Modeling based on the structure of vicilins predicts a histidine cluster in the active site of oxalate oxidase

Abstract

It is known that germin, which is a marker of the onset of growth in germinating wheat, is an oxalate oxidase, and also that germins possess sequence similarity with legumin and vicilin seed storage proteins. These two pieces of information have been combined in order to generate a 3D model of germin based on the structure of vicilin and to examine the model with regard to a potential oxalate oxidase active site. A cluster of three histidine residues has been located within the conserved beta-barrel structure. While there is a relatively low level of overall sequence similarity between the model and the vicilin structures, the conservation of amino acids important in maintaining the scaffold of the beta-barrel lends confidence to the juxtaposition of the histidine residues. The cluster is similar structurally to those found in copper amine oxidase and other proteins, leading to the suggestion that it defines a metal-binding location within the oxalate oxidase active site. It is also proposed that the structural elements involved in intermolecular interactions in vicilins may play a role in oligomer formation in germin/oxalate oxidase.

The Arabidopsis Cupin Domain Protein AtPirin1 Interacts with the G Protein α-Subunit GPA1 and Regulates Seed Germination and Early Seedling Development

“…Based on the three-dimensional structure of several cupin proteins, it was established that the two-motif cupin domain contains residues implicated in forming a ␤ -barrel fold and in metal binding (Gane et al, 1998;Dunwell et al, 2000). The ␤ -barrel fold also is associated with the high levels of thermal stability of cupin superfamily members (Dunwell et al, 2001).…”

Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily

“…This superfamily also includes many of the storage proteins from higher plants (20), and it was the knowledge of the three-dimensional structures of these proteins (155,177) that allowed the molecular modelling of the wheat protein germin (90), an unusual protease-resistant protein with oxalate oxidase (OXO) (EC 1.2.3.4) activity (173). The main characteristic of the cupin domain is a two-motif sequence (69) in which motif 1 corresponds to the C and D strands and motif 2 corresponds to the G and H strands of the unit structure of the bean storage protein phaseolin (177).…”

“…There is, however, a massive accumulation of oxalate (maximum 24% [dry weight]) during early seed development in soybean (131) and presumably in other legumes, and it is tempting to speculate on the possibility that this compound acts as a substrate for a residual oxalate-degrading capacity provided by the storage proteins being produced at that period. Knowledge of the tertiary structure of the two storage proteins phaseolin (177) and canavalin (155) and the finding of certain globally conserved residues (20) provided the basis for the generation of a homology model of wheat germin (90) and all subsequent predictions of cupin structures (Fig. 2).…”

Tobacco Nectarin I

“…1 Germin was first identified in germinating wheat embryos (6). It is a large molecular-weight protein composed of five (6) or six (7,8) monomer subunits. GLPs have subsequently been identified in all species examined to date from mosses to gymnosperms and dicots to monocots (9 -12).…”