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Wang K, Hong Q, Zhu C, Xu Y, Li W, Wang Y, Chen W, Gu X, Chen X, Fang Y, Shen Y, Liu S, Zhang Y. Metal-ligand dual-site single-atom nanozyme mimicking urate oxidase with high substrates specificity. Nat Commun 2024; 15:5705. [PMID: 38977710 PMCID: PMC11231224 DOI: 10.1038/s41467-024-50123-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024] Open
Abstract
In nature, coenzyme-independent oxidases have evolved in selective catalysis using isolated substrate-binding pockets. Single-atom nanozymes (SAzymes), an emerging type of non-protein artificial enzymes, are promising to simulate enzyme active centers, but owing to the lack of recognition sites, realizing substrate specificity is a formidable task. Here we report a metal-ligand dual-site SAzyme (Ni-DAB) that exhibited selectivity in uric acid (UA) oxidation. Ni-DAB mimics the dual-site catalytic mechanism of urate oxidase, in which the Ni metal center and the C atom in the ligand serve as the specific UA and O2 binding sites, respectively, characterized by synchrotron soft X-ray absorption spectroscopy, in situ near ambient pressure X-ray photoelectron spectroscopy, and isotope labeling. The theoretical calculations reveal the high catalytic specificity is derived from not only the delicate interaction between UA and the Ni center but also the complementary oxygen reduction at the beta C site in the ligand. As a potential application, a Ni-DAB-based biofuel cell using human urine is constructed. This work unlocks an approach of enzyme-like isolated dual sites in boosting the selectivity of non-protein artificial enzymes.
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Affiliation(s)
- Kaiyuan Wang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Qing Hong
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Caixia Zhu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yuan Xu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Wang Li
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Ying Wang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Wenhao Chen
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Xiang Gu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Xinghua Chen
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yanfeng Fang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yanfei Shen
- Medical School, Southeast University, Nanjing, 210009, China.
| | - Songqin Liu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yuanjian Zhang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China.
- Department of Oncology, Zhongda Hospital, Southeast University, Nanjing, 210009, China.
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Baraf HSB, Khanna PP, Kivitz AJ, Strand V, Choi HK, Terkeltaub R, Dalbeth N, DeHaan W, Azeem R, Traber PG, Keenan RT. The COMPARE head-to-head, randomized controlled trial of SEL-212 (pegadricase plus rapamycin-containing nanoparticle, ImmTOR™) versus pegloticase for refractory gout. Rheumatology (Oxford) 2024; 63:1058-1067. [PMID: 37449908 PMCID: PMC10986798 DOI: 10.1093/rheumatology/kead333] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/01/2023] [Accepted: 06/17/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVES Serum urate (SU) lowering with PEGylated uricases in gout can reduce flares and tophi. However, treatment-emergent anti-drug antibodies adversely affect safety and efficacy and the currently approved PEGylated uricase pegloticase requires twice-monthly infusions. Investigational SEL-212 therapy aims to promote uricase-specific tolerance via monthly sequential infusions of a proprietary rapamycin-containing nanoparticle (ImmTOR) and pegadricase. METHODS COMPARE was a randomized, phase 2, open-label trial of SEL-212 vs pegloticase in adults with refractory gout. SEL-212 [ImmTOR (0.15 mg/kg) and pegadricase (0.2 mg/kg)] was infused monthly or pegloticase (8 mg) twice monthly for 6 months. The primary endpoint was the proportion of participants with SU <6 mg/dl for ≥80% of the time during 3 and 6 months. Secondary outcomes were mean SU, gout flares, number of tender and/or swollen joints and safety. RESULTS During months 3 and 6 combined, numerically more participants achieved and maintained a SU <6 mg/dl for ≥80% of the time with SEL-212 vs pegloticase (53.0% vs 46.0%, P = 0.181). The percentage reductions in SU levels were statistically greater during months 3 and 6 with SEL-212 vs pegloticase (-73.79% and -47.96%, P = 0.0161). Reductions in gout flare incidence and number of tender and/or swollen joints were comparable between treatments. There were numerical differences between the most common treatment-related adverse events of interest with SEL-212 and pegloticase: gout flares (60.2% vs 50.6%), infections (25.3% vs 18.4%) and infusion-related reactions (15.7% vs 11.5%), respectively. Stomatitis (and related terms) was experienced by eight participants (9.6%) with SEL-212 and none with pegloticase. Stomatitis, a known event for rapamycin, was associated with ImmTOR only. CONCLUSIONS SEL-212 efficacy and tolerability were comparable to pegloticase in refractory gout. This was associated with a substantial reduction in treatment burden with SEL-212 due to decreased infusion frequency vs pegloticase. CLINICAL TRIAL REGISTRATION NCT03905512.
