title: Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway.
abstract: L-Ribose isomerase from Cellulomonas parahominis MB426 (CpL-RI) can catalyze the isomerization between L-ribose and L-ribulose, which are non-abundant in nature and called rare sugars. CpL-RI has a broad substrate specificity and can catalyze the isomerization between D-lyxose and D-xylulose, D-talose and D-tagatose, L-allose and L-psicose, L-gulose and L-sorbose, and D-mannose and D-fructose. To elucidate the molecular basis underlying the substrate recognition mechanism of CpL-RI, the crystal structures of CpL-RI alone and in complexes with L-ribose, L-allose, and L-psicose were determined. The structure of CpL-RI was very similar to that of L-ribose isomerase from Acinetobacter sp. strain DL-28, previously determined by us. CpL-RI had a cupin-type β-barrel structure, and the catalytic site was detected between two large β-sheets with a bound metal ion. The bound substrates coordinated to the metal ion, and Glu113 and Glu204 were shown to act as acid/base catalysts in the catalytic reaction via a cis-enediol intermediate. Glu211 and Arg243 were found to be responsible for the recognition of substrates with various configurations at 4- and 5-positions of sugar. CpL-RI formed a homo-tetramer in crystals, and the catalytic site independently consisted of residues within a subunit, suggesting that the catalytic site acted independently. Crystal structure and site-direct mutagenesis analyses showed that the tetramer structure is essential for the enzyme activity and that each subunit of CpL-RI could be structurally stabilized by intermolecular contacts with other subunits. The results of growth complementation assays suggest that CpL-RI is involved in a novel metabolic pathway using L-ribose as a carbon source.
authors: Rare Sugar Research Center and Faculty of Agriculture, Kagawa University, 2393, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan.
authors: Yuji
authors: Y
authors: Terami
authors: Hiromi
authors: H
authors: Yoshida
authors: Keiko
authors: K
authors: Uechi
authors: Kenji
authors: K
authors: Morimoto
authors: Goro
authors: G
authors: Takata
authors: Shigehiro
authors: S
authors: Kamitori
mesh_terms: D019747:Aldose-Ketose Isomerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D040143:Cellulomonas / Q000201:enzymology*; D018360:Crystallography, X-Ray; D016297:Mutagenesis, Site-Directed; D010429:Pentoses / Q000378:metabolism*; D055503:Protein Multimerization; D012266:Ribose / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D010429:Pentoses; C100182:ribulose; D012266:Ribose; D019747:Aldose-Ketose Isomerases; C022546:ribose isomerase