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Title: Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8

Abstract

The glucose dehydrogenase (GDH) protein from T. thermophilus HB8 was cloned, expressed, purified and crystallized. GDH crystals belong to space group P2{sub 1} and diffract to 1.9 Å resolution. Thermus thermophilus is an aerobic chemoorganotroph that has been found to grow anaerobically in the presence of nitrate. Crystals of glucose dehydrogenase (GDH) from T. thermophilus HB8 belong to space group P2{sub 1}, with unit-cell parameters a = 36.90, b = 132.96, c = 60.78 Å, β = 97.2°. Preliminary studies and molecular-replacement calculations reveal that the asymmetric unit contains two monomers.

Authors:
;  [1]; ; ;  [2];  [2];  [3];  [2];  [4];  [2];  [3];  [2];  [2];  [3];  [2];  [3];  [2];  [1];  [5];  [2] more »;  [3];  [3];  [6] « less
  1. Bioinformatics Centre (Centre of Excellence in Structural Biology and Biocomputing), Indian Institute of Science, Bangalore 560 012 (India)
  2. RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan)
  3. (Japan)
  4. Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Hyogo (Japan)
  5. (India)
  6. (Centre of Excellence in Structural Biology and Biocomputing), Indian Institute of Science, Bangalore 560 012 (India)
Publication Date:
OSTI Identifier:
22360320
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section F; Journal Volume: 63; Journal Issue: Pt 5; Other Information: PMCID: PMC2334996; PMID: 17565193; PUBLISHER-ID: en5221; OAI: oai:pubmedcentral.nih.gov:2334996; Copyright (c) International Union of Crystallography 2007; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United Kingdom
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; CRYSTALS; GLUCOSE; MONOMERS; RESOLUTION; SPACE GROUPS

