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

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

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Structural and immunological characterization of a new nucleotidyltransferase-like antigen from Paracoccidioides brasiliensis.

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.

(2019) Mol Immunol 112: 151-162

  • DOI: https://doi.org/10.1016/j.molimm.2019.04.028
  • Primary Citation of Related Structures:  

  • 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 ( 1 H- 15 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.

  • Organizational Affiliation

    Departamento de Ciências Fisiológicas, Centro de Ciências da Saúde, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleotidyltransferase-like protein221Paracoccidioides brasiliensis Pb18Mutation(s): 0 
Gene Names: PADG_08402
Find proteins for C1GM11 (Paracoccidioides brasiliensis (strain Pb18))
Explore C1GM11 
Go to UniProtKB:  C1GM11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1GM11
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.649α = 90
b = 51.105β = 90
c = 121.19γ = 90
Software Package:
Software NamePurpose
XDSdata processing
DENZOdata processing
XDSdata scaling
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil484466/2007-0

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references, Derived calculations