5KSR

Stationary phase survival protein E (SurE) from Xylella fastidiosa - XFSurE-TB (Tetramer Bigger).

Summary for 5KSR

• Entry DOI: 10.2210/pdb5ksr/pdb
• Related: 5KSQ 5KSS 5KST
• Descriptor: 5'-nucleotidase SurE, MANGANESE (II) ION, IODIDE ION, ... (5 entities in total)
• Functional Keywords: stationary phase survival protein e (sure), xylella fastidiosa, crystallization., hydrolase
• Biological source: Xylella fastidiosa (strain 9a5c)
• Cellular location: Cytoplasm : Q9PF20
• Total number of polymer chains: 4
• Total formula weight: 119083.14

Authors

Machado, A.T.P.,Fonseca, E.M.B.,Dos Reis, M.A.,Saraiva, A.M.,Dos Santos, C.A.,De Toledo, M.A.,Polikarpov, I.,De Souza, A.P.,De Aparicio, R.,Iulek, J. (deposition date: 2016-07-09, release date: 2017-07-19, Last modification date: 2023-10-04)

Primary citation

Machado, A.T.P.,Fonseca, E.M.B.,Reis, M.A.D.,Saraiva, A.M.,Santos, C.A.D.,de Toledo, M.A.S.,Polikarpov, I.,de Souza, A.P.,Aparicio, R.,Iulek, J.
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.
Proteins, 85:1931-1943, 2017

PubMed 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 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.

PubMed: 28677327
DOI: 10.1002/prot.25347

Experimental method

X-RAY DIFFRACTION (1.96 Å)