4Q0P
Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with L-ribose
4Q0P の概要
エントリーDOI | 10.2210/pdb4q0p/pdb |
関連するPDBエントリー | 4Q0Q 4Q0S 4Q0U 4Q0V |
分子名称 | L-Ribose isomerase, COBALT (II) ION, beta-L-ribopyranose, ... (6 entities in total) |
機能のキーワード | cupin barrel, isomerase, sugar binding |
由来する生物種 | Acinetobacter |
タンパク質・核酸の鎖数 | 1 |
化学式量合計 | 29571.82 |
構造登録者 | Yoshida, H.,Yoshihara, A.,Teraoka, M.,Izumori, K.,Kamitori, S. (登録日: 2014-04-02, 公開日: 2014-05-28, 最終更新日: 2024-04-03) |
主引用文献 | 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 主引用文献が同じPDBエントリー |
実験手法 | X-RAY DIFFRACTION (1.93 Å) |
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