Two three-dimensional protein structural similarities accompanied by slight similarities in function are reported to highlight the present difficulties in discerning the relationship between structure and function. The similarity between the structures of uteroglobin and the CAP domain of haloalkane dehalogenase reveals a common four helix hydrophobic ligand binding motif. The similarity between the beta-barrel domains of glutaminyl tRNA synthetase and domain 1 of glutamine synthetase is accompanied by some similarity in the location of nucleotide binding sites and suggests a possible ancient domain common to these two proteins involved in the synthesis or binding of glutaminyl moieties. The problems raised by these two similarities in the structure-function 'twilight zone' are discussed.