proteasome, a highly sophisticated nanomachine essential for life. 26S proteasomes select target proteins via their modification with polyubiquitin chains or, in rare cases, by the recognition of specific motifs. They are made up of different subcomplexes, a 20S core proteasome harboring the proteolytic active sites hidden within its barrel-like structure and two 19S caps that execute regulatory functions. Similar complexes equipped with PA28 regulators instead of 19S caps are a variation of this theme specialized for the production of antigenic peptides required in immune response. Structure analysis as well as extensive biochemical and genetic studies of the 26S proteasome and the ubiquitin system led to a basic model of substrate recognition and degradation. Recent work raised new concepts. Additional factors involved in substrate acquisition and delivery to the proteasome have been discovered. Moreover, first insights in the tasks of individual subunits or subcomplexes of the 19S caps in substrate recognition and binding as well as release and recycling of polyubiquitin tags have been obtained. D 2004 Elsevier B.V. All rights reserved. -
Recent Advances in the Structural Biology of the 26S Proteasome
The International Journal of Biochemistry & Cell Biology 79 (2016) 437–442 Contents lists available at ScienceDirect The International Journal of Biochemistry & Cell Biology jo urnal homepage: www.elsevier.com/locate/biocel Review article Recent advances in the structural biology of the 26S proteasome ∗ Marc Wehmer, Eri Sakata Department of Molecular Structural Biology, Max Planck institute of Biochemistry, 82152, Martinsried, Germany a r t i c l e i n f o a b s t r a c t Article history: There is growing appreciation for the fundamental role of structural dynamics in the function of macro- Received 28 June 2016 molecules. In particular, the 26S proteasome, responsible for selective protein degradation in an ATP Received in revised form 2 August 2016 dependent manner, exhibits dynamic conformational changes that enable substrate processing. Recent Accepted 3 August 2016 cryo-electron microscopy (cryo-EM) work has revealed the conformational dynamics of the 26S protea- Available online 4 August 2016 some and established the function of the different conformational states. Technological advances such as direct electron detectors and image processing algorithms allowed resolving the structure of the pro- Keywords: teasome at atomic resolution. Here we will review those studies and discuss their contribution to our 26S proteasome understanding of proteasome function. Cryoelectron microscopy © 2016 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND Single particle analysis Structural biology license (http://creativecommons.org/licenses/by-nc-nd/4.0/). AAA+ ATPase Contents 1. Introduction . 437 2. Structural dynamics of the 26S proteasome . 438 3. Mechanical insights into the proteasome . -
Topological Distribution of Four-A-Helix Bundles (Folding Motif/Solvent Accessibility/Helix Dipole) SCOTT R
Proc. NatI. Acad. Sci. USA Vol. 86, pp. 6592-6596, September 1989 Biochemistry Topological distribution of four-a-helix bundles (folding motif/solvent accessibility/helix dipole) SCOTT R. PRESNELL* AND FRED E. COHEN*t Departments of *Pharmaceutical Chemistry and tMedicine, University of California, San Francisco, San Francisco, CA 94143-0446 Communicated by Frederic M. Richards, June 19, 1989 ABSTRACT The four-a-helix bundle, a common struc- suggest a set of bundle structures beyond those initially tural motif in globular proteins, provides an excellent forum for reviewed by Weber and Salemme (8). Further, we will the examination of predictive constraints for protein backbone describe robust topological characterizations and categori- topology. An exhaustive examination of the Brookhaven Crys- zations of the discovered structures. In light of our catego- tallographic Protein Data Bank and other literature sources has rization scheme, the past and current topological constraints lead to the discovery of 20 putative four-a-helix bundles. used for the prediction of protein structures containing four- Application of an analytical method that examines the differ- a-helix bundles are reevaluated. ence between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list ofbundles METHODS to 13. In 12 of these bundles, all pairs of neighboring helices To locate putative four-a-helix bundles, two independent were oriented in an anti-parallel fashion. This distribution is in observers employed the graphical display program MIDAS accordance with structure types expected if the helix macro (11) to inspect more than 300 globular protein structures from dipole effect makes a substantial contribution to the stability of the Brookhaven Protein Data Bank (12) (November 14, 1988). -
