New binding site in catalase?

This page complements R.B. Russell & M.J.E. Sternberg, Protein Eng.,9, 107-111, 1996.

During an all-against-all comparison of a database of protein domains, we found a significant similarity between a domain in catalase and the structures of calycins, a group of proteins having no sequence similarity, but which adopt a common up-down-up-down, anti-parallel beta barrel structure.

If you would like to a PDB file containing catalase superimposed onto retinol binding protein (RBP, a lipocalin) and avidin, complete with heteroatoms, etc., click here. The superimposition looks like:

where the catalase domain is coloured red, RBP blue and avidin green. Heteroatoms are shown in spacefill. Note the location of bound biotin (green) and retinol (blue) within avidin and RBP respectively.

Known members of the calycin family (including avidin and RBP) binding molecules in a similar pocket. Lipocalins and fatty acid binding proteins bind to small hydrophobic molecules, and avidins bind biotin with a high affinity. Catalase appears to have a similar, though partially covered pocket. The size of the pocket is shown below (middle) beside biotin (left) and salicylic acid (right), which is known to inhibit some catalases.

The pocket in catalase has a volume (as calculated by Insight) of approximately 115 angstroms, the cavity in avidin has a volume of approximately 224 angstroms, the larger size being explained mostly by the fact that the cavity in avidin is open to solvent on one side.