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Affiliation(s)
- Herbert S B Baraf
- Rheumatology, Center for Rheumatology and Bone Research, Wheaton, MD, USA
- Rheumatology, George Washington University, Washington DC, USA
| | - Puja P Khanna
- Division of Rheumatology, University of Michigan, Ann Arbor, MI, USA
| | - Alan J Kivitz
- Department of Rheumatology, Altoona Center for Clinical Research, Duncansville, PA, USA
| | - Vibeke Strand
- Division of Immunology/Rheumatology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Hyon K Choi
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Robert Terkeltaub
- Rheumatology, Allergy and Immunology Division, San Diego VA Healthcare Service and UCSD, San Diego, CA, USA
| | - Nicola Dalbeth
- Bone and Joint Research Group, Department of Medicine, University of Auckland, Auckland, New Zealand
| | | | | | | | - Robert T Keenan
- Duke University School of Medicine, Durham, NC, USA
- Arthrosi Therapeutics, San Diego, CA, USA
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3
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Mori G, Liuzzi A, Ronda L, Di Palma M, Chegkazi MS, Bui S, Garcia-Maya M, Ragazzini J, Malatesta M, Della Monica E, Rivetti C, Antin PB, Bettati S, Steiner RA, Percudani R. Cysteine Enrichment Mediates Co-Option of Uricase in Reptilian Skin and Transition to Uricotelism. Mol Biol Evol 2023; 40:msad200. [PMID: 37695804 PMCID: PMC10517255 DOI: 10.1093/molbev/msad200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 09/13/2023] Open
Abstract
Uric acid is the main means of nitrogen excretion in uricotelic vertebrates (birds and reptiles) and the end product of purine catabolism in humans and a few other mammals. While uricase is inactivated in mammals unable to degrade urate, the presence of orthologous genes without inactivating mutations in avian and reptilian genomes is unexplained. Here we show that the Gallus gallus gene we name cysteine-rich urate oxidase (CRUOX) encodes a functional protein representing a unique case of cysteine enrichment in the evolution of vertebrate orthologous genes. CRUOX retains the ability to catalyze urate oxidation to hydrogen peroxide and 5-hydroxyisourate (HIU), albeit with a 100-fold reduced efficiency. However, differently from all uricases hitherto characterized, it can also facilitate urate regeneration from HIU, a catalytic property that we propose depends on its enrichment in cysteine residues. X-ray structural analysis highlights differences in the active site compared to known orthologs and suggests a mechanism for cysteine-mediated self-aggregation under H2O2-oxidative conditions. Cysteine enrichment was concurrent with the transition to uricotelism and a shift in gene expression from the liver to the skin where CRUOX is co-expressed with β-keratins. Therefore, the loss of urate degradation in amniotes has followed opposite evolutionary trajectories: while uricase has been eliminated by pseudogenization in some mammals, it has been repurposed as a redox-sensitive enzyme in the reptilian skin.
