Literature DB >> 21821888

Crystallization and X-ray diffraction analysis of nylon-oligomer hydrolase (NylC) from Agromyces sp. KY5R.

Kengo Yasuhira1, Naoki Shibata, Yasuhito Tanaka, Naoya Kumagai, Yusuke Tanaka, Keisuke Nagai, Dai-ichiro Kato, Masahiro Takeo, Seiji Negoro, Yoshiki Higuchi.   

Abstract

6-Aminohexanoate-oligomer hydrolase (NylC) from Agromyces sp. KY5R was expressed in Escherichia coli JM109 and purified by ammonium sulfate fractionation, anion-exchange column chromatography and gel-filtration chromatography. NylC was crystallized by the sitting-drop vapour-diffusion method with sodium citrate as a precipitant in 0.1 M HEPES buffer pH 7.5 containing 0.2 M NaCl. Diffraction data were collected from native and K(2)PtCl(4)-derivative crystals to resolutions of 2.00 and 2.20 Å, respectively. The obtained crystal was plate-shaped, with an I-centred orthorhombic space group and unit-cell parameters a = 155.86, b = 214.45, c = 478.80 Å. The anomalous difference Patterson map of the K(2)PtCl(4)-derivative crystal suggested that the space group was I222 rather than I2(1)2(1)2(1).

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Year:  2011        PMID: 21821888      PMCID: PMC3151121          DOI: 10.1107/S1744309111022858

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


  15 in total

1.  X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme.

Authors:  Seiji Negoro; Taku Ohki; Naoki Shibata; Nobuhiro Mizuno; Yoshiaki Wakitani; Junya Tsurukame; Keiji Matsumoto; Ichitaro Kawamoto; Masahiro Takeo; Yoshiki Higuchi
Journal:  J Biol Chem       Date:  2005-09-14       Impact factor: 5.157

2.  Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities.

Authors:  Taku Ohki; Yoshiaki Wakitani; Masahiro Takeo; Kengo Yasuhira; Naoki Shibata; Yoshiki Higuchi; Seiji Negoro
Journal:  FEBS Lett       Date:  2006-08-28       Impact factor: 4.124

3.  Molecular replacement with MOLREP.

Authors:  Alexei Vagin; Alexei Teplyakov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-12-21

4.  Solvent content of protein crystals.

Authors:  B W Matthews
Journal:  J Mol Biol       Date:  1968-04-28       Impact factor: 5.469

5.  Nylon oligomer degradation gene, nylC, on plasmid pOAD2 from a Flavobacterium strain encodes endo-type 6-aminohexanoate oligomer hydrolase: purification and characterization of the nylC gene product.

Authors:  S Kakudo; S Negoro; I Urabe; H Okada
Journal:  Appl Environ Microbiol       Date:  1993-11       Impact factor: 4.792

6.  Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers.

Authors:  H Okada; S Negoro; H Kimura; S Nakamura
Journal:  Nature       Date:  1983 Nov 10-16       Impact factor: 49.962

7.  6-Aminohexanoate oligomer hydrolases from the alkalophilic bacteria Agromyces sp. strain KY5R and Kocuria sp. strain KY2.

Authors:  Kengo Yasuhira; Yasuhito Tanaka; Hiroshi Shibata; Yasuyuki Kawashima; Akira Ohara; Dai-ichiro Kato; Masahiro Takeo; Seiji Negoro
Journal:  Appl Environ Microbiol       Date:  2007-09-07       Impact factor: 4.792

8.  A new nylon oligomer degradation gene (nylC) on plasmid pOAD2 from a Flavobacterium sp.

Authors:  S Negoro; S Kakudo; I Urabe; H Okada
Journal:  J Bacteriol       Date:  1992-12       Impact factor: 3.490

9.  Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase.

Authors:  Seiji Negoro; Taku Ohki; Naoki Shibata; Kazuhiro Sasa; Haruhisa Hayashi; Hidehiko Nakano; Kengo Yasuhira; Dai-ichiro Kato; Masahiro Takeo; Yoshiki Higuchi
Journal:  J Mol Biol       Date:  2007-04-24       Impact factor: 5.469

10.  Overview of the CCP4 suite and current developments.

Authors:  Martyn D Winn; Charles C Ballard; Kevin D Cowtan; Eleanor J Dodson; Paul Emsley; Phil R Evans; Ronan M Keegan; Eugene B Krissinel; Andrew G W Leslie; Airlie McCoy; Stuart J McNicholas; Garib N Murshudov; Navraj S Pannu; Elizabeth A Potterton; Harold R Powell; Randy J Read; Alexei Vagin; Keith S Wilson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18
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  3 in total

1.  Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis.

Authors:  Seiji Negoro; Naoki Shibata; Yusuke Tanaka; Kengo Yasuhira; Hiroshi Shibata; Haruka Hashimoto; Young-Ho Lee; Shohei Oshima; Ryuji Santa; Shohei Oshima; Kozo Mochiji; Yuji Goto; Takahisa Ikegami; Keisuke Nagai; Dai-Ichiro Kato; Masahiro Takeo; Yoshiki Higuchi
Journal:  J Biol Chem       Date:  2011-12-19       Impact factor: 5.157

2.  Crystallization and X-ray diffraction analysis of nylon hydrolase (NylC) from Arthrobacter sp. KI72.

Authors:  Keisuke Nagai; Kengo Yasuhira; Yusuke Tanaka; Dai-ichiro Kato; Masahiro Takeo; Yoshiki Higuchi; Seiji Negoro; Naoki Shibata
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2013-09-28

3.  Crystals on the cover 2012.

Authors:  Howard Einspahr; Manfred S Weiss
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-12-24
  3 in total

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