5UVD

Crystal structure of an antigenic nucleotidyltransferase-like protein from Paracoccidioides brasiliensis

Summary for 5UVD

• Entry DOI: 10.2210/pdb5uvd/pdb
• Descriptor: Nucleotidyltransferase-like protein, MAGNESIUM ION (3 entities in total)
• Functional Keywords: antigen, putative nucleotidyltransferase, transferase
• Biological source: Paracoccidioides brasiliensis (strain Pb18)
• Total number of polymer chains: 1
• Total formula weight: 24830.15

Authors

Nagem, R.A.P.,Costa, M.A.F.,Rodrigues, F.T.G.,Coitinho, J.B.C. (deposition date: 2017-02-20, release date: 2018-01-31, Last modification date: 2024-03-06)

Primary citation

Coitinho, J.B.,Costa, M.A.F.,Melo, E.M.,Morais, E.A.,de Andrade, L.G.A.,da Rocha, A.M.,de Magalhaes, M.T.Q.,Favaro, D.C.,Bleicher, L.,Pedroso, E.R.P.,Goes, A.M.,Nagem, R.A.P.
Structural and immunological characterization of a new nucleotidyltransferase-like antigen from Paracoccidioides brasiliensis.
Mol.Immunol., 112:151-162, 2019

PubMed Abstract: Pb27 antigen is an interesting alternative to immunological diagnosis of Paracoccidioidomycosis (PCM) and has demonstrated to be protective in experimental PCM. Its tertiary structure and possible function remained unknown till now. To study Pb27 at the atomic level, the recombinant protein was expressed in Escherichia coli BL21(DE3), purified, and its three-dimensional structure was solved by X-ray crystallography. Based on this structure, we performed a residue correlation analysis and in silico ligand search assays to address a possible biological function to Pb27. We identified Pb27 as a member of the extensive nucleotidyltransferase superfamily. The protein has an αβαβαβ topology with two domains (N- and C-terminal domains) and adopts a monomeric form as its biological unit in solution. Structural comparisons with similar members of the superfamily clearly indicate Pb27 C-terminal domain is singular and may play an important role in its biological function. Bioinformatics analysis suggested that Pb27 might bind to ATP and CTP. This suggestion is corroborated by the fact that a magnesium cation is coordinated by two aspartic acid residues present at the active site (between N- and C-terminal domains), as evidenced by X-ray diffraction data. Besides, NMR assays (H-N HSQC spectra) confirmed the binding of CTP to Pb27, demonstrating for the first time an interaction between a nucleotide and this protein. Moreover, we evaluated the reactivity of sera from patients with Paracoccidioides brasiliensis infection against the recombinant form of Pb27 and showed that it was recognized by sera from infected and treated patients. Predicted B and T cell epitopes were synthesized and further evaluated against sera of PCM patients, providing information of the most reactive peptides in Pb27 primary structure which interact with specific Pb27 antibodies.

PubMed: 31108423
DOI: 10.1016/j.molimm.2019.04.028

Experimental method

X-RAY DIFFRACTION (1.86 Å)