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Affiliation(s)
- Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Anastasia Liuzzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Michele Di Palma
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Magda S Chegkazi
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Soi Bui
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Mitla Garcia-Maya
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Jasmine Ragazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Emanuele Della Monica
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Parker B Antin
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, USA
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Roberto A Steiner
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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Cao X, Cai J, Zhang Y, Liu C, Song M, Xu Q, Liu Y, Yan H. Biodegradation of Uric Acid by Bacillus paramycoides-YC02. Microorganisms 2023; 11:1989. [PMID: 37630550 PMCID: PMC10460076 DOI: 10.3390/microorganisms11081989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
High serum uric acid levels, known as hyperuricemia (HUA), are associated with an increased risk of developing gout, chronic kidney disease, cardiovascular disease, diabetes, and other metabolic syndromes. In this study, a promising bacterial strain capable of biodegrading uric acid (UA) was successfully isolated from Baijiu cellar mud using UA as the sole carbon and energy source. The bacterial strain was identified as Bacillus paramycoides-YC02 through 16S rDNA sequence analysis. Under optimal culture conditions at an initial pH of 7.0 and 38 °C, YC02 completely biodegraded an initial UA concentration of 500 mg/L within 48 h. Furthermore, cell-free extracts of YC02 were found to catalyze and remove UA. These results demonstrate the strong biodegradation ability of YC02 toward UA. To gain further insight into the mechanisms underlying UA biodegradation by YC02, the draft genome of YC02 was sequenced using Illumina HiSeq. Subsequent analysis revealed the presence of gene1779 and gene2008, which encode for riboflavin kinase, flavin mononucleotide adenylyl transferase, and flavin adenine dinucleotide (FAD)-dependent urate hydroxylase. This annotation was based on GO or the KEEG database. These enzymes play a crucial role in the metabolism pathway, converting vitamin B2 to FAD and subsequently converting UA to 5-hydroxyisourate (HIU) with the assistance of FAD. Notably, HIU undergoes a slow non-enzymatic breakdown into 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) and (S)-allantoin. The findings of this study provide valuable insights into the metabolism pathway of UA biodegradation by B. paramycoides-YC02 and offer a potential avenue for the development of bacterioactive drugs against HUA and gout.
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Affiliation(s)
| | | | | | | | | | | | | | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (X.C.); (J.C.)
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Maikap A, Karmakar R, Meikap AK, Samanta S. Ultraflexible polyvinylidene fluoride film based amperometric enzyme-free sensor for selective detection of uric acid in a trace level. Biointerphases 2023; 18:041003. [PMID: 37594259 DOI: 10.1116/6.0002792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
The present invention describes a novel flexible nanosensor for the electrochemical detection of uric acid (UA) present in urine. The synthesized graphite-boron nanocomposite with an average thickness of ∼32 nm was grown up on a flexible polyvinylidene fluoride film with an average thickness of ∼50 μm and it acts as a nonenzymatic sensor for UA. The developed flexible sensor showed a prominent reduction peak in cyclic voltammetry and amperometric response with the presence of different concentrations of aqueous UA solution. In the electrochemical study, the redox peak was generated near ∼-0.42 V with a detection limit of around ∼2.09 μM as the bottom level. The high robustness of the developed sensor originated from the polymeric film base and the rapid response time of ∼0.5 s for detecting UA present in human urine. The interference property of the sensor was confirmed in the presence of bilirubin and creatinine as an eventual reference toward selectivity. The phase and morphology of the sensor surface were extensively observed before and after sensing to comprehend the electrochemical interaction between the sensor and target molecules. The generated quantitative results of the integrated system were verified by testing known and unknown concentrations of UA solutions.
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Affiliation(s)
- Abhisek Maikap
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
- Department of Physics, NIT Durgapur, Durgapur 713209, India
| | - Riju Karmakar
- Department of Physics, NIT Durgapur, Durgapur 713209, India
| | | | - Subhra Samanta
- MPML Division, CSIR-Central Mechanical Engineering Research Institute, Durgapur 713209, India
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Guo Y, Huo J, Bai R, Zhang J, Yao J, Ma K, Zhang Z, Li H, Zhang C. The effects of free Cys residues on the structure, activity, and tetrameric stability of mammalian uricase. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12597-y. [PMID: 37256327 DOI: 10.1007/s00253-023-12597-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023]
Abstract
Mammalian uricases contain four conserved cysteine (Cys) residues, but little is known about their structures and functions. In this study, we first confirmed that all four Cys residues are free and not involved in disulfide bond formation, using canine uricase as a model protein. Cys residues had a greater effect on stability than on activity based on single Cys-to-Ser (serine) substitutions. Circular dichroism (CD) and homology modeling indicated that C188S reduces β-sheet contents and inter- and intra-subunit hydrophobic interaction, potentially impairing the core tetrameric β-barrel structure of the tunneling-fold protein, and ultimately decreased the tetrameric stability. Additionally, the inactivation of C188S during the stability tests may be a complex process involving depolymerization followed by irregular aggregation. Double mutations or thiol blockage of Cys188 and Cys195 significantly disrupted the formation and stability of tetrameric uricase, which may be mediated by the free thiols in Cys residues. The present results demonstrated that the free Cys residues are essential for tetrameric formation and stability in mammalian uricase. This implies that free cysteine residues, although not involved in disulfide bonding, may play important structural roles in certain proteins, underscoring the significance of the hydrophobic characteristics of the free thiols in Cys residues. KEY POINTS: • Four Cys residues are not involved in disulfide bonding in mammalian uricase. • The hydrophobicity of free thiols is critical for tetrameric stability in uricase. • Free Cys residues can serve structural roles without involving in disulfide bonds.
