Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand

2010 ◽  
Vol 66 (6) ◽  
pp. 714-724 ◽  
Author(s):  
Laure Gabison ◽  
Mohamed Chiadmi ◽  
Mohamed El Hajji ◽  
Bertrand Castro ◽  
Nathalie Colloc'h ◽  
...  
Keyword(s):  
Uric Acid ◽  
Metal Ion ◽  
Active Sites ◽  
Reaction Pathway ◽  
Catalytic Triad ◽  
Urate Oxidase ◽  
Atomic Resolution ◽  
Base System ◽  
Protonation State ◽  
Large Water

Urate oxidase (uricase; EC 1.7.3.3; UOX) fromAspergillus flavuscatalyzes the oxidation of uric acid in the presence of molecular oxygen to 5-hydroxyisourate in the degradation cascade of purines; intriguingly, catalysis proceeds using neither a metal ion (Fe, Cuetc.) nor a redox cofactor. UOX is a tetrameric enzyme with four active sites located at the interface of two subunits; its structure was refined at atomic resolution (1 Å) using new crystal data in the presence of xanthine and at near-atomic resolution (1.3–1.7 Å) in complexes with the natural substrate (urate) and two inhibitors: 8-nitroxanthine and 8-thiouric acid. Three new features of the structural and mechanistic behaviour of the enzyme were addressed. Firstly, the high resolution of the UOX–xanthine structure allowed the solution of an old structural problem at a contact zone within the tetramer; secondly, the protonation state of the substrate was determined from both a halochromic inhibitor complex (UOX–8-nitroxanthine) and from the H-atom distribution in the active site, using the structures of the UOX–xanthine and the UOX–uric acid complexes; and thirdly, it was possible to extend the general base system, characterized by the conserved catalytic triad Thr–Lys–His, to a large water network that is able to buffer and shuttle protons back and forth between the substrate and the peroxo hole along the reaction pathway.

Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors

2014 ◽  
Vol 70 (2) ◽  
pp. 461-470 ◽  
Author(s):  
Petr Pachl ◽  
Milan Fábry ◽  
Ivan Rosenberg ◽  
Ondřej Šimák ◽  
Pavlína Řezáčová ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Specific Inhibitor ◽  
Detailed Comparison ◽  
Atomic Resolution ◽  
Phosphate Anion ◽  
Protonation State ◽  
Interatomic Distances ◽  
Enzyme Active Site ◽  
Resolution Structure

The human 5′(3′)-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08 Å) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4 Å) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.

Catalytic Resonance Theory: Parallel Reaction Pathway Control

2019 ◽  
Author(s):  
M. Alexander Ardagh ◽  
Manish Shetty ◽  
Anatoliy Kuznetsov ◽  
Qi Zhang ◽  
Phillip Christopher ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
Active Site ◽  
Active Sites ◽  
Reaction Pathway ◽  
Control Strategies ◽  
Oscillation Amplitude ◽  
Catalytic Performance ◽  
Parallel Reaction ◽  
Resonance Theory ◽  
Static Conditions

Catalytic enhancement of chemical reactions via heterogeneous materials occurs through stabilization of transition states at designed active sites, but dramatically greater rate acceleration on that same active site is achieved when the surface intermediates oscillate in binding energy. The applied oscillation amplitude and frequency can accelerate reactions orders of magnitude above the catalytic rates of static systems, provided the active site dynamics are tuned to the natural frequencies of the surface chemistry. In this work, differences in the characteristics of parallel reactions are exploited via selective application of active site dynamics (0 < ΔU < 1.0 eV amplitude, 10<sup>-6</sup> < f < 10<sup>4</sup> Hz frequency) to control the extent of competing reactions occurring on the shared catalytic surface. Simulation of multiple parallel reaction systems with broad range of variation in chemical parameters revealed that parallel chemistries are highly tunable in selectivity between either pure product, even when specific products are not selectively produced under static conditions. Two mechanisms leading to dynamic selectivity control were identified: (i) surface thermodynamic control of one product species under strong binding conditions, or (ii) catalytic resonance of the kinetics of one reaction over the other. These dynamic parallel pathway control strategies applied to a host of chemical conditions indicate significant potential for improving the catalytic performance of many important industrial chemical reactions beyond their existing static performance.

scholarly journals Spin-sate reconfiguration induced by alternating magnetic field for efficient oxygen evolution reaction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gang Zhou ◽  
Peifang Wang ◽  
Hao Li ◽  
Bin Hu ◽  
Yan Sun ◽  
...  
Keyword(s):  
Reaction Kinetics ◽  
Oxygen Evolution ◽  
Oxygen Evolution Reaction ◽  
Active Sites ◽  
Reaction Pathway ◽  
Low Cost ◽  
Orbital Interaction ◽  
New Paradigm ◽  
Metal Organic ◽  
Energy Conversion Devices

