title: X-ray structures of Bacillus pallidus d-arabinose isomerase and its complex with l-fucitol.
abstract: d-Arabinose isomerase (d-AI), also known as l-fucose isomerase (l-FI), catalyzes the aldose-ketose isomerization of d-arabinose to d-ribulose, and l-fucose to l-fuculose. Bacillus pallidus (B. pallidus) d-AI can catalyze isomerization of d-altrose to d-psicose, as well as d-arabinose and l-fucose. Three X-ray structures of B. pallidus d-AI in complexes with 2-methyl-2,4-pentadiol, glycerol and an inhibitor, l-fucitol, were determined at resolutions of 1.77, 1.60 and 2.60 A, respectively. B. pallidus d-AI forms a homo-hexamer, and one subunit has three domains of almost equal size; two Rossmann fold domains and a mimic of the (beta/alpha) barrel fold domain. A catalytic metal ion (Mn(2+)) was found in the active site coordinated by Glu342, Asp366 and His532, and an additional metal ion was found at the channel for the passage of a substrate coordinated by Asp453. The X-ray structures basically supported the ene-diol mechanism for the aldose-ketose isomerization by B. pallidus d-AI, as well as Escherichia coli (E. coli) l-FI, in which Glu342 and Asp366 facing each other at the catalytic metal ion transfer a proton from C2 to C1 and O1 to O2, acting as acid/base catalysts, respectively. However, considering the ionized state of Asp366, the catalytic reaction also possibly occurs through the negatively charged ene-diolate intermediate stabilized by the catalytic metal ion. A structural comparison with E. colil-FI showed that B. pallidus d-AI possibly interconverts between "open" and "closed" forms, and that the additional metal ion found in B. pallidus d-AI may help to stabilize the channel region.
authors.affiliation: Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.
authors.forename: Kosei
authors.initials: K
authors.lastname: Takeda
authors.forename: Hiromi
authors.initials: H
authors.lastname: Yoshida
authors.forename: Ken
authors.initials: K
authors.lastname: Izumori
authors.forename: Shigehiro
authors.initials: S
authors.lastname: Kamitori
mesh_terms: D019747:Aldose-Ketose Isomerases / Q000737:chemistry* / Q000378:metabolism; D001407:Bacillus / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D002384:Catalysis; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology; D007536:Isomerism; D008345:Manganese / Q000737:chemistry* / Q000378:metabolism; D009005:Monosaccharides / Q000737:chemistry / Q000378:metabolism; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013402:Sugar Alcohols / Q000737:chemistry* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D009005:Monosaccharides; D013402:Sugar Alcohols; C473538:fucitol; D008345:Manganese; D019747:Aldose-Ketose Isomerases; C019714:D-arabinose isomerase