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Affiliation(s)
- Yong Guo
- College of Pharmacy, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Jingjing Huo
- College of Pharmacy, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Runchao Bai
- Shandong Center for Food and Drug Evaluation & Inspection, Jinan, 250022, Shandong, People's Republic of China
| | - Jingyuan Zhang
- College of Pharmacy, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Jipeng Yao
- College of Pharmacy, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Kaijie Ma
- College of Pharmacy, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Zengtao Zhang
- Renrui Biotechnology Inc., Rizhao, 276599, Shandong, People's Republic of China
| | - Haigang Li
- College of Pharmacy, Linyi University, Linyi, 276000, Shandong, People's Republic of China.
| | - Chun Zhang
- College of Pharmacy, Linyi University, Linyi, 276000, Shandong, People's Republic of China.
- Renrui Biotechnology Inc., Rizhao, 276599, Shandong, People's Republic of China.
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Vasilev J, Mix AK, Heimerl T, Maier UG, Moog D. Inferred Subcellular Localization of Peroxisomal Matrix Proteins of Guillardia theta Suggests an Important Role of Peroxisomes in Cryptophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:889662. [PMID: 35783940 PMCID: PMC9244630 DOI: 10.3389/fpls.2022.889662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes participate in several important metabolic processes in eukaryotic cells, such as the detoxification of reactive oxygen species (ROS) or the degradation of fatty acids by β-oxidation. Recently, the presence of peroxisomes in the cryptophyte Guillardia theta and other "chromalveolates" was revealed by identifying proteins for peroxisomal biogenesis. Here, we investigated the subcellular localization of candidate proteins of G. theta in the diatom Phaeodactylum tricornutum, either possessing a putative peroxisomal targeting signal type 1 (PTS1) sequence or factors lacking a peroxisomal targeting signal but known to be involved in β-oxidation. Our results indicate important contributions of the peroxisomes of G. theta to the carbohydrate, ether phospholipid, nucleotide, vitamin K, ROS, amino acid, and amine metabolisms. Moreover, our results suggest that in contrast to many other organisms, the peroxisomes of G. theta are not involved in the β-oxidation of fatty acids, which exclusively seems to occur in the cryptophyte's mitochondria.
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Affiliation(s)
- Jana Vasilev
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ann-Kathrin Mix
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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8
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Xu X, Yan Y, Huang J, Zhang Z, Wang Z, Wu M, Liang H. Regulation of uric acid and glyoxylate metabolism by UgmR protein in Pseudomonas aeruginosa. Environ Microbiol 2022; 24:3242-3255. [PMID: 35702827 DOI: 10.1111/1462-2920.16088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa has evolved several systems to adapt to complex environments. The GntR family proteins play important roles in the regulation of metabolic processes and bacterial pathogenesis. In this study, we uncovered that the gene clusters of PA1513-PA1518 and PA1498-PA1502 in P. aeruginosa are required for uric acid and glyoxylate metabolism, respectively. We also identified a GntR family regulator UgmR that is involved in regulation of uric acid and glyoxylate metabolism. Promoter activity measurement and biochemical assays revealed that the UgmR directly represses the transcriptional activity of PA1513-PA1518 and PA1498-PA1502, and this inhibition was relieved by the addition of uric acid. Importantly, further experiments showed that UgmR also participates in the glyoxylate shunt. Collectively, these findings contribute to a better understanding of the UgmR factor involved in uric acid and glyoxylate metabolism, which provide insights into the complex metabolic pathways in P. aeruginosa. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xuejie Xu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Yunfang Yan
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Jiadai Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, SAR, China
| | - Zihao Zhang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Zhihan Wang
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND
| | - Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China.,College of Medicine, Southern University of Science and Technology, Shenzhen, China
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9