AbstractOxygen evolution reaction (OER) plays a determining role in electrochemical energy conversion devices, but challenges remain due to the lack of effective low-cost electrocatalysts and insufficient understanding about sluggish reaction kinetics. Distinguish from complex nano-structuring, this work focuses on the spin-related charge transfer and orbital interaction between catalysts and intermediates to accelerate catalytic reaction kinetics. Herein, we propose a simple magnetic-stimulation approach to rearrange spin electron occupation in noble-metal-free metal-organic frameworks (MOFs) with a feature of thermal-differentiated superlattice, in which the localized magnetic heating in periodic spatial distribution makes the spin flip occur at particular active sites, demonstrating a spin-dependent reaction pathway. As a result, the spin-rearranged Co0.8Mn0.2 MOF displays mass activities of 3514.7 A gmetal−1 with an overpotential of ~0.27 V, which is 21.1 times that of pristine MOF. Our findings provide a new paradigm for designing spin electrocatalysis and steering reaction kinetics.

scholarly journals Molecular Elucidation of a Urate Oxidase from Deinococcus radiodurans for Hyperuricemia and Gout Therapy

2021 ◽  
Vol 22 (11) ◽  
pp. 5611
Author(s):  
Yi-Chih Chiu ◽  
Ting-Syuan Hsu ◽  
Chen-Yu Huang ◽  
Chun-Hua Hsu
Keyword(s):  
Uric Acid ◽  
High Stability ◽  
Deinococcus Radiodurans ◽  
Catalytic Efficiency ◽  
Enzyme Characterization ◽  
Urate Oxidase ◽  
Medical Applications ◽  
Physiological Conditions ◽  
Extremophile Microorganism ◽  
Mesophilic Conditions

Urate oxidase initiates the uric acid degradation pathways and is extensively used for protein drug development for gout therapy and serum uric acid diagnosis. We first present the biochemical and structural elucidation of a urate oxidase from the extremophile microorganism Deinococcus radiodurans (DrUox). From enzyme characterization, DrUox showed optimal catalytic ability at 30 °C and pH 9.0 with high stability under physiological conditions. Only the Mg2+ ion moderately elevated its activity, which indicates the characteristic of the cofactor-free urate oxidase family. Of note, DrUox is thermostable in mesophilic conditions. It retains almost 100% activity when incubated at 25 °C and 37 °C for 24 h. In this study, we characterized a thermostable urate oxidase, DrUox with high catalytic efficiency and thermal stability, which strengthens its potential for medical applications.

Effect and Mechanism of Total Saponin of Dioscorea on Animal Experimental Hyperuricemia

2006 ◽  
Vol 34 (01) ◽  
pp. 77-85 ◽  
Author(s):  
Guang-Liang Chen ◽  
Wei Wei ◽  
Shu-Yun Xu
Keyword(s):  
Uric Acid ◽  
Serum Uric Acid ◽  
Acid Concentration ◽  
Serum Uric Acid Level ◽  
Urate Oxidase ◽  
Uric Acid Concentration ◽  
Total Saponin ◽  
Test Kit ◽  
Serum Uric Acid Concentration ◽  
Potassium Oxonate

In this study, we investigated the effects and mechanisms of Total Saponin of Dioscorea (TSD) on animal experimental hyperuricemia. Mouse and rat hyperuricemic models were made by orally administering yeast extract paste once a day (30 and 20 g/kg, respectively), for 7 days. Yeast would disturb normal purine metabolism by increasing xanthine oxidase (XOD) activity and generating large quantities of uric acid. This model is similar to human hyperuricemia, which is induced by high-protein diets, due to a purine and nucleic acid metabolic disturbance. Another mouse hyperuricemia model was generated by intraperitoneal injection once with uric acid 250 mg/kg or potassium oxonate 300 mg/kg. Potassium oxonate, a urate oxidase inhibitor, can raise the serum uric acid level by inhibiting the decomposition of uric acid. Likewise, injecting uric acid can also increase serum uric acid concentration. The concentration of uric acid in serum or urine was detected by the phosphotungstic acid method, and the activity of XOD was assayed by a test kit. The results showed that TSD (240, 120 and 60 mg/kg, ig) could significantly lower the level of serum uric acid in hyperuricemic mice. TSD (120 and 60 mg/kg, ig) could also lower the level of serum uric acid in hyperuricemic rats, reduce the activity of XOD in the serum and liver of hyperuricemic rats, and increase the level of urine uric acid concentration as well as 24-hour total uric acid excretion. In conclusion, TSD possesses a potent anti-hyperuricemic effect on hyperuricemic animals, and the mechanism may be relevant in accelerating the excretion and decreasing the production of uric acid.

