Substrate Distortion Contributes to the Catalysis of Orotidine 5′-Monophosphate Decarboxylase

Orotidine 5′-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of orotidine 5′-monophosphate (OMP) to uridine 5′-monophosphate (UMP) by 17 orders of magnitude. Eight new crystal structures with ligand analogues combined with computational analyses of the enzyme’s short-lived intermediates and the intrinsic electronic energies to distort the substrate and other ligands improve our understanding of the still controversially discussed reaction mechanism. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl and ethyl esters of OMP both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. Molecular dynamics and quantum mechanics/molecular mechanics computations of the enzyme–substrate complex also show the bond between the carboxylate group and the pyrimidine ring to be distorted, with the distortion contributing a 10–15% decrease of the ΔΔ<i>G</i>^⧧ value. These results are consistent with ODCase using both substrate distortion and transition-state stabilization, primarily exerted by K72, in its catalysis of the OMP decarboxylation reaction

Additional file 4: Figure S4. of Low-intensity pulsed ultrasound rescues insufficient salivary secretion in autoimmune sialadenitis

Bands of Western blot analysis for the cropped images in Fig. 3a (A), 3b (B) and 3c (C) are provided in this file. (TIFF 5449 kb

Additional file 2: Figure S2. of Low-intensity pulsed ultrasound rescues insufficient salivary secretion in autoimmune sialadenitis

Quantification of the fluorescence intensity in Fig. 1C. **p < 0.01 (n = 4). (TIFF 897 kb

Additional file 3: Figure S3. of Low-intensity pulsed ultrasound rescues insufficient salivary secretion in autoimmune sialadenitis

Bands of Western blot analysis for the cropped images in Fig. 2c are provided in this file. (TIFF 1856 kb

Additional file 1: Figure S1. of Low-intensity pulsed ultrasound rescues insufficient salivary secretion in autoimmune sialadenitis

Schematic representation of the in vitro LIPUS system used. A cell culture plate with medium was placed in the ultrasound field at a distance of about 1 mm from the transducer to optimize beam uniformity across the target region. (TIFF 1093 kb