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Pugin B, Plüss S, Mujezinovic D, Nielsen RC, Lacroix C. Optimized UV-Spectrophotometric Assay to Screen Bacterial Uricase Activity Using Whole Cell Suspension. Front Microbiol 2022; 13:853735. [PMID: 35495677 PMCID: PMC9043897 DOI: 10.3389/fmicb.2022.853735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Uricase catalyzes the conversion of uric acid into allantoin with concomitant reduction of molecular oxygen to hydrogen peroxide. In humans, uricase is not functional, thereby predisposing individuals to hyperuricemia, a metabolic disturbance associated with gout, chronic kidney disorders, and cardiovascular diseases. The efficacy of current therapies to treat hyperuricemia is limited, and novel approaches are therefore desired, for instance using uricase-expressing probiotic strains. Here, we evaluated UV-spectrophotometric and H2O2-based fluorescent assays to enable the rapid identification of uricase activity in a broad panel of lactobacilli, Bacillus, and Bifidobacterium species. We highlighted abiotic (medium composition and mode of sterilization) and biotic (H2O2-producing strains) factors impacting the measurements' accuracy, and reported on the stepwise optimization of a simple, fast, and robust high-throughput UV-spectrophotometric method to screen uricase activity using whole bacterial suspension, thereby assessing both cell-associated and extracellular activity. The validity of the optimized assay, based on the monitoring of uric acid degradation at 300 nm, was confirmed via liquid chromatography. Finally, a panel of 319 Qualified Presumption of Safety (QPS) strains of lactobacilli (18 species covering nine genera), Bacillus (three species), and Bifidobacterium (four species) were screened for uricase activity using the optimized method. All 319 strains, but the positive control Bacillus sp. DSM 1306, were uricase-negative, indicating that this activity is rare among these genera, especially in isolates from food or feces. Altogether, the UV-spectrophotometric high-throughput assay based on whole bacterial suspension reported here can be used to rapidly screen large microbial collections, by simultaneously detecting cell-associated and extracellular uricase activity, thereby accelerating the identification of uricolytic strains with therapeutic potential to treat hyperuricemia.
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Affiliation(s)
- Benoit Pugin
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Serafina Plüss
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Denisa Mujezinovic
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
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Structural and biochemical insights into a hyperthermostable urate oxidase from Thermobispora bispora for hyperuricemia and gout therapy. Int J Biol Macromol 2021; 188:914-923. [PMID: 34403675 DOI: 10.1016/j.ijbiomac.2021.08.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 01/21/2023]
Abstract
Microbial urate oxidase has emerged as a potential source of therapeutic properties for hyperuricemia in arthritic gout and renal disease. The thermostability and long-term thermal tolerance of the enzyme need to be established to prolong its therapeutic effects. Here, we present the biochemical and structural aspects of a hyperthermostable urate oxidase (TbUox) from the thermophilic microorganism Thermobispora bispora. Enzymatic characterization of TbUox revealed that it was active over a wide range of temperatures, from 30 to 70 °C, with optimal activity at 65 °C and pH 8.0, which suggests its applicability under physiological conditions. Moreover, TbUox exhibits high thermostability from 10 to 65 °C, with Tm of 70.3 °C and near-neutral pH stability from pH 7.0 to 8.0 and high thermal tolerance. The crystal structures of TbUox revealed a distinct feature of the C-terminal loop extensions that may help with protein stability via inter-subunit interactions. In addition, the high thermal tolerance of TbUox may be contributed by the extensive inter-subunit contacts via salt bridges, hydrogen bonds, and hydrophobic interactions. The findings in this study provide a molecular basis for the thermophilic TbUox urate oxidase for application in hyperuricemia and gout therapy.
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Wang X, Shan J, Liu W, Li J, Tan H, Li X, Chen G. Theoretical Studies on the Binding Mode and Reaction Mechanism of TLP Hydrolase kpHIUH. Molecules 2021; 26:molecules26133884. [PMID: 34202153 PMCID: PMC8272043 DOI: 10.3390/molecules26133884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 11/16/2022] Open
Abstract
In this work, we have investigated the binding conformations of the substrate in the active site of 5-HIU hydrolase kpHIUH and its catalytic hydrolysis mechanism. Docking calculations revealed that the substrate adopts a conformation in the active site with its molecular plane laying parallel to the binding interface of the protein dimer of kpHIUH, in which His7 and His92 are located adjacent to the hydrolysis site C6 and have hydrogen bond interactions with the lytic water. Based on this binding conformation, density functional theory calculations indicated that the optimal catalytic mechanism consists of two stages: (1) the lytic water molecule is deprotonated by His92 and carries out nucleophilic attack on C6=O of 5-HIU, resulting in an oxyanion intermediate; (2) by accepting a proton transferred from His92, C6–N5 bond is cleaved to completes the catalytic cycle. The roles of His7, His92, Ser108 and Arg49 in the catalytic reaction were revealed and discussed in detail.
