Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d

Abstract

BackgroundAromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB) for coplanar aromatic motifs similar to those found in known glycan-binding proteins.ResultsThe proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO) enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192) in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry.ConclusionsBased on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.

Redox-dependent interaction between thaumatin-like protein and β-glucan influences malting quality of barley

“…We conducted a systematic search of the TLP models to locate regions that might interact with (1, 3) β-D glucan (13). The search suggested that the glucan could be docked at the primary polysaccharide-binding site (CQTGDCGG) located in the cleft (26). In our study, this motif was observed exclusively in TLP1, -2, and -8 (Table S2).…”

Identification of Amino Acids Important for Binding of Clostridium perfringens Epsilon Toxin to Host Cells and to HAVCR1

“…(26, 27) Two or three coplanar, closely-spaced, surface-accessible aromatic amino acids are frequently involved in glycan binding. (28) In the present study, we investigate the role of clustered, surface-accessible aromatic amino acids within epsilon toxin in mediating binding of the toxin to cells and to its putative receptor, HAVCR1.…”

Horizontal Gene Transfer Contributed to the Evolution of Extracellular Surface Structures: The Freshwater Polyp Hydra Is Covered by a Complex Fibrous Cuticle Containing Glycosaminoglycans and Proteins of the PPOD and SWT (Sweet Tooth) Families

“…9A). Trp is typically rare on the protein surface, with the exception of carbohydrate-binding sites where it is an overrepresented residue and can play a crucial role in C-H/π-stacking with the B-face of the pyranose ring [38]–[40].…”