3WW2

X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-psicose

Summary for 3WW2

• Entry DOI: 10.2210/pdb3ww2/pdb
• Related: 3WW1 3WW3 3WW4
• Descriptor: L-ribose isomerase, MANGANESE (II) ION, alpha-L-psicofuranose, ... (6 entities in total)
• Functional Keywords: cupin-type beta-barrel, isomerase
• Biological source: Cellulomonas parahominis
• Total number of polymer chains: 2
• Total formula weight: 57335.70

Authors

Terami, Y.,Yoshida, H.,Takata, G.,Kamitori, S. (deposition date: 2014-06-13, release date: 2015-04-29, Last modification date: 2024-05-29)

Primary citation

Terami, Y.,Yoshida, H.,Uechi, K.,Morimoto, K.,Takata, G.,Kamitori, S.
Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway.
Appl.Microbiol.Biotechnol., 99:6303-6313, 2015

PubMed 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.

PubMed: 25661811
DOI: 10.1007/s00253-015-6417-4

Experimental method

X-RAY DIFFRACTION (2 Å)