Literature DB >> 22232170

Crystallization and preliminary neutron diffraction studies of ADP-ribose pyrophosphatase-I from Thermus thermophilus HB8.

Nobuo Okazaki1, Motoyasu Adachi, Taro Tamada, Kazuo Kurihara, Takushi Ooga, Nobuo Kamiya, Seiki Kuramitsu, Ryota Kuroki.   

Abstract

ADP-ribose pyrophosphatase-I from Thermus thermophilus HB8 (TtADPRase-I) prevents the intracellular accumulation of ADP-ribose by hydrolyzing it to AMP and ribose 5'-phosphate. To understand the catalytic mechanism of TtADPRase-I, it is necessary to investigate the role of glutamates and metal ions as well as the coordination of water molecules located at the active site. A macroseeding method was developed in order to obtain a large TtADPRase-I crystal which was suitable for a neutron diffraction study to provide structural information. Neutron and X-ray diffraction experiments were performed at room temperature using the same crystal. The crystal diffracted to 2.1 and 1.5 Å resolution in the neutron and X-ray diffraction experiments, respectively. The crystal belonged to the primitive space group P3(2)21, with unit-cell parameters a = b = 50.7, c = 119 Å.
© 2012 International Union of Crystallography. All rights reserved.

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Year:  2011        PMID: 22232170      PMCID: PMC3253833          DOI: 10.1107/S1744309111044551

Source DB:  PubMed          Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun        ISSN: 1744-3091


  14 in total

1.  The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family.

Authors:  S B Gabelli; M A Bianchet; M J Bessman; L M Amzel
Journal:  Nat Struct Biol       Date:  2001-05

Review 2.  Structural genomics projects in Japan.

Authors:  S Yokoyama; Y Matsuo; H Hirota; T Kigawa; M Shirouzu; Y Kuroda; H Kurumizaka; S Kawaguchi; Y Ito; T Shibata; M Kainosho; Y Nishimura; Y Inoue; S Kuramitsu
Journal:  Prog Biophys Mol Biol       Date:  2000       Impact factor: 3.667

3.  Overproduction, crystallization and preliminary diffraction data of ADP-ribose pyrophosphatase from Thermus thermophilus HB8.

Authors:  Sachiko Yoshiba; Noriko Nakagawa; Ryoji Masui; Takehiko Shibata; Yorinao Inoue; Shigeyuki Yokoyama; Seiki Kuramitsu
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2003-09-19

4.  The 15-K neutron structure of saccharide-free concanavalin A.

Authors:  M P Blakeley; A J Kalb; J R Helliwell; D A A Myles
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-03       Impact factor: 11.205

5.  Molecular mechanism of the Thermus thermophilus ADP-ribose pyrophosphatase from mutational and kinetic studies.

Authors:  Takushi Ooga; Sachico Yoshiba; Noriko Nakagawa; Seiki Kuramitsu; Ryoji Masui
Journal:  Biochemistry       Date:  2005-07-05       Impact factor: 3.162

6.  Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8.

Authors:  Taisuke Wakamatsu; Noriko Nakagawa; Seiki Kuramitsu; Ryoji Masui
Journal:  J Bacteriol       Date:  2007-11-26       Impact factor: 3.490

Review 7.  The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes.

Authors:  M J Bessman; D N Frick; S F O'Handley
Journal:  J Biol Chem       Date:  1996-10-11       Impact factor: 5.157

8.  Structural genomics projects in Japan.

Authors:  S Yokoyama; H Hirota; T Kigawa; T Yabuki; M Shirouzu; T Terada; Y Ito; Y Matsuo; Y Kuroda; Y Nishimura; Y Kyogoku; K Miki; R Masui; S Kuramitsu
Journal:  Nat Struct Biol       Date:  2000-11

Review 9.  Neutron protein crystallography: current status and a brighter future.

Authors:  Dean A A Myles
Journal:  Curr Opin Struct Biol       Date:  2006-09-11       Impact factor: 6.809

10.  Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.

Authors:  Sachiko Yoshiba; Takushi Ooga; Noriko Nakagawa; Takehiko Shibata; Yorinao Inoue; Shigeyuki Yokoyama; Seiki Kuramitsu; Ryoji Masui
Journal:  J Biol Chem       Date:  2004-06-21       Impact factor: 5.157

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