Conversion of functionally undefined homopentameric protein PbaA into a proteasome activator by mutational modification of its C-terminal segment conformation

Published on Jan 1, 2018in Protein Engineering Design & Selection 1.88
· DOI :10.1093/protein/gzx066
Maho Yagi-Utsumi6
Estimated H-index: 6
(Nagoya City University),
Arunima Sikdar2
Estimated H-index: 2
(Graduate University for Advanced Studies)
+ 6 AuthorsKoichi Kato52
Estimated H-index: 52
(Nagoya City University)
  • References (18)
  • Citations (2)
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References18
Published on Sep 1, 2007in Molecular Cell 14.25
David M. Smith31
Estimated H-index: 31
(Harvard University),
Shih-Chung Chang8
Estimated H-index: 8
(Harvard University)
+ 3 AuthorsAlfred L. Goldberg132
Estimated H-index: 132
(Harvard University)
Summary The 20S proteasome functions in protein degradation in eukaryotes together with the 19S ATPases or in archaea with the homologous PAN ATPase complex. These ATPases contain a conserved C-terminal hydrophobic-tyrosine-X motif (HbYX). We show that these residues are essential for PAN to associate with the 20S and open its gated channel for substrate entry. Upon ATP binding, these C-terminal residues bind to pockets between the 20S's α subunits. Seven-residue or longer peptides from PAN's C ...
342 Citations Source Cite
Published on Apr 28, 1995in Science 41.06
Jan Löwe59
Estimated H-index: 59
,
Daniela Stock14
Estimated H-index: 14
+ 3 AuthorsRobert Huber132
Estimated H-index: 132
The three-dimensional structure of the proteasome from the archaebacterium Thermoplasma acidophilum has been elucidated by x-ray crystallographic analysis by means of isomorphous replacement and cyclic averaging. The atomic model was built and refined to a crystallographic R factor of 22.1 percent. The 673-kilodalton protease complex consists of 14 copies of two different subunits, alpha and beta, forming a barrel-shaped structure of four stacked rings. The two inner rings consist of seven beta ...
1,219 Citations Source Cite
Published on Apr 1, 1993in Journal of Applied Crystallography 3.42
Roman A. Laskowski43
Estimated H-index: 43
,
Malcolm W. MacArthur20
Estimated H-index: 20
+ 1 AuthorsJanet M. Thornton116
Estimated H-index: 116
The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure. Its outputs comprise a number of plots in PostScript format and a comprehensive residue-by-residue listing. These give an assessment of the overall quality of the structure as compared with well refined structures of the same resolution and also highlight regions that may need further investigation. The PROCHECK programs are useful for assessing the quality not only of protein structures in th...
17.3k Citations Source Cite
Published on Feb 1, 1998in Cell 31.40
Wolfgang Baumeister92
Estimated H-index: 92
,
J. Walz24
Estimated H-index: 24
+ 1 AuthorsErika Seemüller13
Estimated H-index: 13
(Max Planck Society)
The work of one of us (W. B.) was supported by a grant of the Human Frontiers Science Program. We wish to thank Drs. C. P. Hill (Salt Lake City) and J. M. Flanagan (Brookhaven) for making available to us structural data prior to publication. We are grateful to Drs. F. U. Hartl and M. Kania for critically reading the manuscript.
1,214 Citations Source Cite
Published on Nov 1, 2008in Progress in Surface Science 9.00
Toshio Ando40
Estimated H-index: 40
(Kanazawa University),
Takayuki Uchihashi35
Estimated H-index: 35
(Kanazawa University),
Takeshi Fukuma24
Estimated H-index: 24
(Kanazawa University)
The atomic force microscope (AFM) has a unique capability of allowing the high-resolution imaging of biological samples on substratum surfaces in physiological solutions. Recent technological progress of AFM in biological research has resulted in remarkable improvements in both the imaging rate and the tip force acting on the sample. These improvements have enabled the direct visualization of dynamic structural changes and dynamic interactions occurring in individual biological macromolecules, w...
