4q0p

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with L-ribose

spinqualitylabelsall models 4q0p, resolution 1.93Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4q0p is a 1 chain structure with sequence from Acinetobacter sp. DL-28. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.93Å Ligands: 0MK, CO, NCO, Z6J Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q93UQ5_9GAMM Publication Abstract from PubMed 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 beta-barrel structure, and the catalytic site was found between two large beta-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. DATABASE: The atomic coordinates and structure factors of AcL-RbI/l-ribose, AcL-RbI/l-ribulose, AcL-RbI/ribitol, E204Q/l-ribose and E204Q/l-ribulose have been deposited in the Protein Data Bank under accession codes, 4Q0P, 4Q0Q, 4Q0S, 4Q0U and 4Q0V. STRUCTURED DIGITAL ABSTRACT: * AcL-RbI and AcL-RbI bind by x-ray crystallography (View interaction). X-ray structure of a novel l-ribose isomerase acting on a non-natural sugar l-ribose as its ideal substrate.,Yoshida H, Yoshihara A, Teraoka M, Terami Y, Takata G, Izumori K, Kamitori S FEBS J. 2014 May 20. doi: 10.1111/febs.12850. PMID:24846739 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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