Sequence similarity between xylose isomerase and replicase: Another TIM-barrel in the replicase structure?

Abstract

The BLAST search using the strand β2 (46_GAHGVTFHDDDLIP) of the ( α/ β) 8-barrel of xylose isomerase from Streptomyces olivochromogenes resulted in retrieving the sequentially similar segment of replicase from garlic latent virus (692_GGHGIGFHRDD). The detailed analysis of the entire amino acid sequences of both xylose isomerase and replicase suggested that the polypeptide segment 644–1046 of replicase (the entire length of this enzyme is 1924 residues) could share the structure of xylose isomerase (20.7% identity using the entire sequence of xylose isomerase). The relatedness of replicase and xylose isomerase is supported by the fact that the sequence similarity can be observed along the whole sequence of xylose isomerase (386 amino acid residues). The sequence of replicase exhibits moreover the similarity with that of lycopene cyclase, an enzyme implicated in the β-carotene biosynthesis, that was previously found to share similarity with xylose isomerase. Thus the relevant segment of replicase is predicted to adopt an ( α/ β) 8-barrel topology similar to that of xylose isomerase.