Supplemental Methods
Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection. -
B Number Gene Name Mrna Intensity Mrna
sample) total list predicted B number Gene name assignment mRNA present mRNA intensity Gene description Protein detected - Membrane protein membrane sample detected (total list) Proteins detected - Functional category # of tryptic peptides # of tryptic peptides # of tryptic peptides detected (membrane b0002 thrA 13624 P 39 P 18 P(m) 2 aspartokinase I, homoserine dehydrogenase I Metabolism of small molecules b0003 thrB 6781 P 9 P 3 0 homoserine kinase Metabolism of small molecules b0004 thrC 15039 P 18 P 10 0 threonine synthase Metabolism of small molecules b0008 talB 20561 P 20 P 13 0 transaldolase B Metabolism of small molecules chaperone Hsp70; DNA biosynthesis; autoregulated heat shock b0014 dnaK 13283 P 32 P 23 0 proteins Cell processes b0015 dnaJ 4492 P 13 P 4 P(m) 1 chaperone with DnaK; heat shock protein Cell processes b0029 lytB 1331 P 16 P 2 0 control of stringent response; involved in penicillin tolerance Global functions b0032 carA 9312 P 14 P 8 0 carbamoyl-phosphate synthetase, glutamine (small) subunit Metabolism of small molecules b0033 carB 7656 P 48 P 17 0 carbamoyl-phosphate synthase large subunit Metabolism of small molecules b0048 folA 1588 P 7 P 1 0 dihydrofolate reductase type I; trimethoprim resistance Metabolism of small molecules peptidyl-prolyl cis-trans isomerase (PPIase), involved in maturation of b0053 surA 3825 P 19 P 4 P(m) 1 GenProt outer membrane proteins (1st module) Cell processes b0054 imp 2737 P 42 P 5 P(m) 5 GenProt organic solvent tolerance Cell processes b0071 leuD 4770 P 10 P 9 0 isopropylmalate -
Structural Plasticity of 4-Α-Helical Bundles Exemplified by the Puzzle-Like Molecular Assembly of the Rop Protein
Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein Maria Amprazia,b, Dina Kotsifakib, Mary Providakib, Evangelia G. Kapetanioub, Georgios Fellasa, Ioannis Kyriazidisa, Javier Pérezc, and Michael Kokkinidisa,b,1 aDepartment of Biology, University of Crete, GR 71409 Heraklion, Crete, Greece; bInstitute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR 70013 Heraklion, Crete, Greece; and cSynchrotron SOLEIL, 91192 Gif-sur-Yvette, France Edited by José N. Onuchic, Rice University, Houston, TX, and approved June 20, 2014 (received for review December 12, 2013) The dimeric Repressor of Primer (Rop) protein, a widely used “loopless” mutant, the α-helical hairpin of the monomer is model system for the study of coiled-coil 4-α-helical bundles, is converted into a single helix (15, 16). The complete LLR mol- characterized by a remarkable structural plasticity. Loop region ecule is a tetramer that is completely reorganized relative to the mutations lead to a wide range of topologies, folding states, dimeric wild-type (WT) Rop, thereby becoming a hyper-ther- and altered physicochemical properties. A protein-folding study mostable protein (16). On the other hand, establishment of an of Rop and several loop variants has identified specific residues uninterrupted heptad periodicity through a two-residue insertion and sequences that are linked to the observed structural plasticity. in the loop produces minimal changes relative to WT in terms of Apart from the native state, native-like and molten-globule states structure and properties (12). Thus, these two mutants with have been identified; these states are sensitive to reducing agents uninterrupted patterns of heptads reveal that there is a consid- due to the formation of nonnative disulfide bridges. -
Principles of Helix-Helix Packing in Proteins: the Helical Lattice Superposition Model Dirk Walther1*, Frank Eisenhaber1,2 and Patrick Argos1
J. Mol. Biol. (1996) 255, 536–553 Principles of Helix-Helix Packing in Proteins: The Helical Lattice Superposition Model Dirk Walther1*, Frank Eisenhaber1,2 and Patrick Argos1 1European Molecular Biology The geometry of helix-helix packing in globular proteins is comprehen- Laboratory, Meyerhofstraße 1 sively analysed within the model of the superposition of two helix lattices Postfach 10.2209, 69012 which result from unrolling the helix cylinders onto a plane containing Heidelberg, Germany points representing each residue. The requirements for the helix geometry (the radius R, the twist angle v and the rise per residue D) under perfect 2Biochemisches Institut der match of the lattices are studied through a consistent mathematical model Charite´, der Humboldt- that allows consideration of all possible associations of all helix types (a-, Universita¨t zu Berlin, p- and 310). The corresponding