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 E scherichia coli   O 157 :  H 7 (18%) and B acillus 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 β‐barrel structure, and the catalytic site was found between two large β‐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 ( G lu113 and G lu204) 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. Database The atomic coordinates and structure factors of AcL‐RbI / l ‐ribose, AcL‐RbI / l ‐ribulose, AcL‐RbI /ribitol, E 204 Q / l ‐ribose and E 204 Q / l ‐ribulose have been deposited in the Protein Data Bank under accession codes, 4Q0P , 4Q0Q , 4Q0S , 4Q0U and 4Q0V . Structured digital abstract • AcL-RbI and AcL-RbI bind by x-ray crystallography ( View interaction ).