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Title: Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110

Abstract

A haloalkane dehalogenase, DbjA, was crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The crystal belongs to the orthorhombic system, space group P2{sub 1}2{sub 1}2 and diffracts to 1.75 Å resolution. Haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. The haloalkane dehalogenase DbjA constitutes a novel substrate-specificity class with high catalytic activity for β-methylated haloalkanes. In order to reveal the mechanism of its substrate specificity, DbjA has been crystallized using the hanging-drop vapour-diffusion method. The best crystals were obtained using the microseeding technique with a reservoir solution consisting of 17–19.5%(w/v) PEG 4000, 0.2 M calcium acetate and 0.1 M Tris–HCl pH 7.7–8.0. The space group of the DbjA crystal is P2{sub 1}2{sub 1}2, with unit-cell parameters a = 212.9, b = 117.8, c = 55.8 Å. The crystal diffracts to 1.75 Å resolution.

Authors:
 [1];  [2];  [3];  [1];  [4];  [1];  [5];  [6]
  1. Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan)
  2. (JBIRC), Japan Biological Informatics Consortium (JBIC), 2-42 Aomi, Koto-ku, Tokyo 135-0064 (Japan)
  3. Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium (JBIC), 2-42 Aomi, Koto-ku, Tokyo 135-0064 (Japan)
  4. Loschmidt Laboratories, Masaryk University, Kamenice 5/A4, 625 00 Brno (Czech Republic)
  5. Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064 (Japan)
  6. (Japan)
Publication Date:
OSTI Identifier:
22360305
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section F; Journal Volume: 63; Journal Issue: Pt 4; Other Information: PMCID: PMC2330215; PMID: 17401198; PUBLISHER-ID: ll5100; OAI: oai:pubmedcentral.nih.gov:2330215; 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; ACETATES; BIODEGRADATION; CALCIUM; CRYSTALLIZATION; CRYSTALS; DIFFUSION; MATHEMATICAL SOLUTIONS; RESOLUTION; SOLUTIONS; SPACE GROUPS; SPECIFICITY; SUBSTRATES

Citation Formats

Sato, Yukari, Japan Biological Information Research Center, Natsume, Ryo, Tsuda, Masataka, Damborsky, Jiri, Nagata, Yuji, Senda, Toshiya, E-mail: tsenda@jbirc.aist.go.jp, and Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577. Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110. United Kingdom: N. p., 2007. Web. doi:10.1107/S1744309107008652.
Sato, Yukari, Japan Biological Information Research Center, Natsume, Ryo, Tsuda, Masataka, Damborsky, Jiri, Nagata, Yuji, Senda, Toshiya, E-mail: tsenda@jbirc.aist.go.jp, & Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577. Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110. United Kingdom. doi:10.1107/S1744309107008652.
Sato, Yukari, Japan Biological Information Research Center, Natsume, Ryo, Tsuda, Masataka, Damborsky, Jiri, Nagata, Yuji, Senda, Toshiya, E-mail: tsenda@jbirc.aist.go.jp, and Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577. Sun . "Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110". United Kingdom. doi:10.1107/S1744309107008652.
@article{osti_22360305,
title = {Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110},
author = {Sato, Yukari and Japan Biological Information Research Center and Natsume, Ryo and Tsuda, Masataka and Damborsky, Jiri and Nagata, Yuji and Senda, Toshiya, E-mail: tsenda@jbirc.aist.go.jp and Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577},
abstractNote = {A haloalkane dehalogenase, DbjA, was crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The crystal belongs to the orthorhombic system, space group P2{sub 1}2{sub 1}2 and diffracts to 1.75 Å resolution. Haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. The haloalkane dehalogenase DbjA constitutes a novel substrate-specificity class with high catalytic activity for β-methylated haloalkanes. In order to reveal the mechanism of its substrate specificity, DbjA has been crystallized using the hanging-drop vapour-diffusion method. The best crystals were obtained using the microseeding technique with a reservoir solution consisting of 17–19.5%(w/v) PEG 4000, 0.2 M calcium acetate and 0.1 M Tris–HCl pH 7.7–8.0. The space group of the DbjA crystal is P2{sub 1}2{sub 1}2, with unit-cell parameters a = 212.9, b = 117.8, c = 55.8 Å. The crystal diffracts to 1.75 Å resolution.},
doi = {10.1107/S1744309107008652},
journal = {Acta Crystallographica. Section F},
number = Pt 4,
volume = 63,
place = {United Kingdom},
year = {Sun Apr 01 00:00:00 EDT 2007},
month = {Sun Apr 01 00:00:00 EDT 2007}
}