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      Structure of a bd oxidase indicates similar mechanisms for membraneintegrated oxygen reductases

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          Abstract

          The cytochrome bd oxidases are terminal oxidases that are present in bacteria and archaea. They reduce molecular oxygen (dioxygen) to water, avoiding the production of reactive oxygen species. In addition to their contribution to the proton motive force, they mediate viability under oxygen-related stress conditions and confer tolerance to nitric oxide, thus contributing to the virulence of pathogenic bacteria. Here we present the atomic structure of the bd oxidase from Geobacillus thermodenitrificans, revealing a pseudosymmetrical subunit fold. The arrangement and order of the heme cofactors support the conclusions from spectroscopic measurements that the cleavage of the dioxygen bond may be mechanistically similar to that in the heme-copper containing oxidases, even though the structures are completely different.

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          Basic Local Alignment Search Tool

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            Protein structure prediction using Rosetta.

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              The Phenix software for automated determination of macromolecular structures.

              X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. Copyright © 2011 Elsevier Inc. All rights reserved.
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                Author and article information

                Journal
                0404511
                7473
                Science
                Science
                Science (New York, N.Y.)
                0036-8075
                1095-9203
                22 April 2017
                29 April 2016
                18 July 2017
                : 352
                : 6285
                : 583-586
                Affiliations
                [1 ]Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany
                [2 ]Department of Biochemistry, University of Washington, Seattle, WA, USA
                [3 ]Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
                Author notes
                []Corresponding author. hartmut.michel@ 123456biophys.mpg.de
                [*]

                Present address: Faculty of Biology and Preclinical Medicine, University of Regensburg, Universitätsstrasse 31, D-93051 Regensburg, Germany.

                [†]

                Present address: Department of Molecular Membrane Biology, Max Planck Institute for Brain Research, Max-von-Laue-Straße 4, D-60438 Frankfurt/Main, Germany.

                Article
                PMC5515584 PMC5515584 5515584 nihpa869069
                10.1126/science.aaf2477
                5515584
                27126043
                497bd215-8828-4ff2-a198-18e1b8a90fee
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