Follow-Up Study on Management of Tumour Lysis Syndrome with Single Low Fixed Dose (1.5 mg) of Rasburicase - A Tertiary Cancer Centre Experience from India

2021 ◽  
Vol 8 (25) ◽  
pp. 2149-2154
Author(s):  
Alok Ranjan ◽  
Nisha Khanna ◽  
Vivek Ranjan ◽  
Ashwin Kumar
Keyword(s):  
Uric Acid ◽  
Single Dose ◽  
Tumour Lysis Syndrome ◽  
Urate Oxidase ◽  
Fixed Dose ◽  
Additional Dose ◽  
Tumour Lysis ◽  
Follow Up Study ◽  
Study Results

BACKGROUND Rasburicase (recombinant urate oxidase) has been proven to be an effective therapy for prevention of tumour lysis syndrome (TLS). The recommended daily dosing regimen of rasburicase is 0.2 mg/kg/day for 5 days which is expensive and unaffordable to many patients in the developing countries. The purpose of the present study was to evaluate the effect of single 1.5 mg dose rasburicase in the management of tumour lysis syndrome. METHODS This is a follow-up study done at our institute. Fifty (50) patients with tumour lysis syndrome who received rasburicase from August 2015 to January 2020 were enrolled in this study RESULTS Single dose of rasburicase is effective in decreasing serum uric acid level in significant number (N = 41) of patients. Percentage of patients having uric acid less than 7 mg after single dose of rasburicase in 48 hours - 82.9 % (N = 34) while 17 % (N = 7) were found to have uric acid levels of more than 7 mg/dl. The percentage of patients with uric acid levels more than 7 mg/dl reduced from 36.5 % after 24 hours to 17 % after 48 hours. This indicates that the uric acid levels show a declining trend even after 24 hours without giving an additional dose of rasburicase. There was no relationship between uric acid levels at 24 hours and percentage change in creatinine level from baseline to 24 hours (correlation coefficient (r) = -0.047, P = 0.770. Patients who required additional dose (N = 9) had high base line value of uric acid and their high value was maintained over the follow up period of three days. Patients with pre exiting kidney disease and high level of baseline uric acid also needed dialysis (N = 3). CONCLUSIONS In majority of patients, a single 1.5 mg dose of rasburicase is an effective way to reduce raised uric acid in appropriate circumstances. KEYWORDS Single Dose, Recombinant Urate Oxidase, Uric Acid, Leukemia, Tumour Lysis Syndrome, Rasburicase

Efficient N2 Reduction with VS2 Electrocatalyst: Identifying the Active Sites and Unraveling the Reaction Pathway

2021 ◽  
Author(s):  
Liang Zhao ◽  
Rui Zhao ◽  
Yixiang Zhou ◽  
Xiaoxuan Wang ◽  
Xinyue Chi ◽  
...  
Keyword(s):  
Active Sites ◽  
Reaction Pathway ◽  
Reduction Reaction ◽  
Sustainable Production ◽  
Nitrogen Reduction

Electrochemical nitrogen reduction reaction (NRR) is an effective method for sustainable production of NH3. However, a robust NRR electrocatalyst is predominantly required in order to active the inert N2 molecule....

High uric acid induces liver fat accumulation via ROS/JNK/AP-1 signaling

2021 ◽  
Author(s):  
De Xie ◽  
Hairong Zhao ◽  
Jiaming Lu ◽  
Furong He ◽  
Weidong Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Uric Acid ◽  
Fatty Acid Synthase ◽  
Specific Inhibitor ◽  
Urate Oxidase ◽  
Alcoholic Fatty Liver ◽  
Fat Accumulation ◽  
Lipogenic Gene ◽  
Lipogenic Gene Expression ◽  
Jnk Activation

Uric acid is the end metabolite derived from the oxidation of purine compounds. Overwhelming evidence shows the vital interrelation between hyperuricemia (HUA) and non-alcoholic fatty liver disease (NAFLD). However, the mechanisms for this association remain unclear. In this study, we investigated the effect of HUA on fat accumulation in human HepG2 hepatoma cells and urate oxidase-knockout (Uox-KO) mice. HUA activated c-Jun N-terminal kinase (JNK) in vivo and in vitro. Furthermore, inhibiting JNK activation by a JNK-specific inhibitor, SP600125, decreased fat accumulation and lipogenic gene expression induced by HUA. Overexpression of the lipogenic enzymes fatty acid synthase and acetyl-CoA carboxylase 1 was via activation of JNK, which was blocked by the JNK inhibitor SP600125. HUA activated AP-1 to upregulate lipogenic gene expression via JNK activation. In addition, HUA caused mitochondrial dysfunction and reactive oxygen species production. Pre-treatment with the antioxidant N-acetyl-L-cysteine could ameliorate HUA-activated JNK and hepatic steatosis. These data suggest that ROS/JNK/AP-1 signaling plays an important role in HUA-mediated fat accumulation in liver.

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