Three-dimensional structures have been determined of a large number of proteins characterized by a repetitive fold where each of the repeats (coils) supplies a strand to one or more parallel beta-sheets. Some of these proteins form superfamilies of proteins, which have probably arisen by divergent evolution from a common ancestor. The classical example is the family including four families of pectinases without obviously related primary sequences, the phage P22 tailspike endorhamnosidase, chrondroitinase B and possibly pertactin from Bordetella pertusis. These show extensive stacking of similar residues to give aliphatic, aromatic and polar stacks such as the asparagine ladder. This suggests that coils can be added or removed by duplication or deletion of the DNA corresponding to one or more coils and explains how homologous proteins can have different numbers of coils. This process can also account for the evolution of other families of proteins such as the beta-rolls, the leucine-rich repeat proteins, the hexapeptide repeat family, two separate families of beta-helical antifreeze proteins and the spiral folds. These families need not be related to each other but will share features such as relative untwisted beta-sheets, stacking of similar residues and turns between beta-strands of approximately 90 degrees often stabilized by hydrogen bonding along the direction of the parallel beta-helix.Repetitive folds present special problems in the comparison of structures but offer attractive targets for structure prediction. The stacking of similar residues on a flat parallel beta-sheet may account for the formation of amyloid with beta-strands at right-angles to the fibril axis from many unrelated peptides.

to a superfamily of 8-fold /]/a-barrels with similar amino acid residues at their active sites. In the three families that these enzymes represent, the nucleophile is a glutamate, which is located close to the carboxy-terminus of/]-strand seven. In addition all three enzymes have the sequence asparagine-glutamate close to the carboxy-terminus of /]-strand four. This glutamate has been identified as the acid/base in the family F xylanases and is essential for catalysis in /]-galactosidase. We suggest that the equivalent residue in the barley glucanases is the acid/base. Analysis of the sequences of family 1 /]-glucosidases and family 5 cellulases shows that these enzymes also belong to this superfamily which we call the 4/7 superfamily.

X-ray studies of acid proteases indicate a bilobal structure with a well defined active site cleft. An intramolecular twofold symmetry axis relates two topologically similar domains and the active site residues. A possible mechanism for evolution by gene duplication, divergence and gene fusion is presented.

The substrate-binding clefts and catalytic machinery of pectin and pectate lyases have diverged significantly. Specificity is dictated by both the nature of the protein-carbohydrate interaction and long-range electrostatic forces. Three potential catalytic residues have been identified in pectin lyase, two of these are common to pectate lyases. Pectin lyase A does not bind Ca2+ but an arginine residue is found in an equivalent position to the Ca2+ ion in pectate lyase, suggesting a similar role in catalysis. The activity of pectin lyase A is pH -dependent with an optimum activity at pH 5.5. The activity drops above pH 7.0 due to a conformational change at the binding cleft, triggered by the proximity of two buried aspartate residues.

IntroductionTwo of the major unanswered questions in food allergy research are what makes one person, and not another, become allergic and what are the attributes of some foods and food proteins that make them more allergenic than others? Seeking to answer these questions is much more difficult than investigating the allergenic potency of inhalant or contact allergens since the proteins involved in sensitising or elicting allergic reactions may have undergone extensive modification during food processing and be presented within complex structures within food.These physicochemical changes will alter the way in which they are broken down during digestion and may modify the form in which they are taken up across the gut mucosal barrier and presented to the immune system. Certainly the structure of the food matrix can have a great impact on the elicitation of allergic reactions and fat-rich matrices may affect the kinetics of allergen release, potentiating the severity of allergic reactions (Grimshaw et al., 2003). However, because of its complex nature the impact of food processing and the food matrix on allergenicity of proteins has only recently become a subject of research. Such investigations are fraught with difficulties, not least the fact that food processing often renders food proteins insoluble in the simple salt solutions frequently employed in serological or clinical studies. As a consequence our understanding of the impact of food processing on allergenicity is limited to the more soluble and extractable residues in foods and the allergenic potential of insoluble protein complexes is virtually unstudied despite representing the vast bulk of food proteins consumed. Proteins in fabricated food structuresMuch of our understanding of the effects of food processing on food protein structure and the fabrication of different types of food structure has been gained from studying model food,

Most plant food allergens belong to only 4 structural families, indicating that conserved structures and biological activities may play a role in determining or promoting allergenic properties. Structural bioinformatic analysis shows that conservation of 3-dimensional structure should be included in any assessment of potential IgE cross-reactivity in, for example, novel proteins.

The crystal structure of the 40-kDa endo-polygalacturonase from Erwinia carotovora ssp. carotovora was solved by multiple isomorphous replacement and refined at 1.9 Å to a conventional crystallographic R-factor of 0.198 and R free of 0.239. This is the first structure of a polygalacturonase and comprises a 10 turn righthanded parallel ␤-helix domain with two loop regions forming a "tunnel like" substrate-binding cleft. Sequence conservation indicates that the active site of polygalacturonase is between these two loop regions, and comparison of the structure of polygalacturonase with that of rhamnogalacturonase A from Aspergillus aculeatus enables two conserved aspartates, presumed to be catalytic residues, to be identified. An adjacent histidine, in accord with biochemical results, is also seen. A similarity in overall electrostatic properties of the substrate-binding clefts of polygalacturonase and pectate lyase, which bind and cleave the same substrate, polygalacturonic acid, is also revealed.

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