Jack bean urease imaged at 49kX nominal magnification
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ABSTRACT:
SUBMITTER: J. Christopher Fromme
PROVIDER: EMPIAR-10547 | biostudies-other |
REPOSITORIES: biostudies-other
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| EMPIAR-10656 | biostudies-other
Project description:1. Urease of specific activity 160-180 Sumner units/g. (Sumner, 1951) was purified from jack-bean meal. The preparation was pure on the basis of polyacryl-amide-gel electrophoresis and N-terminal studies. 2. By using both the 1-fluoro-2,4-dinitrobenzene method and the phenyl isothiocyanate method a single N-terminal methionine residue was found. 3. A single C-terminal sequence -Tyr-Leu-Phe was found by studies with carboxypeptidase A, carboxypeptidase B and hydrazinolysis. 4. N-Bromosuccinimide cleavage showed that five unique tryptophan sequences were present: Trp-Ala, Trp-Glu, Trp-Gly, Trp-Met and Trp-Arg. 5. Polyacrylamide-gel electrophoresis in sodium dodecyl sulphate showed that urease had a subunit molecular weight of 76000. 6. The yield of N- and C-terminal amino acids, the number of tryptic peptides and tryptophan sequences and the above polyacrylamide-gel electrophoretic measurement all suggest that urease contains a single structural subunit of molecular weight 75000.
| S-EPMC1184748 | biostudies-other
Project description:Preliminary results of an extended X-ray absorption fine structure (e.x.a.f.s.) and X-ray absorption near edge structure study of jack bean urease have recently been reported [Hasnain & Piggott (1983) Biochem. Biophys. Res. Commun. 112, 279]. These results indicate that the environment of the nickel ion in the enzyme is similar to that in the model compounds Ni(L)2(L')1(ClO4)1 (where L is 1-n-propyl-2-alpha-hydroxybenzylbenzimidazole and L' is the deprotonated form) and Ni(HMB)3(Br)2 (where HMB is 2-hydroxymethylbenzimidazole), the closest similarity being with Ni(L)2-(L')1(ClO4)1. A detailed e.x.a.f.s. analysis has now been carried out and the crystal structures of the two model compounds solved. These results are reported here.
| S-EPMC1153664 | biostudies-other
Project description:Baicalin (BA) is the principal component of Radix Scutellariae responsible for its pharmacological activity. In this study, kinetics and mechanism of inhibition by BA against jack-bean urease were investigated for its therapeutic potential. It was revealed that the IC?? of BA against jack-bean urease was 2.74 ± 0.51 mM, which was proved to be a competitive and concentration-dependent inhibition with slow-binding progress curves. The rapid formation of initial BA-urease complex with an inhibition constant of K(i) = 3.89 × 10?³?mM was followed by a slow isomerization into the final complex with an overall inhibition constant of K(i)* = 1.47 × 10???mM. High effectiveness of thiol protectors against BA inhibition indicated that the strategic role of the active-site sulfhydryl group of the urease was involved in the blocking process. Moreover, the inhibition of BA was proved to be reversible due to the fact that urease could be reactivated by dithiothreitol but not reactant dilution. Molecular docking assay suggested that BA made contacts with the important activating sulfhydryl group Cys-592 residues and restricted the mobility of the active-site flap. Taken together, it could be deduced that BA was a competitive inhibitor targeting thiol groups of urease in a slow-binding manner both reversibly and concentration-dependently, serving as a promising urease inhibitor for treatments on urease-related diseases.
| S-EPMC3807542 | biostudies-literature
Project description:Plant urease is a seed protein that is common in most legumes. It is also common in many bacteria and fungi and several species of yeast. Urease allows organisms to use exogenous and internally generated urea as a nitrogen source by catalyzing the hydrolysis of urea to ammonia and carbon dioxide. Urease from jack bean meal was purified to electrophoretic homogeneity using a series of steps involving acetone precipitation and size-exclusion and ion-exchange chromatography. The jack bean urease was crystallized and the resulting crystals diffracted to 2.05 A resolution using synchrotron radiation. The crystals belonged to the hexagonal space group P6(3)22, with unit-cell parameters a = b = 138.57, c = 198.36 A.
| S-EPMC2795609 | biostudies-literature
Project description:A series of halo-substituted mixed ester/amide-based analogues 4a-l have been prepared as jack bean urease inhibitor, which showed good to excellent inhibition of enzyme activity. The role of halo-substituted benzoyl moieties and alkyl substituted anilines in urease inhibitory kinetics was also investigated. The alkyl-substituted anilines 1a–b reacted with chloroacetyl chloride to afford intermediates 2a-b, which were then reacted with different halo-substituted benzoic acids 3a–f to prepare the title compounds 4a-l. The chemical structures of final products 4a-l were ascertained by FTIR, 1H NMR, 13C NMR, and mass spectra. The compound 4b showed remarkable activity with IC501.6 ± 0.2?nM, better than the standard thiourea having IC50472.1 ± 135.1?nM. The 2-chloro-substituted phenyl ring on one side of compound 4b and 4-isopropyl-substituted benzene on the other side play an essential role in inhibition of urease activity. Lineweaver–Burk plots (kinetics study) indicated about 4b derivative as a mixed type of inhibitor. The virtual screening performed against urease enzyme (PDBID 4H9M) showed that compounds 4b and 4e have binding energies of ?7.8 and ?7.9?Kcal/mol, respectively. Based upon our results, it was found that derivative 4b is a highly potent urease inhibitor, better than the standard thiourea.
| S-EPMC7775144 | biostudies-literature
Project description:Sulfonamide derivatives serve as an important building blocks in the drug design discovery and development (4D) process. Ciprofloxacin-, sulfadiazine- and amantadine-based sulfonamides were synthesized as potent inhibitors of jack bean urease and free radical scavengers. Molecular diversity was explored and electronic factors were also examined. All 24 synthesized compounds exhibited excellent potential against urease enzyme. Compound 3e (IC50 = 0.081 ± 0.003 µM), 6a (IC50 = 0.0022 ± 0.0002 µM), 9e (IC50 = 0.0250 ± 0.0007 µM) and 12d (IC50 = 0.0266 ± 0.0021 µM) were found to be the lead compounds compared to standard (thiourea, IC50 = 17.814 ± 0.096 µM). Molecular docking studies were performed to delineate the binding affinity of the molecules and a kinetic mechanism of enzyme inhibition was propounded. Compounds 3e, 6a and 12d exhibited a mixed type of inhibition, while derivative 9e revealed a non-competitive mode of inhibition. Compounds 12a, 12b, 12d, 12e and 12f showed excellent radical scavenging potency in comparison to the reference drug vitamin C.
| S-EPMC6152116 | biostudies-literature
Project description:We provide a detailed description of a serial femtosecond crystallography (SFX) dataset collected at the European X-ray free-electron laser facility (EuXFEL). The EuXFEL is the first high repetition rate XFEL delivering MHz X-ray pulse trains at 10 Hz. The short spacing (<1 µs) between pulses requires fast flowing microjets for sample injection and high frame rate detectors. A data set was recorded of a microcrystalline mixture of at least three different jack bean proteins (urease, concanavalin A, concanavalin B). A one megapixel Adaptive Gain Integrating Pixel Detector (AGIPD) was used which has not only a high frame rate but also a large dynamic range. This dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development and for data analysis training for prospective XFEL users.
| S-EPMC6472352 | biostudies-literature