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(es)

Pereira Machado, Agnes Thiane ^[1] ; Barreto Fonseca, Emanuella Maria ^[2] ; dos Reis, Marcelo Augusto ^{[2, 3]} ; Saraiva, Antonio Marcos ^{[4, 5]} ; dos Santos, Clelton Aparecido ^[4] ; Szymanski de Toledo, Marcelo Augusto ^[4] ; Polikarpov, Igor ^[6] ; de Souza, Anete Pereira ^{[4, 7]} ; Aparicio, Ricardo ^[2] ; Iulek, Jorge ^[1]

Afiliação do(s) autor(es)

^[1] Univ Estadual Ponta Grossa, Dept Chem, Ponta Grossa - Brazil

^[2] Univ Estadual Campinas, Inst Chem, Sao Paulo - Brazil

^[3] Fed Inst Educ Sci & Technol South Minas Gerais, Inconfidentes, MG - Brazil

^[4] Univ Estadual Campinas, Mol Biol & Genet Engn Ctr, Sao Paulo - Brazil

^[5] Natl Inst Metrol Qual & Technol INMETRO, Metrol Appl Life Sci Dimav, BR-25250020 Duque De Caxias, RJ - Brazil

^[6] Univ Sao Paulo, Sao Carlos Inst Phys, Sao Carlos, SP - Brazil

^[7] Univ Estadual Campinas, Biol Inst, Dept Plant Biol, Sao Paulo - Brazil

• Tipo de documento: Artigo Científico
• Fonte: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS; v. 85, n. 10, p. 1931-1943, OCT 2017.
• Citações Web of Science: 0

Resumo

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 30-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 SmallAngle 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. (AU)

• Processo FAPESP: 12/51580-4 - Caracterização funcional e molecular de proteínas potencialmente relacionadas a fitopatogenicidade da bactéria formadora de biofilme Xylella fastidiosa
• Beneficiário: Anete Pereira de Souza
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 08/55690-3 - Expressão, purificação e caracterização estrutural e funcional de proteínas relacionadas à patogenicidade de Xylella fastidiosa
• Beneficiário: Clelton Aparecido dos Santos
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 05/03234-6 - Estudos estruturais da LGI1 humana
• Beneficiário: Ricardo Aparicio
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 04/02540-3 - Caracterização funcional e estrutural de proteínas relacionadas a patogenicidade de Xylella fastidiosa
• Beneficiário: Antonio Marcos Saraiva
• Modalidade de apoio: Bolsas no Brasil - Doutorado Direto
• Processo FAPESP: 11/15792-4 - Novos inibidores de LMW-PTP e CDC25B: planejamento baseado em fragmentos moleculares com uso de métodos in silico, ensaios de inibição e Cristalografia de Proteínas
• Beneficiário: Emanuella Maria Barreto Fonseca
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 06/52844-4 - Clonagem e expressão, purificação e caracterização estrutural de duas proteínas relacionadas a patogenicidade de Xylella fastidiosa
• Beneficiário: Marcelo Augusto Szymanski de Toledo
• Modalidade de apoio: Bolsas no Brasil - Iniciação Científica
• Processo FAPESP: 01/07533-7 - Resolução da estrutura tridimensional de proteínas relacionadas à patogenicidade de Xyllela fastidiosa
• Beneficiário: Anete Pereira de Souza
• Modalidade de apoio: Auxílio à Pesquisa - Regular