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Title: Crystallization and preliminary X-ray analysis of PH1566, a putative ribosomal RNA-processing factor from the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Abstract

A putative ribosomal RNA-processing factor consisting of two KH domains from Pyrococcus horikoshii OT3 (PH1566; 25 kDa) was crystallized by the sitting-drop vapour-diffusion method using PEG 3000 as the precipitant. The space group of the crystals was determined as primitive orthorhombic P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 45.9, b = 47.4, c = 95.7 Å. A putative ribosomal RNA-processing factor consisting of two KH domains from Pyrococcus horikoshii OT3 (PH1566; 25 kDa) was crystallized by the sitting-drop vapour-diffusion method using PEG 3000 as the precipitant. The crystals diffracted X-rays to beyond 2.0 Å resolution using a synchrotron-radiation source. The space group of the crystals was determined as primitive orthorhombic P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 45.9, b = 47.4, c = 95.7 Å. The crystals contain one molecule in the asymmetric unit (V{sub M} = 2.5 Å{sup 3} Da{sup −1}) and have a solvent content of 50%.

Authors:
; ;  [1]; ;  [1];  [2]
  1. Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan)
  2. (Japan)
Publication Date:
OSTI Identifier:
22356251
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section F; Journal Volume: 62; Journal Issue: Pt 1; Other Information: PMCID: PMC2150936; PMID: 16511260; PUBLISHER-ID: pu5113; OAI: oai:pubmedcentral.nih.gov:2150936; Copyright (c) International Union of Crystallography 2006; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United Kingdom
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; CRYSTALLIZATION; CRYSTALS; DIFFUSION; MOLECULES; PROCESSING; RESOLUTION; SOLVENTS; SPACE GROUPS