equations have three well-separated Hessische Straße 3–4 10115 solutions for the interhelical packing angle, V, as a function of the helix Berlin, Germany geometric parameters allowing optimal packing. The resulting functional relations also show unexpected behaviour. For a typically observed a-helix ° − ° (v = 99.1 , D = 1.45 Å), the three optimal packing angles are Va,b,c = 37.1 , −97.4° and +22.0° with a periodicity of 180° and respective helix radii Ra,b,c = 3.0 Å, 3.5 Å and 4.3 Å. However, the resulting radii are very sensitive ° to variations in the twist angle v. At vtriple = 96.9 , all three solutions yield identical radii at D = 1.45 Å where Rtriple = 3.46 Å. This radius is close to that of a poly(Ala) helix, indicating a great packing flexibility when alanine is involved in the packing core, and vtriple is close to the mean observed twist angle. -
(12) Patent Application Publication (10) Pub. No.: US 2006/0110747 A1 Ramseier Et Al
US 200601 10747A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2006/0110747 A1 Ramseier et al. (43) Pub. Date: May 25, 2006 (54) PROCESS FOR IMPROVED PROTEIN (60) Provisional application No. 60/591489, filed on Jul. EXPRESSION BY STRAIN ENGINEERING 26, 2004. (75) Inventors: Thomas M. Ramseier, Poway, CA Publication Classification (US); Hongfan Jin, San Diego, CA (51) Int. Cl. (US); Charles H. Squires, Poway, CA CI2O I/68 (2006.01) (US) GOIN 33/53 (2006.01) CI2N 15/74 (2006.01) Correspondence Address: (52) U.S. Cl. ................................ 435/6: 435/7.1; 435/471 KING & SPALDING LLP 118O PEACHTREE STREET (57) ABSTRACT ATLANTA, GA 30309 (US) This invention is a process for improving the production levels of recombinant proteins or peptides or improving the (73) Assignee: Dow Global Technologies Inc., Midland, level of active recombinant proteins or peptides expressed in MI (US) host cells. The invention is a process of comparing two genetic profiles of a cell that expresses a recombinant (21) Appl. No.: 11/189,375 protein and modifying the cell to change the expression of a gene product that is upregulated in response to the recom (22) Filed: Jul. 26, 2005 binant protein expression. The process can improve protein production or can improve protein quality, for example, by Related U.S. Application Data increasing solubility of a recombinant protein. Patent Application Publication May 25, 2006 Sheet 1 of 15 US 2006/0110747 A1 Figure 1 09 010909070£020\,0 10°0 Patent Application Publication May 25, 2006 Sheet 2 of 15 US 2006/0110747 A1 Figure 2 Ester sers Custer || || || || || HH-I-H 1 H4 s a cisiers TT closers | | | | | | Ya S T RXFO 1961. -
Structural and Mechanistic Characterization of the Bacterial Proteasome-Related Proteins Bpa and Dop
Research Collection Doctoral Thesis Structural and Mechanistic Characterization of the Bacterial Proteasome-related Proteins Bpa and Dop Author(s): Bolten, Marcel Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010814710 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 23817 STRUCTURAL AND MECHANISTIC CHARACTERIZATION OF THE BACTERIAL PROTEASOME-RELATED PROTEINS BPA AND DOP A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by MARCEL BOLTEN M.Sc. in Chemical Biology, TU Dortmund born on 25.07.1986 citizen of Germany accepted on the recommendation of Prof. Dr. Eilika Weber-Ban Prof. Dr. Rudi Glockshuber Prof. Dr. Donald Hilvert 2016 Chapter3 of this thesis has appeared in the following publication: Bolten, M.1; Delley, C.L.1; Leibundgut, M.; Boehringer, D.; Ban, N. & Weber-Ban, E. Structural analysis of the bacterial proteasome activator Bpa in complex with the 20S proteasome. Structure 2016, 24, 2138–2151 doi: 10.1016/j.str.2016.10.008 1contributed equally Zusammenfassung Proteinhomöostase ist ein fundamentaler Prozess des Lebens und beschreibt die Kontrolle der Proteinkonzentrationen und der Funktionalität des Proteoms in le- benden Zellen. Ein wichtiger Aspekt dieses Kontrollprozesses ist der Proteinabbau, bei welchem Proteasen selektiv beschädigte oder nicht länger benötigte Proteine verdauen. Diese Aufgabe wird üblicherweise von kompartmentalisierenden Pro- teasekomplexen übernommen, die abgeschlossene Abbaukompartimente mit Zu- gangskontrolle besitzen, wodurch deren proteolytische Aktivität gegenüber dem Zytosol abgeschottet ist. -
Das Proteasomsystem