Citation Formats

Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Nishida, Masami, Kitamura, Yoshiaki, Baba, Seiki, Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Ebihara, Akio, Shimizu, Nobutaka, Nakagawa, Noriko, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Hyogo, Shinkai, Akeo, Yamamoto, Masaki, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Hyogo, Kuramitsu, Seiki, Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Shiro, Yoshitsugu, Sekar, Kanagaraj, E-mail: sekar@physics.iisc.ernet.in, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, Yokoyama, Shigeyuki, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, and Bioinformatics Centre. Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8. United Kingdom: N. p., 2007. Web. doi:10.1107/S1744309107014819.
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Nishida, Masami, Kitamura, Yoshiaki, Baba, Seiki, Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Ebihara, Akio, Shimizu, Nobutaka, Nakagawa, Noriko, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Hyogo, Shinkai, Akeo, Yamamoto, Masaki, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Hyogo, Kuramitsu, Seiki, Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Shiro, Yoshitsugu, Sekar, Kanagaraj, E-mail: sekar@physics.iisc.ernet.in, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, Yokoyama, Shigeyuki, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, & Bioinformatics Centre. Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8. United Kingdom. doi:10.1107/S1744309107014819.
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Nishida, Masami, Kitamura, Yoshiaki, Baba, Seiki, Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Ebihara, Akio, Shimizu, Nobutaka, Nakagawa, Noriko, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Hyogo, Shinkai, Akeo, Yamamoto, Masaki, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Hyogo, Kuramitsu, Seiki, Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Shiro, Yoshitsugu, Sekar, Kanagaraj, E-mail: sekar@physics.iisc.ernet.in, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, Yokoyama, Shigeyuki, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, and Bioinformatics Centre. Tue . "Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8". United Kingdom. doi:10.1107/S1744309107014819.
@article{osti_22360320,
title = {Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8},
author = {Kanaujia, Shankar Prasad and Ranjani, Chellamuthu Vasuki and Jeyakanthan, Jeyaraman and Nishida, Masami and Kitamura, Yoshiaki and Baba, Seiki and Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 and Ebihara, Akio and Shimizu, Nobutaka and Nakagawa, Noriko and Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Hyogo and Shinkai, Akeo and Yamamoto, Masaki and Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Hyogo and Kuramitsu, Seiki and Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 and Shiro, Yoshitsugu and Sekar, Kanagaraj, E-mail: sekar@physics.iisc.ernet.in and Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012 and Yokoyama, Shigeyuki and RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 and Bioinformatics Centre},
abstractNote = {The glucose dehydrogenase (GDH) protein from T. thermophilus HB8 was cloned, expressed, purified and crystallized. GDH crystals belong to space group P2{sub 1} and diffract to 1.9 Å resolution. Thermus thermophilus is an aerobic chemoorganotroph that has been found to grow anaerobically in the presence of nitrate. Crystals of glucose dehydrogenase (GDH) from T. thermophilus HB8 belong to space group P2{sub 1}, with unit-cell parameters a = 36.90, b = 132.96, c = 60.78 Å, β = 97.2°. Preliminary studies and molecular-replacement calculations reveal that the asymmetric unit contains two monomers.},
doi = {10.1107/S1744309107014819},
journal = {Acta Crystallographica. Section F},
number = Pt 5,
volume = 63,
place = {United Kingdom},
year = {Tue May 01 00:00:00 EDT 2007},
month = {Tue May 01 00:00:00 EDT 2007}
}
  • The crystallization and preliminary X-ray diffraction analysis of the l-fuculose-1-phosphate aldolase (FucA) from T. thermophilus HB8. Native diffraction data set was collected to a resolution of 1.9 Å. Fuculose phosphate aldolase catalyzes the reversible cleavage of l-fuculose-1-phosphate to dihydroxyacetone phosphate and l-lactaldehyde. The protein from Thermus thermophilus HB8 is a biological tetramer with a subunit molecular weight of 21 591 Da. Purified FucA has been crystallized using sitting-drop vapour-diffusion and microbatch techniques at 293 K. The crystals belong to space group P4, with unit-cell parameters a = b = 100.94, c = 45.87 Å. The presence of a dimer ofmore » the enzyme in the asymmetric unit was estimated to give a Matthews coefficient (V{sub M}) of 2.7 Å{sup 3} Da{sup −1} and a solvent content of 54.2%(v/v). Three-wavelength diffraction MAD data were collected to 2.3 Å from zinc-containing crystals. Native diffraction data to 1.9 Å resolution have been collected using synchrotron radiation at SPring-8.« less
  • The molybdopterin synthase from T. thermophilus HB8 was cloned, expressed, purified and crystallized. The crystals belong to space group P2{sub 1} and diffracted to a resolution of 1.64 Å. Thermus thermophilus is a Gram-negative aerobic thermophilic eubacterium which can grow at temperatures ranging from 323 to 355 K. In addition to their importance in thermostability or adaptation strategies for survival at high temperatures, the thermostable enzymes in thermophilic organisms contribute to a wide range of biotechnological applications. The molybdenum cofactor in all three kingdoms consists of a tricyclic pyranopterin termed molybdopterin that bears the cis-dithiolene group responsible for molybdenum ligation.more » The crystals of molybdopterin synthase from T. thermophilus HB8 belong to the primitive monoclinic space group P2{sub 1}, with unit-cell parameters a = 33.94, b = 103.32, c = 59.59 Å, β = 101.3°. Preliminary studies and molecular-replacement calculations reveal the presence of three monomers in the asymmetric unit.« less
  • The pyrimidine nucleoside phosphorylase TTHA1771 from T. thermophilus HB8 has been overexpressed, purified and crystallized. The crystals diffract X-rays to 1.8 Å resolution using synchrotron radiation. Pyrimidine nucleoside phosphorylase (PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide-synthesis salvage pathway. In order to study the structure–thermostability relationship of this enzyme, PYNP from the extreme thermophile Thermus thermophilus HB8 (TTHA1771) has been cloned, overexpressed and purified. The TTHA1771 protein was crystallized at 291 K using the oil-microbatch method with PEG 4000 as a precipitant. A native data set was collected to 1.8 Å resolution using synchrotron radiation. The crystal belongsmore » to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 58.83, b = 76.23, c = 103.86 Å, β = 91.3°.« less
  • Crystals of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase from T. thermophilus HB8 were obtained which diffracted synchrotron X-rays to a resolution of 1.6 Å. The 4-hydroxyphenylacetate (4HPA) 3-monooxygenase enzyme catalyzes the hydroxylation of 4HPA to 3,4-dihydroxyphenylacetate in the initial step of the degradation pathway of 4HPA. This enzyme consists of two components: an oxygenase (HpaB) and a reductase (HpaC). HpaB hydroxylates 4HPA using an oxygen molecule and a reduced flavin, which is supplied by HpaC. HpaB from Thermus thermophilus HB8 was overexpressed in Escherichia coli and crystallized. Crystals of HpaB were grown in 0.4 M 1,6-hexanediol, 0.1 M sodiummore » acetate pH 5.0 and 25%(v/v) glycerol and diffracted X-rays to a resolution of 1.60 Å. The crystals belong to the orthorhombic space group I222, with unit-cell parameters a = 91.8, b = 99.6, c = 131.1 Å. The asymmetric unit volume provides space for only one subunit of the tetrameric HpaB molecule, giving a Matthews coefficient V{sub M} of 2.8 Å{sup 3} Da{sup −1} and a solvent content of 55.1%. Platinum-derivatized crystals of HpaB were prepared by soaking native crystals in a solution containing 1 mM ammonium tetrachloroplatinate(II) for 1 d and diffracted X-rays to a resolution of 2.50 Å. MAD data were successfully collected for structural determination using these crystals.« less
  • The putative fumarylacetoacetase TTHA0809 from T. thermophilus HB8 has been overexpressed, purified and crystallized. The crystals diffracted X-rays to 2.2 Å resolution using synchrotron radiation. Fumarylacetoacetase catalyzes the final step of tyrosine and phenylalanine catabolism. A recombinant form of the fumarylacetoacetase family member TTHA0809 from Thermus thermophilus HB8 has been crystallized by the oil-microbatch method using sodium chloride as a precipitating agent. The crystals belong to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 93.3, b = 73.4, c = 122.6 Å, β = 111.8°. The crystals are most likely to contain two dimers in the asymmetricmore » unit, with a V{sub M} value of 3.32 Å{sup 3} Da{sup −1}. Diffraction data were collected at 2.2 Å resolution using synchrotron radiation at beamline BL26B1 of SPring-8, Japan.« less