Cupin: A candidate molecular structure for the Nep1-like protein family
1 Programa de Pós-Graduação em Computação Aplicada, Unisinos, Av. Unisinos – 950, São Leopoldo, Brasil
2 Departamento de Física e Biofísica, UNESP, Dist. Rubião Jr. sn, Botucatu, Brasil
3 Instituto de Biotecnologia, UCS, R. Francisco Getúlio Vargas 1130, Caxias do Sul, Brasil
4 Departamento de Genética e Evolução, IB/UNICAMP, Campinas, Brasil
5 Centro de Ciências Rurais, UFPampa/UFSM, São Gabriel, Brasil
BMC Plant Biology 2008, 8:50 doi:10.1186/1471-2229-8-50Published: 30 April 2008
NEP1-like proteins (NLPs) are a novel family of microbial elicitors of plant necrosis. Some NLPs induce a hypersensitive-like response in dicot plants though the basis for this response remains unclear. In addition, the spatial structure and the role of these highly conserved proteins are not known.
We predict a 3d-structure for the β-rich section of the NLPs based on alignments, prediction tools and molecular dynamics. We calculated a consensus sequence from 42 NLPs proteins, predicted its secondary structure and obtained a high quality alignment of this structure and conserved residues with the two Cupin superfamily motifs. The conserved sequence GHRHDWE and several common residues, especially some conserved histidines, in NLPs match closely the two cupin motifs. Besides other common residues shared by dicot Auxin-Binding Proteins (ABPs) and NLPs, an additional conserved histidine found in all dicot ABPs was also found in all NLPs at the same position.
We propose that the necrosis inducing protein class belongs to the Cupin superfamily. Based on the 3d-structure, we are proposing some possible functions for the NLPs.