Literature DB >> 21041927

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

Julian C H Chen1, Marat Mustyakimov, Benno P Schoenborn, Paul Langan, Marc Michael Blum.   

Abstract

Diisopropyl fluorophosphatase (DFPase) is a calcium-dependent phosphotriesterase that acts on a variety of highly toxic organophosphorus compounds that act as inhibitors of acetylcholinesterase. The mechanism of DFPase has been probed using a variety of methods, including isotopic labelling, which demonstrated the presence of a phosphoenzyme intermediate in the reaction mechanism. In order to further elucidate the mechanism of DFPase and to ascertain the protonation states of the residues and solvent molecules in the active site, the neutron structure of DFPase was solved at 2.2 Å resolution. The proposed nucleophile Asp229 is deprotonated, while the active-site solvent molecule W33 was identified as water and not hydroxide. These data support a mechanism involving direct nucleophilic attack by Asp229 on the substrate and rule out a mechanism involving metal-assisted water activation. These data also allowed for the re-engineering of DFPase through rational design to bind and productively orient the more toxic S(P) stereoisomers of the nerve agents sarin and cyclosarin, creating a modified enzyme with enhanced overall activity and significantly increased detoxification properties.

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Year:  2010        PMID: 21041927      PMCID: PMC2967418          DOI: 10.1107/S0907444910034013

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  26 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.  Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase.

Authors:  Matthew P Blakeley; Federico Ruiz; Raul Cachau; Isabelle Hazemann; Flora Meilleur; Andre Mitschler; Stephan Ginell; Pavel Afonine; Oscar N Ventura; Alexandra Cousido-Siah; Michael Haertlein; Andrzej Joachimiak; Dean Myles; Alberto Podjarny
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-04       Impact factor: 11.205

3.  Combined high-resolution neutron and X-ray analysis of inhibited elastase confirms the active-site oxyanion hole but rules against a low-barrier hydrogen bond.

Authors:  Taro Tamada; Takayoshi Kinoshita; Kazuo Kurihara; Motoyasu Adachi; Takashi Ohhara; Keisuke Imai; Ryota Kuroki; Toshiji Tada
Journal:  J Am Chem Soc       Date:  2009-08-12       Impact factor: 15.419

4.  Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography.

Authors:  Motoyasu Adachi; Takashi Ohhara; Kazuo Kurihara; Taro Tamada; Eijiro Honjo; Nobuo Okazaki; Shigeki Arai; Yoshinari Shoyama; Kaname Kimura; Hiroyoshi Matsumura; Shigeru Sugiyama; Hiroaki Adachi; Kazufumi Takano; Yusuke Mori; Koushi Hidaka; Tooru Kimura; Yoshio Hayashi; Yoshiaki Kiso; Ryota Kuroki
Journal:  Proc Natl Acad Sci U S A       Date:  2009-03-09       Impact factor: 11.205

5.  A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 A resolution.

Authors:  Daichi Yagi; Taro Yamada; Kazuo Kurihara; Yuki Ohnishi; Masahiro Yamashita; Taro Tamada; Ichiro Tanaka; Ryota Kuroki; Nobuo Niimura
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-08-06

6.  Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose.

Authors:  Andrey Y Kovalevsky; Amy K Katz; H L Carrell; Leif Hanson; Marat Mustyakimov; S Zoe Fisher; Leighton Coates; Benno P Schoenborn; Gerard J Bunick; Jenny P Glusker; Paul Langan
Journal:  Biochemistry       Date:  2008-06-26       Impact factor: 3.162

7.  Reversed enantioselectivity of diisopropyl fluorophosphatase against organophosphorus nerve agents by rational design.

Authors:  Marco Melzer; Julian C-H Chen; Anne Heidenreich; Jürgen Gäb; Marianne Koller; Kai Kehe; Marc-Michael Blum
Journal:  J Am Chem Soc       Date:  2009-12-02       Impact factor: 15.419

8.  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

9.  Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.

Authors:  Paul D Adams; Marat Mustyakimov; Pavel V Afonine; Paul Langan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-05-15

10.  Protein structures by spallation neutron crystallography.

Authors:  Paul Langan; Zoë Fisher; Andrii Kovalevsky; Marat Mustyakimov; Amanda Sutcliffe Valone; Cliff Unkefer; Mary Jo Waltman; Leighton Coates; Paul D Adams; Pavel V Afonine; Brad Bennett; Chris Dealwis; Benno P Schoenborn
Journal:  J Synchrotron Radiat       Date:  2008-04-18       Impact factor: 2.616

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  11 in total

1.  Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin.

Authors:  Julian C-H Chen; Zoë Fisher; Andrey Y Kovalevsky; Marat Mustyakimov; B Leif Hanson; Vladimir V Zhurov; Paul Langan
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-01-21

2.  Seeing the chemistry in biology with neutron crystallography.

Authors:  Paul Langan; Julian C-H Chen
Journal:  Phys Chem Chem Phys       Date:  2013-07-15       Impact factor: 3.676

Review 3.  Organophosphate-Hydrolyzing Enzymes as First-Line of Defence Against Nerve Agent-Poisoning: Perspectives and the Road Ahead.

Authors:  A R Satvik Iyengar; Abhay H Pande
Journal:  Protein J       Date:  2016-12       Impact factor: 2.371

Review 4.  Catalytic mechanisms for phosphotriesterases.

Authors:  Andrew N Bigley; Frank M Raushel
Journal:  Biochim Biophys Acta       Date:  2012-04-26

5.  Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography.

Authors:  Julian C-H Chen; B Leif Hanson; S Zoë Fisher; Paul Langan; Andrey Y Kovalevsky
Journal:  Proc Natl Acad Sci U S A       Date:  2012-09-04       Impact factor: 11.205

6.  Theoretical Studies on Catalysis Mechanisms of Serum Paraoxonase 1 and Phosphotriesterase Diisopropyl Fluorophosphatase Suggest the Alteration of Substrate Preference from Paraoxonase to DFP.

Authors:  Hao Zhang; Ling Yang; Ying-Ying Ma; Chaoyuan Zhu; Shenghsien Lin; Rong-Zhen Liao
Journal:  Molecules       Date:  2018-07-07       Impact factor: 4.411

7.  A KLK4 proteinase substrate capture approach to antagonize PAR1.

Authors:  Eitan Rabinovitch; Koishiro Mihara; Amiram Sananes; Marianna Zaretsky; Michael Heyne; Julia Shifman; Amir Aharoni; Morley D Hollenberg; Niv Papo
Journal:  Sci Rep       Date:  2021-08-09       Impact factor: 4.379

8.  Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: implications for engineering bioscavengers.

Authors:  Troy Wymore; Martin J Field; Paul Langan; Jeremy C Smith; Jerry M Parks
Journal:  J Phys Chem B       Date:  2014-04-21       Impact factor: 2.991

9.  Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering.

Authors:  Miha Purg; Mikael Elias; Shina Caroline Lynn Kamerlin
Journal:  J Am Chem Soc       Date:  2017-11-21       Impact factor: 15.419

10.  Theoretical Studies Applied to the Evaluation of the DFPase Bioremediation Potential against Chemical Warfare Agents Intoxication.

Authors:  Flávia V Soares; Alexandre A de Castro; Ander F Pereira; Daniel H S Leal; Daiana T Mancini; Ondrej Krejcar; Teodorico C Ramalho; Elaine F F da Cunha; Kamil Kuca
Journal:  Int J Mol Sci       Date:  2018-04-23       Impact factor: 5.923

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