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12
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Hibi T, Itoh T. Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity. J Biochem 2021; 169:15-23. [PMID: 33002140 DOI: 10.1093/jb/mvaa114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 09/24/2020] [Indexed: 11/13/2022] Open
Abstract
Urate oxidases (UOs) catalyze the cofactor-independent oxidation of uric acid, and an extensive water network in the active site has been suggested to play an essential role in the catalysis. For our present analysis of the structure and function of the water network, the crystal qualities of Bacillus sp. TB-90 urate oxidase were improved by controlled dehydration using the humid air and glue-coating method. After the dehydration, the P21212 crystals were transformed into the I222 space group, leading to an extension of the maximum resolution to 1.42 Å. The dehydration of the crystals revealed a significant change in the five-water-molecules' binding mode in the vicinity of the catalytic diad, indicating that these molecules are quasi-stable. The pH profile analysis of log(kcat) gave two pKa values: pKa1 at 6.07 ± 0.07 and pKa2 at 7.98 ± 0.13. The site-directed mutagenesis of K13, T73 and N276 involved in the formation of the active-site water network revealed that the activities of these mutant variants were significantly reduced. These structural and kinetic data suggest that the five quasi-stable water molecules play an essential role in the catalysis of the cofactor-independent urate oxidation by reducing the energy penalty for the substrate-binding or an on-off switching for the proton-relay rectification.
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Affiliation(s)
- Takao Hibi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Yoshida, Fukui 910-1195, Japan
| | - Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Yoshida, Fukui 910-1195, Japan
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13
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Molecular Elucidation of a Urate Oxidase from Deinococcus radiodurans for Hyperuricemia and Gout Therapy. Int J Mol Sci 2021; 22:ijms22115611. [PMID: 34070642 PMCID: PMC8199477 DOI: 10.3390/ijms22115611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 12/02/2022] Open
Abstract
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.
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14
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McGregor L, Földes T, Bui S, Moulin M, Coquelle N, Blakeley MP, Rosta E, Steiner RA. Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis. IUCRJ 2021; 8:46-59. [PMID: 33520242 PMCID: PMC7792999 DOI: 10.1107/s2052252520013615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 06/12/2023]
Abstract
Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O2 to de-hydro-isourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5-hy-droxy-isourate (5HIU). At different stages of the reaction both catalytic O2 and water occupy the 'peroxo hole' above the organic substrate. Here, high-resolution neutron/X-ray crystallographic analysis at room temperature has been integrated with molecular dynamics simulations to investigate the hydration step of the reaction. The joint neutron/X-ray structure of perdeuterated Aspergillus flavus UOX in complex with its 8-azaxanthine (8AZA) inhibitor shows that the catalytic water molecule (W1) is present in the peroxo hole as neutral H2O, oriented at 45° with respect to the ligand. It is stabilized by Thr57 and Asn254 on different UOX protomers as well as by an O-H⋯π interaction with 8AZA. The active site Lys10-Thr57 dyad features a charged Lys10-NH3 + side chain engaged in a strong hydrogen bond with Thr57OG1, while the Thr57OG1-HG1 bond is rotationally dynamic and oriented toward the π system of the ligand, on average. Our analysis offers support for a mechanism in which W1 performs a nucleophilic attack on DHUC5 with Thr57HG1 central to a Lys10-assisted proton-relay system. Room-temperature crystallography and simulations also reveal conformational heterogeneity for Asn254 that modulates W1 stability in the peroxo hole. This is proposed to be an active mechanism to facilitate W1/O2 exchange during catalysis.