Citation Formats

Jia, Min Ze, Ohtsuka, Jun, Lee, Woo Cheol, Nagata, Koji, Tanokura, Masaru, E-mail: amtanok@mail.ecc.u-tokyo.ac.jp, and Biological Supramolecular Crystallography Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Koto, Mikadzuki-cho, Sayo-gun, Hyogo 679-5148. Crystallization and preliminary X-ray analysis of PH1566, a putative ribosomal RNA-processing factor from the hyperthermophilic archaeon Pyrococcus horikoshii OT3. United Kingdom: N. p., 2006. Web. doi:10.1107/S1744309105040613.
Jia, Min Ze, Ohtsuka, Jun, Lee, Woo Cheol, Nagata, Koji, Tanokura, Masaru, E-mail: amtanok@mail.ecc.u-tokyo.ac.jp, & Biological Supramolecular Crystallography Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Koto, Mikadzuki-cho, Sayo-gun, Hyogo 679-5148. Crystallization and preliminary X-ray analysis of PH1566, a putative ribosomal RNA-processing factor from the hyperthermophilic archaeon Pyrococcus horikoshii OT3. United Kingdom. doi:10.1107/S1744309105040613.
Jia, Min Ze, Ohtsuka, Jun, Lee, Woo Cheol, Nagata, Koji, Tanokura, Masaru, E-mail: amtanok@mail.ecc.u-tokyo.ac.jp, and Biological Supramolecular Crystallography Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Koto, Mikadzuki-cho, Sayo-gun, Hyogo 679-5148. Sun . "Crystallization and preliminary X-ray analysis of PH1566, a putative ribosomal RNA-processing factor from the hyperthermophilic archaeon Pyrococcus horikoshii OT3". United Kingdom. doi:10.1107/S1744309105040613.
@article{osti_22356251,
title = {Crystallization and preliminary X-ray analysis of PH1566, a putative ribosomal RNA-processing factor from the hyperthermophilic archaeon Pyrococcus horikoshii OT3},
author = {Jia, Min Ze and Ohtsuka, Jun and Lee, Woo Cheol and Nagata, Koji and Tanokura, Masaru, E-mail: amtanok@mail.ecc.u-tokyo.ac.jp and Biological Supramolecular Crystallography Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Koto, Mikadzuki-cho, Sayo-gun, Hyogo 679-5148},
abstractNote = {A putative ribosomal RNA-processing factor consisting of two KH domains from Pyrococcus horikoshii OT3 (PH1566; 25 kDa) was crystallized by the sitting-drop vapour-diffusion method using PEG 3000 as the precipitant. The space group of the crystals was determined as primitive orthorhombic P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 45.9, b = 47.4, c = 95.7 Å. A putative ribosomal RNA-processing factor consisting of two KH domains from Pyrococcus horikoshii OT3 (PH1566; 25 kDa) was crystallized by the sitting-drop vapour-diffusion method using PEG 3000 as the precipitant. The crystals diffracted X-rays to beyond 2.0 Å resolution using a synchrotron-radiation source. The space group of the crystals was determined as primitive orthorhombic P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 45.9, b = 47.4, c = 95.7 Å. The crystals contain one molecule in the asymmetric unit (V{sub M} = 2.5 Å{sup 3} Da{sup −1}) and have a solvent content of 50%.},
doi = {10.1107/S1744309105040613},
journal = {Acta Crystallographica. Section F},
number = Pt 1,
volume = 62,
place = {United Kingdom},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}
  • l-Threonine dehydrogenase from the hyperthermophilic archaeon P. horikoshii was crystallized and preliminary X-ray crystallographic analysis was carried out. Recombinant l-threonine dehydrogenase from the hyperthermophilic archaeon Pyrococcus horikoshii was prepared using an Escherichia coli expression system. The hyperthermostable l-threonine dehydrogenase consists of 348 amino acids with a molecular weight of 37.7 kDa. The enzyme was crystallized by the hanging-drop vapour-diffusion method at 277 K and preliminary X-ray crystallographic analysis was carried out. Diffraction data were collected to 2.20 Å resolution under cryogenic conditions. P. horikoshiil-threonine dehydrogenase crystals belong to space group I4{sub 1}22, with unit-cell parameters a = b = 143.84,more » c = 304.13 Å. The presence of three subunits of the enzyme per asymmetric unit was estimsted to give a Matthews coefficient (V{sub M}) of 3.5 Å{sup 3} Da{sup −1} and a solvent content of 64.7%(v/v)« less
  • A putative UDP-N-acetyl-d-mannosamine dehydrogenase from P. horikoshii OT3 has been crystallized in space group P2{sub 1}, with unit-cell parameters a = 80.28, b = 69.24, c = 83.10 Å, β = 114.4°. X-ray diffraction data have been collected to 1.80 Å resolution. A putative UDP-N-acetyl-d-mannosamine dehydrogenase from Pyrococcus horikoshii OT3, an essential enzyme for polysaccharide biosynthesis, has been overexpressed in Escherichia coli and purified. Crystals were obtained using the oil-microbatch method at 291 K. A native data set extending to 1.8 Å resolution has been collected and processed in space group P2{sub 1}. Assuming the presence of a dimer inmore » the asymmetric unit, the V{sub M} value is calculated to be 2.3 Å{sup 3} Da{sup −1}, which is consistent with the result of a dynamic light-scattering experiment that shows a dimeric state of the protein in solution.« less
  • The putative GTPase PH0525 from P. horikoshii OT3 was crystallized using the microbatch method. Crystals were formed under two different conditions, providing two distinct crystal forms. Diffraction data from the two forms were measured to resolution limits of 2.30 and 2.40 Å and processed in space groups P2{sub 1} and C222{sub 1}, respectively. GTPases are involved in diverse cellular functions including cell proliferation, cytoskeleton organization and intracellular traffic. The putative GTPase PH0525 from Pyrococcus horikoshii OT3 has been overexpressed in Escherichia coli and purified. Two distinct crystal forms were grown by the microbatch method at 291 K using a verymore » high protein concentration (80 mg ml{sup −1}). Native data sets extending to resolutions of 2.3 and 2.4 Å have been collected and processed in space groups P2{sub 1} and C222{sub 1}, respectively. Assuming the presence of one monomer per asymmetric unit gives V{sub M} values of 2.6 and 2.4 Å{sup 3} Da{sup −1} for the P2{sub 1} and C222{sub 1} forms, respectively, which is consistent with dynamic light-scattering experiments, which show a monomeric state of the protein in solution.« less
  • A plant- and prokaryote-conserved domain (PPC) has been crystallized. The crystal diffracted to 1.7 Å resolution and belonged to space group P6{sub 3}22. A plant- and prokaryote-conserved domain (PPC) has previously been found in AT-hook motif nuclear localized protein 1 (AHL1) localized in the nuclear matrix of Arabidopsis thaliana (AtAHL1). AtAHL1 has a DNA-binding function. Mutation analyses of AtAHL1 has previously revealed that the hydrophobic region of the PPC domain is essential for its nuclear localization. In this study, the PPC of the hyperthermophilic archaebacterium Pyrococcus horikoshii (PhPPC) was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to themore » hexagonal space group P6{sub 3}22, with unit-cell parameters a = b = 53.69, c = 159.2 Å. Data were obtained at 100 K, with diffraction being observed to a resolution of 1.7 Å. A complete data set from crystals of the SeMet-substituted protein was also obtained.« less
  • The archaeal phosphoglycerate mutase PH0037 from P. horikoshii OT3 has been crystallized in space group R32, with unit-cell parameters a = 155.62, c = 230.35 Å. A 2.2 Å resolution data was collected at SPring-8 beamline BL26B1. Phosphoglycerate mutases catalyze the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in glycolysis and gluconeogenesis pathways. The archaeal phosphoglycerate mutase PH0037 from Pyrococcus horikoshii OT3 has been overexpressed in Escherichia coli and purified. Crystals were obtained using the oil-microbatch method at 291 K. A native data set extending to a resolution of 2.2 Å has been collected and processed in space group R32. Assuming themore » presence of a dimer in the asymmetric unit, the V{sub M} value is calculated to be 3.0 Å{sup 3} Da{sup −1}, consistent with the dynamic light-scattering experiment result, which shows a dimeric state of the protein in solution. Molecular-replacement trials using the crystal structure of Bacilllus stearothermophilus phosphoglycerate mutase as a search model did not provide a satisfactory solution, indicating substantially different structures of these two phophoglycerate mutases.« less