title: Cupin: a candidate molecular structure for the Nep1-like protein family.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  We predict a 3d-structure for the beta-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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Programa de Pós-Graduação em Computação Aplicada, Unisinos, Av. Unisinos - 950, São Leopoldo, Brasil. acechin@unisinos.br
authors.forename: Adelmo L
authors.initials: AL
authors.lastname: Cechin
authors.forename: Marialva
authors.initials: M
authors.lastname: Sinigaglia
authors.forename: Ney
authors.initials: N
authors.lastname: Lemke
authors.forename: Sérgio
authors.initials: S
authors.lastname: Echeverrigaray
authors.forename: Odalys G
authors.initials: OG
authors.lastname: Cabrera
authors.forename: Gonçalo A G
authors.initials: GA
authors.lastname: Pereira
authors.forename: José C M
authors.initials: JC
authors.lastname: Mombach
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D016001:Confidence Intervals; D016384:Consensus Sequence; D003545:Cysteine / Q000737:chemistry; D006031:Glycosylation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010940:Plant Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D010940:Plant Proteins; D003545:Cysteine