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Affiliation(s)
- Lindsay McGregor
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Tamás Földes
- Department of Chemistry, King’s College London, London SE1 1DB, United Kingdom
- Department of Physics and Astronomy, University College, London WC1E 6BT, United Kingdom
| | - Soi Bui
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Martine Moulin
- Life Sciences Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Nicolas Coquelle
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Edina Rosta
- Department of Chemistry, King’s College London, London SE1 1DB, United Kingdom
- Department of Physics and Astronomy, University College, London WC1E 6BT, United Kingdom
| | - Roberto A. Steiner
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
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15
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Li S, Shao M, Li D, Tang B, Cao W, Sun X. Association of serum uric acid levels with primary open-angle glaucoma: a 5-year case-control study. Acta Ophthalmol 2019; 97:e356-e363. [PMID: 29673085 DOI: 10.1111/aos.13789] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 03/17/2018] [Indexed: 01/03/2023]
Abstract
PURPOSE It has been hypothesised that uric acid (UA) has a protective effect against oxidative damage in the central nervous system. Therefore, we investigated serum UA concentrations in patients with primary open-angle glaucoma (POAG) and explored the relationship between serum UA concentration and glaucoma severity. METHODS This prospective, cross-sectional, case-control study was conducted in 163 POAG patients and 103 normal controls. Clinical and demographic information was obtained from the medical data platform of the Eye & ENT Hospital of Fudan University, Shanghai, China. The POAG patients were categorised into mild [median deviation (MD) ≤ 6.00 dB], moderate (MD > 6 Db-≥12 dB) and severe (MD > 12 dB) subgroups, based on their visual field MD results. RESULTS The level of serum UA in the POAG group (0.321 ± 0.084 mmol/l) was approximately 12.77% lower (p < 0.001) than that of the control group (0.362 ± 0.053 mmol/l). The UA/creatinine (Cr) ratio was approximately 14.99% lower (p < 0.001) in patients with POAG (4.47 ± 1.15), compared with the control group (5.14 ± 1.05). The mean level of UA was lowest in the severe POAG group, followed by the moderate POAG group, and the mild POAG group (p < 0.001). A similar trend was observed when UA levels were compared between the POAG and control groups in males. Multivariate regression analyses showed a significant negative correlation between UA and vertical cup-disc ratio (B = -0.320, p = 0.034), and UA and MD (B = -0.441, p = 0.031) in males. CONCLUSION Primary open-angle glaucoma patients have lower UA levels; however, a negative association between UA levels and disease severity was evident in male patients.
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Affiliation(s)
- Shengjie Li
- Department of Clinical Laboratory Eye & ENT Hospital, Shanghai Medical College Fudan University Shanghai China
| | - Mingxi Shao
- Department of Clinical Laboratory Eye & ENT Hospital, Shanghai Medical College Fudan University Shanghai China
| | - Danhui Li
- Key Laboratory of Environment and Genes Related to Diseases Ministry of Education Medical School Xi'an Jiaotong University Xi'an China
| | - Binghua Tang
- Department of Clinical Laboratory Eye & ENT Hospital, Shanghai Medical College Fudan University Shanghai China
| | - Wenjun Cao
- Department of Clinical Laboratory Eye & ENT Hospital, Shanghai Medical College Fudan University Shanghai China
- Department of Ophthalmology & Visual Science Eye & ENT Hospital, Shanghai Medical College Fudan University Shanghai China
| | - Xinghuai Sun
- Department of Ophthalmology & Visual Science Eye & ENT Hospital, Shanghai Medical College Fudan University Shanghai China
- State Key Laboratory of Medical Neurobiology Institutes of Brain Science and Collaborative Innovation Center for Brain Science Fudan University Shanghai China
- Key Laboratory of Myopia Ministry of Health (Fudan University) Shanghai China
- Shanghai Key Laboratory of Visual Impairment and Restoration (Fudan University) Shanghai China
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16
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Association between Pretreatment Serum Uric Acid Levels and Progression of Newly Diagnosed Primary Angle-Closure Glaucoma: A Prospective Cohort Study. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:7919836. [PMID: 30881597 PMCID: PMC6383391 DOI: 10.1155/2019/7919836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/03/2018] [Accepted: 12/16/2018] [Indexed: 12/17/2022]
Abstract
Purpose Increased evidence reveals that uric acid (UA) may have an important neuroprotective effect through its antioxidant properties. The aim of the present study was to investigate the relationship between pretreatment serum UA levels and the progression of newly diagnosed primary angle-closure glaucoma (PACG). Methods This prospective observational cohort study included 64 patients with newly diagnosed PACG who were followed up for a mean period of 12.77 months (range: 3–28 months). All subjects underwent a complete ophthalmological examination during the baseline and final follow-up visits, together with the acquisition of blood samples for UA measurements. During the follow-up period, the progression of PACG was defined as a clinical diagnosis of medically uncontrolled intraocular pressure and a loss of visual field with a mean deviation of >1 dB/year. Univariable and multivariable Cox regression models were used to investigate the association between baseline serum UA levels and the progression of PACG. The cumulative probability of progression of glaucoma was analyzed using the Kaplan-Meier method. Results During follow-up, 32 subjects were defined as progressive PACG, among whom baseline UA values were significantly higher in nonprogressing subjects than in progressing subjects (0.314 ± 0.069 mmol/l versus [vs.] 0.258 ± 0.069 mmol/l, respectively; P = 0.002). Similar results were also observed in male and female subgroups (P < 0.05). In a multivariable model, a decreased baseline serum UA level was associated with an increased risk for progressing PACG: both in male (hazard ratio [HR] 6.088 [95% confidence interval (CI) 1.163–31.8638]; P = 0.032) and female subjects (HR 3.565 [95% CI 1.131–11.236]; P = 0.030). Subjects with high UA levels demonstrated higher cumulative probabilities of nonprogressing PACG than those with low UA levels (male [16.67% vs. 80.00%; P = 0.0084] and female [29.41% vs. 68.00%; P = 0.0182]). Conclusion An association between high baseline serum UA levels and a decreased risk for progressing PACG was found. This primary finding suggests that high serum UA levels may have a protective role against PACG and could slow disease progression.
