4Q0P
Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with L-ribose
Summary for 4Q0P
| Entry DOI | 10.2210/pdb4q0p/pdb |
| Related | 4Q0Q 4Q0S 4Q0U 4Q0V |
| Descriptor | L-Ribose isomerase, COBALT (II) ION, beta-L-ribopyranose, ... (6 entities in total) |
| Functional Keywords | cupin barrel, isomerase, sugar binding |
| Biological source | Acinetobacter |
| Total number of polymer chains | 1 |
| Total formula weight | 29571.82 |
| Authors | Yoshida, H.,Yoshihara, A.,Teraoka, M.,Izumori, K.,Kamitori, S. (deposition date: 2014-04-02, release date: 2014-05-28, Last modification date: 2024-04-03) |
| Primary citation | Yoshida, H.,Yoshihara, A.,Teraoka, M.,Terami, Y.,Takata, G.,Izumori, K.,Kamitori, S. X-ray structure of a novel L-ribose isomerase acting on a non-natural sugar L-ribose as its ideal substrate. Febs J., 281:3150-3164, 2014 Cited by PubMed Abstract: 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 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 (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. PubMed: 24846739DOI: 10.1111/febs.12850 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.93 Å) |
Structure validation
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