The model structure of the copper-dependent ammonia monooxygenase
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ORIGINAL PAPER
The model structure of the copper‑dependent ammonia monooxygenase Francesco Musiani1 · Valquiria Broll1 · Elisa Evangelisti1 · Stefano Ciurli1 Received: 24 July 2020 / Accepted: 2 September 2020 / Published online: 14 September 2020 © The Author(s) 2020
Abstract Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. Graphic abstract
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00775-020-01820-0) contains supplementary material, which is available to authorized users. Extended author information available on the last page of the article
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996
JBIC Journal of Biological Inorganic Chemistry (2020) 25:995–1007
Keywords Ammonia monooxygenase · Homology modelling · Nitrogen cycle · Nitrification · Copper enzyme · Nitrosomonas europaea
Introduction It has been estimated that the world population will reach 9 billion by the year 2050 [1], and that to sustain the consequential food demand, a 70–100% expansion in global agricultural production will be needed [2]. Nitrogen (N) is an essential element for life on Earth [3] as well as a critical nutrient for agriculture and food production [4]; due to its tremendous importance on agriculture, soil nitrogen fertilization must thus be carried out to increase crop yield [5]. According to the Food and Agriculture Organization of the United Nations (FAO), the world nitrogen fertilizer demand is expected to increase continuously for the period between 2017 and 2022 [6], and only in the United States of America (USA), nitrogen fertilizers use has increased more than 40 times fro
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