307 Citations Source Cite
Published on May 1, 2002in Structure 4.91
Masaki Unno14
Estimated H-index: 14
(Osaka University),
Tsunehiro Mizushima9
Estimated H-index: 9
(Osaka University)
+ 4 AuthorsTomitake Tsukihara45
Estimated H-index: 45
(Osaka University)
Abstract The 20S proteasome is the catalytic portion of the 26S proteasome. Constitutively expressed mammalian 20S proteasomes have three active subunits, β1, β2, and β5, which are replaced in the immunoproteasome by interferon-γ-inducible subunits β1i, β2i, and β5i, respectively. Here we determined the crystal structure of the bovine 20S proteasome at 2.75 A resolution. The structures of α2, β1, β5, β6, and β7 subunits of the bovine enzyme were different from the yeast enzyme but enabled the bo...
377 Citations Source Cite
Published on Feb 1, 2007in Nature 41.58
Remco Sprangers24
Estimated H-index: 24
(University of Toronto),
Lewis E. Kay97
Estimated H-index: 97
(University of Toronto)
The machinery used by the cell to perform essential biological processes is made up of large molecular assemblies. One such complex, the proteasome, is the central molecular machine for removal of damaged and misfolded proteins from the cell. Here we show that for the 670-kilodalton 20S proteasome core particle it is possible to overcome the molecular weight limitations that have traditionally hampered quantitative nuclear magnetic resonance (NMR) spectroscopy studies of such large systems. This...
327 Citations Source Cite
Published on Feb 1, 2009in Nature Reviews Molecular Cell Biology 35.61
Shigeo Murata45
Estimated H-index: 45
(University of Tokyo),
Hideki Yashiroda16
Estimated H-index: 16
(University of Tokyo),
Keiji Tanaka119
Estimated H-index: 119
The 26S proteasome is a large protein complex that consists of a catalytic 20S core and a 19S regulatory particle, each of which contains numerous subunits. Proteasome-dedicated chaperones guarantee the efficient and correct assembly of this degradation machine, which is essential for its function.
332 Citations Source Cite
Garib N. Murshudov40
Estimated H-index: 40
,
A.A. Vagin8
Estimated H-index: 8
,
Eleanor J. Dodson54
Estimated H-index: 54
This paper reviews the mathematical basis of maximum likelihood. The likelihood function for macromolecular structures is extended to include prior phase information and experimental standard uncertainties. The assumption that different parts of a structure might have different errors is considered. A method for estimating σA using `free' reflections is described and its effects analysed. The derived equations have been implemented in the program REFMAC. This has been tested on several proteins ...
11.5k Citations Source Cite
Arunima Sikdar2
Estimated H-index: 2
(Nagoya City University),
Tadashi Satoh14
Estimated H-index: 14
(Nagoya City University)
+ 1 AuthorsKoichi Kato52
Estimated H-index: 52
(Nagoya City University)
Abstract Formation of the eukaryotic proteasome is not a spontaneous process but a highly ordered process assisted by several assembly chaperones. In contrast, archaeal proteasome subunits can spontaneously assemble into an active form. Recent bioinformatic analysis identified the proteasome-assembly chaperone-like proteins, PbaA and PbaB, in archaea. Our previous study showed that the PbaB homotetramer functions as a proteasome activator through its tentacle-like C-terminal segments. However, a...
4 Citations Source Cite
  • References (18)
  • Citations (2)
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Cited By2
Published on Dec 14, 2017in Biophysical Reviews
Koichi Kato52
Estimated H-index: 52
(Nagoya City University),
Tadashi Satoh14
Estimated H-index: 14
(Nagoya City University)
Molecular organization in biological systems comprises elaborately programmed processes involving metastable complex formation of biomolecules. This is exemplified by the formation of the proteasome, which is one of the largest and most complicated biological supramolecular complexes. This biomolecular machinery comprises approximately 70 subunits, including structurally homologous, but functionally distinct, ones, thereby exerting versatile proteolytic functions. In eukaryotes, proteasome forma...
1 Citations Source Cite
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