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Stachowicz M, Jokubauskas P, Bagiński B, MacDonald R, Harlov D. A revised structure for the rare earth fluoride gagarinite-(Ce) from experimental synthesis by fluid-induced alteration of chevkinite-(Ce). Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322092294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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Freier R, Aragón E, Bagiński B, Pluta R, Martin-Malpartida P, Ruiz L, Condeminas M, Gonzalez C, Macias MJ. Structures of the germline-specific Deadhead and thioredoxin T proteins from Drosophila melanogaster reveal unique features among thioredoxins. IUCrJ 2021; 8:281-294. [PMID: 33708404 PMCID: PMC7924233 DOI: 10.1107/s2052252521000221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Thioredoxins (Trxs) are ubiquitous enzymes that regulate the redox state in cells. In Drosophila, there are two germline-specific Trxs, Deadhead (Dhd) and thioredoxin T (TrxT), that belong to the lethal(3)malignant brain tumor signature genes and to the 'survival network' of genes that mediate the cellular response to DNA damage. Dhd is a maternal protein required for early embryogenesis that promotes protamine-histone exchange in fertilized eggs and midblastula transition. TrxT is testis-specific and associates with the lampbrush loops of the Y chromosome. Here, the first structures of Dhd and TrxT are presented, unveiling new features of these two thioredoxins. Dhd has positively charged patches on its surface, in contrast to the negatively charged surfaces commonly found in most Trxs. This distinctive charge distribution helps to define initial encounter complexes with DNA/RNA that will lead to final specific interactions with cofactors to promote chromatin remodeling. TrxT contains a C-terminal extension, which is mostly unstructured and highly flexible, that wraps the conserved core through a closed conformation. It is believed that these new structures can guide future work aimed at understanding embryo development and redox homeostasis in Drosophila. Moreover, due to their restricted presence in Schizophora (a section of the true flies), these structures can help in the design of small-molecular binders to modulate native redox homeostasis, thereby providing new applications for the control of plagues that cause human diseases and/or bring about economic losses by damaging crop production.
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Affiliation(s)
- Regina Freier
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Eric Aragón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Błażej Bagiński
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Radoslaw Pluta
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lidia Ruiz
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Miriam Condeminas
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Cayetano Gonzalez
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Maria J. Macias
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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Abstract
MODOMICS is an established database of RNA modifications that provides comprehensive information concerning chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. This chapter covers the resources available on MODOMICS web server and the basic steps that can be undertaken by the user to explore them. MODOMICS is available at http://www.genesilico.pl/modomics .
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Affiliation(s)
- Pietro Boccaletto
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
| | - Błażej Bagiński
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
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