X-ray structure of a novel L-ribose isomerase acting on a non-natural sugar L-ribose as its ideal substrate

L-Ribose, a pentose, is not known to exist in nature. Although organisms typically do not have a metabolic pathway that uses L-ribose as a carbon source, prokaryotes use various sugars as carbon sources for survival. Acinetobacter sp. DL-28 has been shown to express the novel enzyme, L-ribose isomerase (AcL-RbI), which catalyzes reversible isomerization between L-ribose and L-ribulose. AcL-RbI showed the highest activity to L-ribose, followed by D-lyxose with 47% activity, and had no significant amino acid sequence similarity to structure-known proteins, except for weak homology with the D-lyxose isomerases from Escherichia coli O157 : H7 (18%) and Bacillus subtilis strain (19%). Thus, AcL-RbI is expected to have the unique three-dimensional structure to recognize L-ribose as its ideal substrate. The X-ray structures of AcL-RbI in complexes with substrates were determined. AcL-RbI had a cupin-type beta-barrel structure, and the catalytic site was found between two large beta-sheets with a bound metal ion. The catalytic site structures clearly showed that AcL-RbI adopted a cis-enediol intermediate mechanism for the isomerization reaction using two glutamate residues (Glu113 and Glu204) as acid/base catalysts. In its crystal form, AcL-RbI formed a unique homotetramer with many substrate sub-binding sites, which likely facilitated capture of the substrate.