Literature DB >> 32152099

Visualizing the protons in a metalloenzyme electron proton transfer pathway.

Hanna Kwon1, Jaswir Basran2,3, Juliette M Devos4, Reynier Suardíaz1,5, Marc W van der Kamp5, Adrian J Mulholland1, Tobias E Schrader6, Andreas Ostermann7, Matthew P Blakeley8, Peter C E Moody9,3, Emma L Raven10.   

Abstract

In redox metalloenzymes, the process of electron transfer often involves the concerted movement of a proton. These processes are referred to as proton-coupled electron transfer, and they underpin a wide variety of biological processes, including respiration, energy conversion, photosynthesis, and metalloenzyme catalysis. The mechanisms of proton delivery are incompletely understood, in part due to an absence of information on exact proton locations and hydrogen bonding structures in a bona fide metalloenzyme proton pathway. Here, we present a 2.1-Å neutron crystal structure of the complex formed between a redox metalloenzyme (ascorbate peroxidase) and its reducing substrate (ascorbate). In the neutron structure of the complex, the protonation states of the electron/proton donor (ascorbate) and all of the residues involved in the electron/proton transfer pathway are directly observed. This information sheds light on possible proton movements during heme-catalyzed oxygen activation, as well as on ascorbate oxidation.

Entities:  

Keywords:  ascorbate; heme; neutron; peroxidase; proton transfer

Year:  2020        PMID: 32152099      PMCID: PMC7104402          DOI: 10.1073/pnas.1918936117

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


  50 in total

1.  On the role of water in peroxidase catalysis: a theoretical investigation of HRP compound I formation.

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Journal:  J Phys Chem B       Date:  2010-04-22       Impact factor: 2.991

2.  A proton delivery pathway in the soluble fumarate reductase from Shewanella frigidimarina.

Authors:  Katherine L Pankhurst; Christopher G Mowat; Emma L Rothery; Janette M Hudson; Anne K Jones; Caroline S Miles; Malcolm D Walkinshaw; Fraser A Armstrong; Graeme A Reid; Stephen K Chapman
Journal:  J Biol Chem       Date:  2006-05-12       Impact factor: 5.157

3.  Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography.

Authors:  S J Fisher; M P Blakeley; E I Howard; I Petit-Haertlein; M Haertlein; A Mitschler; A Cousido-Siah; A G Salvay; A Popov; C Muller-Dieckmann; T Petrova; A Podjarny
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-11-28

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.  The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.

Authors:  Naomine Yano; Kazumasa Muramoto; Atsuhiro Shimada; Shuhei Takemura; Junpei Baba; Hidenori Fujisawa; Masao Mochizuki; Kyoko Shinzawa-Itoh; Eiki Yamashita; Tomitake Tsukihara; Shinya Yoshikawa
Journal:  J Biol Chem       Date:  2016-09-07       Impact factor: 5.157

6.  Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans.

Authors:  S Iwata; C Ostermeier; B Ludwig; H Michel
Journal:  Nature       Date:  1995-08-24       Impact factor: 49.962

7.  The catalytic pathway of cytochrome p450cam at atomic resolution.

Authors:  I Schlichting; J Berendzen; K Chu; A M Stock; S A Maves; D E Benson; R M Sweet; D Ringe; G A Petsko; S G Sligar
Journal:  Science       Date:  2000-03-03       Impact factor: 47.728

8.  Low-barrier hydrogen bond in photoactive yellow protein.

Authors:  Shigeo Yamaguchi; Hironari Kamikubo; Kazuo Kurihara; Ryota Kuroki; Nobuo Niimura; Nobutaka Shimizu; Yoichi Yamazaki; Mikio Kataoka
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-02       Impact factor: 11.205

9.  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

10.  Neutron crystallography of photoactive yellow protein reveals unusual protonation state of Arg52 in the crystal.

Authors:  Kento Yonezawa; Nobutaka Shimizu; Kazuo Kurihara; Yoichi Yamazaki; Hironari Kamikubo; Mikio Kataoka
Journal:  Sci Rep       Date:  2017-08-24       Impact factor: 4.379

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  7 in total

1.  An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network.

Authors:  Igor D Petrik; Roman Davydov; Maximilian Kahle; Braddock Sandoval; Sudharsan Dwaraknath; Pia Ädelroth; Brian Hoffman; Yi Lu
Journal:  Biochemistry       Date:  2021-01-19       Impact factor: 3.162

2.  Production of perdeuterated fucose from glyco-engineered bacteria.

Authors:  Lukas Gajdos; V Trevor Forsyth; Matthew P Blakeley; Michael Haertlein; Anne Imberty; Eric Samain; Juliette M Devos
Journal:  Glycobiology       Date:  2021-02-09       Impact factor: 4.313

3.  Structure-activity relationship and mechanism of four monostilbenes with respect to ferroptosis inhibition.

Authors:  Xiaojian Ouyang; Xican Li; Jie Liu; Yangping Liu; Yulu Xie; Zhongcun Du; Hong Xie; Ban Chen; Wenbiao Lu; Dongfeng Chen
Journal:  RSC Adv       Date:  2020-08-21       Impact factor: 4.036

4.  Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis.

Authors:  Qun Wan; Brad C Bennett; Troy Wymore; Zhihong Li; Mark A Wilson; Charles L Brooks; Paul Langan; Andrey Kovalevsky; Chris G Dealwis
Journal:  ACS Catal       Date:  2021-04-28       Impact factor: 13.084

5.  Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in FeIV =O Formation.

Authors:  Marina Lučić; Dimitri A Svistunenko; Michael T Wilson; Amanda K Chaplin; Bradley Davy; Ali Ebrahim; Danny Axford; Takehiko Tosha; Hiroshi Sugimoto; Shigeki Owada; Florian S N Dworkowski; Ivo Tews; Robin L Owen; Michael A Hough; Jonathan A R Worrall
Journal:  Angew Chem Int Ed Engl       Date:  2020-09-23       Impact factor: 15.336

Review 6.  Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of FeIV = O formation in bacterial dye-decolorizing peroxidases.

Authors:  Marina Lučić; Michael T Wilson; Dimitri A Svistunenko; Robin L Owen; Michael A Hough; Jonathan A R Worrall
Journal:  J Biol Inorg Chem       Date:  2021-09-03       Impact factor: 3.358

7.  Direct Aerobic Generation of a Ferric Hydroperoxo Intermediate Via a Preorganized Secondary Coordination Sphere.

Authors:  Kate A Jesse; Sophie W Anferov; Kelsey A Collins; Juan A Valdez-Moreira; Maia E Czaikowski; Alexander S Filatov; John S Anderson
Journal:  J Am Chem Soc       Date:  2021-10-26       Impact factor: 15.419

  7 in total

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