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

Author(s)

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]

Affiliation

^[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

• Document type: Journal article
• Source: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS; v. 85, n. 10, p. 1931-1943, OCT 2017.
• Web of Science Citations: 0

Abstract

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)

• FAPESP's process: 12/51580-4 - Molecular and functional characterization of proteins potentially related to the phytopatogenicity of biofilm-forming bacteria Xylella fastidiosa
• Grantee: Anete Pereira de Souza
• Support Opportunities: Regular Research Grants
• FAPESP's process: 11/15792-4 - New inhibitors of LMW-PTP and CDC25B: fragment-based drug design using in silico methods, inhibition assays and Protein Crystallography
• Grantee: Emanuella Maria Barreto Fonseca
• Support Opportunities: Scholarships in Brazil - Doctorate