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      Crystal structure of Type IX secretion system PorE C-terminal domain from Porphyromonas gingivalis in complex with a peptidoglycan fragment

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          Abstract

          Porphyromonas gingivalis, the major human pathogen associated to periodontal diseases, utilizes the Bacteroidetes-specific type IX secretion system (T9SS) to export virulence factors. PorE is a periplasmic multi-domain lipoprotein associated to the outer membrane that was recently identified as essential for T9SS function. Little is known on T9SS at the structural level, and in particular its interaction with peptidoglycan. This prompted us to carry out structural studies on PorE full length as well as on its four isolated domains. Here we report the crystal structure of the C-terminal OmpA_C-like putative peptidoglycan-binding domain at 1.55 Å resolution. An electron density volume was identified in the protein cleft, making it possible to build a naturally-occurring peptidoglycan fragment. This result suggests that PorE interacts with peptidoglycan and that PorE could anchor T9SS to the cell wall.

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          Most cited references39

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          T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

          This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.
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            Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT.

            BUSTER-TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coordinates, B factors and occupancies. In real space, in addition to the traditional atomic and bulk-solvent models, BUSTER models the parts of the structure for which an atomic model is not yet available ('missing structure') as low-resolution probability distributions for the random positions of the missing atoms. In reciprocal space, the BUSTER structure-factor distribution in the complex plane is a two-dimensional Gaussian centred around the structure factor calculated from the atomic, bulk-solvent and missing-structure models. The errors associated with these three structural components are added to compute the overall spread of the Gaussian. When the atomic model is very incomplete, modelling of the missing structure and the consistency of the BUSTER statistical model help structure building and completion because (i) the accuracy of the overall scale factors is increased, (ii) the bias affecting atomic model refinement is reduced by accounting for some of the scattering from the missing structure, (iii) the addition of a spatial definition to the source of incompleteness improves on traditional Luzzati and sigmaA-based error models and (iv) the program can perform selective density modification in the regions of unbuilt structure alone.
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              RF cloning: a restriction-free method for inserting target genes into plasmids.

              Restriction-free (RF) cloning provides a simple, universal method to precisely insert a DNA fragment into any desired location within a circular plasmid, independent of restriction sites, ligation, or alterations in either the vector or the gene of interest. The technique uses a PCR fragment encoding a gene of interest as a pair of primers in a linear amplification reaction around a circular plasmid. In contrast to QuickChange site-directed mutagenesis, which introduces single mutations or small insertions/deletions, RF cloning inserts complete genes without the introduction of unwanted extra residues. The absence of any alterations to the protein as well as the simplicity of both the primer design and the procedure itself makes it suitable for high-throughput expression and ideal for structural genomics.
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                Author and article information

                Contributors
                Philippe.Leone@afmb.univ-mrs.fr
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                30 April 2020
                30 April 2020
                2020
                : 10
                : 7384
                Affiliations
                [1 ]ISNI 0000 0004 1798 275X, GRID grid.463764.4, Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, ; 13009 Marseille, France
                [2 ]GRID grid.428531.9, Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, ; 13009 Marseille, France
                [3 ]Institute of Biotechnology, Vietnam Academy of Science and Technology. 18 Hoang Quoc Viet, Ha Noi, Vietnam
                [4 ]University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 18 Hoang Quoc Viet, Ha Noi, Vietnam
                Article
                64115
                10.1038/s41598-020-64115-z
                7192894
                32355178
                c4170b72-6aef-4b29-94c1-59ee94149777
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 13 February 2020
                : 31 March 2020
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                x-ray crystallography,bacterial secretion,bacterial pathogenesis
                Uncategorized
                x-ray crystallography, bacterial secretion, bacterial pathogenesis

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