Structure and plasticity of the peptidyl-prolyl isomerase Par27 of Bordetella pertussis revealed by X-ray diffraction and small-angle X-ray scattering.
Par27 from Bordetella pertussis belongs to a newly discovered class of dimeric peptidyl-prolyl isomerase (PPIase)/chaperones from the parvulin family. It is a tripartite protein with a central PPIase domain surrounded by N- and C-terminal sub-domains (NTD and CTD). Here, the Par27 structure was characterized by X-ray crystallography, small-angle X-ray scattering and template-based modeling. In the crystal lattice, Par27 consists of alternating well ordered and poorly ordered domains. The PPIase domains gave rise to diffuse scattering and could not be solved, whereas a 2.2A resolution crystal structure was obtained for the NTD and CTD, revealing a cradle-shaped dimeric platform. Despite a lack of sequence similarity with corresponding sub-domains, the topology of the peptide chain in the NTD/CTD core is similar to that of other monomeric PPIase/chaperones such as SurA and trigger factor from Escherichia coli. In Par27, dimerization occurs by sub-domain swapping. Because of the strong amino acid sequence similarity to other parvulin domains, a model for the Par27 PPIase domain was built by template-based modeling and validated against small-angle X-ray scattering (SAXS) data. A model of the full-length dimeric Par27 structure was built by rigid-body modeling and filtering against SAXS data using the partial crystal structure of the NTD/CTD core and the template-based PPIase model. The flexibility of protein was accounted for by representing the structure as an ensemble of different conformations that collectively reproduce the scattering data. The refined models exhibit a cradle-like shape reminiscent of other PPIase/chaperones, and the variability in the orientation of the PPIase domains relative to the NTD/CTD core platform observed in the different models suggests inter-domain flexibility that could be important for the biological activity of this protein.
Clantin
Bernard
B
UMR8161 CNRS, Institut de Biologie de Lille, Institut Pasteur de Lille, Université de Lille 1 - Université de Lille 2, 1 rue Calmette, 59021 Lille Cedex, France.
Leyrat
Cédric
C
Wohlkönig
Alex
A
Hodak
Hélène
H
Ribeiro
Euripedes de Almeida
Ede A
Martinez
Nicolas
N
Baud
Catherine
C
Smet-Nocca
Caroline
C
Villeret
Vincent
V
Jacob-Dubuisson
Françoise
F
Jamin
Marc
M
D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001886:Bordetella pertussis / Q000201:enzymology*; D056004:Molecular Dynamics Simulation; D019696:Peptidylprolyl Isomerase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
D001426:Bacterial Proteins; D011994:Recombinant Proteins; D019696:Peptidylprolyl Isomerase