Literature DB >> 17183172

Preliminary time-of-flight neutron diffraction study on diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris.

Marc-Michael Blum1, Alexander Koglin, Heinz Rüterjans, Benno Schoenborn, Paul Langan, Julian C-H Chen.   

Abstract

The enzyme diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris is capable of decontaminating a wide variety of toxic organophosphorus nerve agents. DFPase is structurally related to a number of enzymes, such as the medically important paraoxonase (PON). In order to investigate the reaction mechanism of this phosphotriesterase and to elucidate the protonation state of the active-site residues, large-sized crystals of DFPase have been prepared for neutron diffraction studies. Available H atoms have been exchanged through vapour diffusion against D2O-containing mother liquor in the capillary. A neutron data set has been collected to 2.2 A resolution on a relatively small (0.43 mm3) crystal at the spallation source in Los Alamos. The sample size and asymmetric unit requirements for the feasibility of neutron diffraction studies are summarized.

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Year:  2006        PMID: 17183172      PMCID: PMC2330113          DOI: 10.1107/S1744309106052924

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


  26 in total

1.  Crystallization and preliminary neutron analysis of the dissimilatory sulfite reductase D (DsrD) protein from the sulfate-reducing bacterium Desulfovibrio vulgaris.

Authors:  Toshiyuki Chatake; Nobuhiro Mizuno; Gerrit Voordouw; Yoshiki Higuchi; Shigeki Arai; Ichiro Tanaka; Nobuo Niimura
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2003-11-27

2.  Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules.

Authors:  Kazuo Kurihara; Ichiro Tanaka; Toshiyuki Chatake; Michael W W Adams; Francis E Jenney; Natalia Moiseeva; Robert Bau; Nobuo Niimura
Journal:  Proc Natl Acad Sci U S A       Date:  2004-07-22       Impact factor: 11.205

3.  Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction.

Authors:  Amy K Katz; Xinmin Li; H L Carrell; B Leif Hanson; Paul Langan; Leighton Coates; Benno P Schoenborn; Jenny P Glusker; Gerard J Bunick
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-17       Impact factor: 11.205

4.  Mutational and structural studies of the diisopropylfluorophosphatase from Loligo vulgaris shed new light on the catalytic mechanism of the enzyme.

Authors:  Vicky Katsemi; Christian Lücke; Juergen Koepke; Frank Löhr; Steffen Maurer; Günter Fritzsch; Heinz Rüterjans
Journal:  Biochemistry       Date:  2005-06-28       Impact factor: 3.162

5.  Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris.

Authors:  E I Scharff; J Koepke; G Fritzsch; C Lücke; H Rüterjans
Journal:  Structure       Date:  2001-06       Impact factor: 5.006

6.  A preliminary neutron diffraction study of rasburicase, a recombinant urate oxidase enzyme, complexed with 8-azaxanthin.

Authors:  Monika Budayova-Spano; Françoise Bonneté; Natalie Ferté; Mohamed El Hajji; Flora Meilleur; Matthew Paul Blakeley; Bertrand Castro
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2006-02-28

7.  Crystallography & NMR system: A new software suite for macromolecular structure determination.

Authors:  A T Brünger; P D Adams; G M Clore; W L DeLano; P Gros; R W Grosse-Kunstleve; J S Jiang; J Kuszewski; M Nilges; N S Pannu; R J Read; L M Rice; T Simonson; G L Warren
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1998-09-01

8.  Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography.

Authors:  N Niimura; Y Minezaki; T Nonaka; J C Castagna; F Cipriani; P Høghøj; M S Lehmann; C Wilkinson
Journal:  Nat Struct Biol       Date:  1997-11

9.  Binding of a designed substrate analogue to diisopropyl fluorophosphatase: implications for the phosphotriesterase mechanism.

Authors:  Marc-Michael Blum; Frank Löhr; Andre Richardt; Heinz Rüterjans; Julian C-H Chen
Journal:  J Am Chem Soc       Date:  2006-10-04       Impact factor: 15.419

10.  Structure of insulin: results of joint neutron and X-ray refinement.

Authors:  A Wlodawer; H Savage; G Dodson
Journal:  Acta Crystallogr B       Date:  1989-02-01
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  14 in total

1.  X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction.

Authors:  Marc Michael Blum; Stephen J Tomanicek; Harald John; B Leif Hanson; Heinz Rüterjans; Benno P Schoenborn; Paul Langan; Julian C H Chen
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2010-03-26

2.  Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase).

Authors:  Julian C H Chen; Marat Mustyakimov; Benno P Schoenborn; Paul Langan; Marc Michael Blum
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-10-20

3.  A preliminary neutron crystallographic study of an A-DNA crystal.

Authors:  Ricardo M F Leal; Susana C M Teixeira; Matthew P Blakeley; Edward P Mitchell; V Trevor Forsyth
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2009-02-12

4.  Macromolecular neutron crystallography at the Protein Crystallography Station (PCS).

Authors:  Andrey Kovalevsky; Zoe Fisher; Hannah Johnson; Marat Mustyakimov; Mary Jo Waltman; Paul Langan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-10-20

5.  Computational Modeling of Human Paraoxonase 1: Preparation of Protein Models, Binding Studies, and Mechanistic Insights.

Authors:  Toby T Sanan; Sivaramakrishnan Muthukrishnan; Jeremy M Beck; Peng Tao; Carrigan J Hayes; Tamara C Otto; Douglas M Cerasoli; David E Lenz; Christopher M Hadad
Journal:  J Phys Org Chem       Date:  2010-04-01       Impact factor: 2.391

6.  Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP).

Authors:  S Z Fisher; S Anderson; R Henning; K Moffat; P Langan; P Thiyagarajan; A J Schultz
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-10-17

7.  Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.

Authors:  Marc-Michael Blum; Marat Mustyakimov; Heinz Rüterjans; Kai Kehe; Benno P Schoenborn; Paul Langan; Julian C-H Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-09       Impact factor: 11.205

8.  Perdeuteration, purification, crystallization and preliminary neutron diffraction of an ocean pout type III antifreeze protein.

Authors:  Isabelle Petit-Haertlein; Matthew P Blakeley; Eduardo Howard; Isabelle Hazemann; Andre Mitschler; Michael Haertlein; Alberto Podjarny
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2009-03-26

Review 9.  Neutron crystallography: opportunities, challenges, and limitations.

Authors:  Matthew P Blakeley; Paul Langan; Nobuo Niimura; Alberto Podjarny
Journal:  Curr Opin Struct Biol       Date:  2008-08-07       Impact factor: 6.809

10.  Preliminary time-of-flight neutron diffraction study of human deoxyhemoglobin.

Authors:  A Y Kovalevsky; T Chatake; N Shibayama; S-Y Park; T Ishikawa; M Mustyakimov; S Z Fisher; P Langan; Y Morimoto
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2008-03-21
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