Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis
| Autor: | Agnes Thiane Pereira Machado, Ricardo Aparicio, Igor Polikarpov, Anete Pereira de Souza, Marcelo Augusto dos Reis, Jorge Iulek, Clelton A. Santos, A.M. Saraiva, Emanuella Maria Barreto Fonseca, Marcelo A.S. Toledo |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Stereochemistry Protomer Crystallography X-Ray Xylella Biochemistry Oligomer 03 medical and health sciences chemistry.chemical_compound Tetramer Bacterial Proteins Structural Biology Normal mode Scattering Small Angle Molecular Biology Conformational isomerism biology Chemistry Small-angle X-ray scattering Plants biology.organism_classification Crystallography 030104 developmental biology CRISTALOGRAFIA Protein quaternary structure Xylella fastidiosa |
| Zdroj: | Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual) Universidade de São Paulo (USP) instacron:USP |
| ISSN: | 1097-0134 |
| Popis: | Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein. |
| Databáze: | OpenAIRE |
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