4. Literaturverzeichnis Apcher GS, Maitland J, Dawson S, Sheppard P, Mayer RJ (2004) The alpha4 and alpha7 subunits and assembly of the 20S proteasome. FEBS Lett. 569(1-3):211-6. Aki M, Shimbara N, Takashina M, Akiyama K, Kagawa S, Tamura T, Tanahashi N, Yoshimura T, Tanaka K, Ichihara A (1994) Interferon-gamma induces different subunit organizations and functional diversity of proteasomes. J Biochem (Tokyo) 115:257-269 Bienkowska JR, Hartman H, Smith TF. (2003) A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells? Protein Eng. 16(12):897-904. Bochtler M, Ditzel L, Groll M, Hartmann C, Huber R (1999) The proteasome. Annu Rev Biophys Biomol Struct, 28, 295-317. Bochtler M, Hartmann C, Song HK, Bourenkov GP, Bartunik HD, Huber R (2000) The structures of HslU and the ATP-dependent protease HslU-HslV. Nature 403, 800-805. Branninigan JA, Dodson G, Duggleby HJ, Moody PC, Smith JL, Tomchick, DR, Murzin AG (1995) A protein catalytic framework with an N-terminal nucleophile is capable of self- activation. Nature 378:414–419 Braun BC, Glickman M, Kraft R, Dahlmann B, Kloetzel PM, Finley D, Schmidt M. (1999) The base of the proteasome regulatory particle exhibits chaperone-like activity. Nat Cell Biol. 1(4):221-6. Brotz-Oesterhelt H, Beyer D, Kroll HP, Endermann R, Ladel C, Schroeder W, Hinzen B, Raddatz S, Paulsen H, Henninger K, Bandow JE, Sahl HG, Labischinski H. (2005) Dysregulation of bacterial proteolytic machinery by a new class of antibiotics. Nat Med. 11(10):1082-7. Bukau, B. (1997) The heat shock response in Escherichia coli. -
Structural Basis for the Alternating Access Mechanism of the Cation Diffusion Facilitator Yiip
Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP Maria Luisa Lopez-Redondoa,1, Nicolas Coudraya,1, Zhening Zhanga,2, John Alexopoulosa, and David L. Stokesa,3 aSkirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016 Edited by Robert M. Stroud, University of California, San Francisco, CA, and approved January 31, 2018 (received for review August 24, 2017) YiiP is a dimeric antiporter from the cation diffusion facilitator representatives. Both superfamilies are characterized by internal family that uses the proton motive force to transport Zn2+ across sequence repeats which fold into two distinct domains. The con- bacterial membranes. Previous work defined the atomic structure of formational changes from IF to OF states are described as either + an outward-facing conformation, the location of several Zn2 bind- rocking-bundle or elevator-like movements of one domain relative ing sites, and hydrophobic residues that appear to control access to to the other, and these movements typically involve coordinated, the transport sites from the cytoplasm. A low-resolution cryo-EM symmetric structural changes in the respective repeats (15–17). structure revealed changes within the membrane domain that were CDF transporters, however, do not have an obvious sequence associated with the alternating access mechanism for transport. In repeat, and although many are reported to form homodimers, an the current work, the resolution of this cryo-EM structure has been X-ray structure of YiiP shows that independent transport sites are extended to 4.1 Å. Comparison with the X-ray structure defines the present within each monomer (18, 19). -
Implications for Proteasome Nuclear Localization Revealed by the Structure of the Nuclear Proteasome Tether Protein Cut8
Implications for proteasome nuclear localization revealed by the structure of the nuclear proteasome tether protein Cut8 Kojiro Takedaa, Nam K. Tonthatb, Tiffany Gloverc, Weijun Xuc, Eugene V. Koonind, Mitsuhiro Yanagidaa, and Maria A. Schumacherb,1 aG0 Cell Unit; Okinawa Institute of Science and Technology (OIST); 1919-1 Tancha, Onna, Okinawa, Japan; bDepartment of Biochemistry, Duke University Medical Center, Room 243A Nanaline H. Duke Building, Box 3711, Durham, NC 27710; cDepartment of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Unit 1000, Houston, TX 77030; and dNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892 Edited by Axel T. Brunger, Stanford University, Stanford, CA, and approved August 29, 2011 (received for review March 7, 2011) Degradation of nuclear proteins by the 26S proteasome is essential ultimately found to be a delay in the destruction of the mitotic for cell viability. In yeast, the nuclear envelope protein Cut8 med- cyclin and securin (13). However, the polyubiquitination of these iates nuclear proteasomal sequestration by an uncharacterized proteins was normal, suggesting a role for the proteasome. Sub- mechanism. Here we describe structures of Schizosaccharomyces sequent studies showed that Cut8 is responsible for sequestering pombe Cut8, which shows that it contains a unique, modular the 26S proteasome to the nucleus (10, 11). Cut8 was found to be fold composed of an extended N-terminal, lysine-rich segment localized to the nuclear envelope and overlapping the location that when ubiquitinated binds the proteasome, a dimer domain of the proteasome (17–21). An interaction between Cut8 and followed by a six-helix bundle connected to a flexible C tail.