Literature DB >> 32371483

Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.

Takeshi Murakawa1, Kazuo Kurihara2, Mitsuo Shoji3,4, Chie Shibazaki2, Tomoko Sunami2, Taro Tamada2, Naomine Yano5, Taro Yamada5, Katsuhiro Kusaka5, Mamoru Suzuki6, Yasuteru Shigeta3, Ryota Kuroki7, Hideyuki Hayashi8, Takato Yano9, Katsuyuki Tanizawa10, Motoyasu Adachi2, Toshihide Okajima11,10.   

Abstract

Recent advances in neutron crystallographic studies have provided structural bases for quantum behaviors of protons observed in enzymatic reactions. Thus, we resolved the neutron crystal structure of a bacterial copper (Cu) amine oxidase (CAO), which contains a prosthetic Cu ion and a protein-derived redox cofactor, topa quinone (TPQ). We solved hitherto unknown structures of the active site, including a keto/enolate equilibrium of the cofactor with a nonplanar quinone ring, unusual proton sharing between the cofactor and the catalytic base, and metal-induced deprotonation of a histidine residue that coordinates to the Cu. Our findings show a refined active-site structure that gives detailed information on the protonation state of dissociable groups, such as the quinone cofactor, which are critical for catalytic reactions.

Entities:  

Keywords:  copper amine oxidase; metal-induced deprotonation; neutron crystallography; proton sharing; quinone cofactor

Year:  2020        PMID: 32371483      PMCID: PMC7245091          DOI: 10.1073/pnas.1922538117

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  37 in total

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Authors:  W W Cleland
Journal:  Arch Biochem Biophys       Date:  2000-10-01       Impact factor: 4.013

2.  PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.

Authors:  Alexander W Schüttelkopf; Daan M F van Aalten
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-07-21

3.  Geometric and electronic structures of the synthetic Mn₄CaO₄ model compound mimicking the photosynthetic oxygen-evolving complex.

Authors:  Mitsuo Shoji; Hiroshi Isobe; Jian-Ren Shen; Kizashi Yamaguchi
Journal:  Phys Chem Chem Phys       Date:  2016-04-28       Impact factor: 3.676

4.  Processing of X-ray diffraction data collected in oscillation mode.

Authors:  Z Otwinowski; W Minor
Journal:  Methods Enzymol       Date:  1997       Impact factor: 1.600

5.  Kinetic and structural studies on the catalytic role of the aspartic acid residue conserved in copper amine oxidase.

Authors:  Yen-Chen Chiu; Toshihide Okajima; Takeshi Murakawa; Mayumi Uchida; Masayasu Taki; Shun Hirota; Misa Kim; Hiroshi Yamaguchi; Yoshiaki Kawano; Nobuo Kamiya; Shun'ichi Kuroda; Hideyuki Hayashi; Yukio Yamamoto; Katsuyuki Tanizawa
Journal:  Biochemistry       Date:  2006-04-04       Impact factor: 3.162

6.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu.

Authors:  Stefan Grimme; Jens Antony; Stephan Ehrlich; Helge Krieg
Journal:  J Chem Phys       Date:  2010-04-21       Impact factor: 3.488

7.  Crystal structures of the copper-containing amine oxidase from Arthrobacter globiformis in the holo and apo forms: implications for the biogenesis of topaquinone.

Authors:  M C Wilce; D M Dooley; H C Freeman; J M Guss; H Matsunami; W S McIntire; C E Ruggiero; K Tanizawa; H Yamaguchi
Journal:  Biochemistry       Date:  1997-12-23       Impact factor: 3.162

8.  Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin.

Authors:  F Shu; V Ramakrishnan; B P Schoenborn
Journal:  Proc Natl Acad Sci U S A       Date:  2000-04-11       Impact factor: 11.205

9.  Energetics of short hydrogen bonds in photoactive yellow protein.

Authors:  Keisuke Saito; Hiroshi Ishikita
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-15       Impact factor: 11.205

10.  PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Authors:  Paul D Adams; Pavel V Afonine; Gábor Bunkóczi; Vincent B Chen; Ian W Davis; Nathaniel Echols; Jeffrey J Headd; Li-Wei Hung; Gary J Kapral; Ralf W Grosse-Kunstleve; Airlie J McCoy; Nigel W Moriarty; Robert Oeffner; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger; Peter H Zwart
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-01-22
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  5 in total

1.  Current status of neutron crystallography in structural biology.

Authors:  Fumiaki Kono; Kazuo Kurihara; Taro Tamada
Journal:  Biophys Physicobiol       Date:  2022-04-01

2.  Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement.

Authors:  Takeshi Murakawa; Kazuo Kurihara; Motoyasu Adachi; Katsuhiro Kusaka; Katsuyuki Tanizawa; Toshihide Okajima
Journal:  IUCrJ       Date:  2022-04-08       Impact factor: 5.588

3.  Microcrystal preparation for serial femtosecond X-ray crystallography of bacterial copper amine oxidase.

Authors:  Takeshi Murakawa; Mamoru Suzuki; Toshi Arima; Michihiro Sugahara; Tomoyuki Tanaka; Rie Tanaka; So Iwata; Eriko Nango; Kensuke Tono; Hideyuki Hayashi; Kenji Fukui; Takato Yano; Katsuyuki Tanizawa; Toshihide Okajima
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2021-09-21       Impact factor: 1.072

4.  Unique protonation states of aspartate and topaquinone in the active site of copper amine oxidase.

Authors:  Mitsuo Shoji; Takeshi Murakawa; Mauro Boero; Yasuteru Shigeta; Hideyuki Hayashi; Toshihide Okajima
Journal:  RSC Adv       Date:  2020-10-21       Impact factor: 4.036

Review 5.  Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography.

Authors:  Gabriela C Schröder; Flora Meilleur
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-09-27       Impact factor: 7.652

  5 in total

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