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17
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Paight C, Slamovits CH, Saffo MB, Lane CE. Nephromyces Encodes a Urate Metabolism Pathway and Predicted Peroxisomes, Demonstrating That These Are Not Ancient Losses of Apicomplexans. Genome Biol Evol 2019; 11:41-53. [PMID: 30500900 PMCID: PMC6320678 DOI: 10.1093/gbe/evy251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 12/21/2022] Open
Abstract
The phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasitic sister taxon, Cardiosporidium, revealing an ancestral purine degradation pathway thought to have been lost early in apicomplexan evolution. The predicted localization of many of the purine degradation enzymes to peroxisomes, and the in silico identification of a full set of peroxisome proteins, indicates that loss of both features in other apicomplexans occurred multiple times. The degradation of purines is thought to play a key role in the unusual relationship between Nephromyces and its host. Transcriptome data confirm previous biochemical results of a functional pathway for the utilization of uric acid as a primary nitrogen source for this unusual apicomplexan.
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Affiliation(s)
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mary Beth Saffo
- Department of Biological Sciences, University of Rhode Island
- Smithsonian National Museum of Natural History, Washington, District of Columbia
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18
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Turner R, Brennan SO, Ashby LV, Dickerhof N, Hamzah MR, Pearson JF, Stamp LK, Kettle AJ. Conjugation of urate-derived electrophiles to proteins during normal metabolism and inflammation. J Biol Chem 2018; 293:19886-19898. [PMID: 30385504 DOI: 10.1074/jbc.ra118.005237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/31/2018] [Indexed: 12/19/2022] Open
Abstract
Urate is often viewed as an antioxidant. Here, we present an alternative perspective by showing that, when oxidized, urate propagates oxidative stress. Oxidation converts urate to the urate radical and the electrophilic products dehydrourate, 5-hydroxyisourate, and urate hydroperoxide, which eventually break down to allantoin. We investigated whether urate-derived electrophiles are intercepted by nucleophilic amino acid residues to form stable adducts on proteins. When urate was oxidized in the presence of various peptides and proteins, two adducts derived from urate (M r 167 Da) were detected and had mass additions of 140 and 166 Da, occurring mainly on lysine residues and N-terminal amines. The adduct with a 140-Da mass addition was detected more frequently and was stable. Dehydrourate (M r 166 Da) also formed transient adducts with cysteine residues. Urate-derived adducts were detected on human serum albumin in plasma of healthy donors. Basal adduct levels increased when neutrophils were added to plasma and stimulated, and relied on the NADPH oxidase, myeloperoxidase, hydrogen peroxide, and superoxide. Adducts of oxidized urate on serum albumin were elevated in plasma and synovial fluid from individuals with gout and rheumatoid arthritis. We propose that rather than acting as an antioxidant, urate's conversion to electrophiles contributes to oxidative stress. The addition of urate-derived electrophiles to nucleophilic amino acid residues, a process we call oxidative uratylation, will leave a footprint on proteins that could alter their function when critical sites are modified.
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Affiliation(s)
- Rufus Turner
- From the Centre for Free Radical Research.,the Department of Pathology and Biomedical Science
| | | | - Louisa V Ashby
- From the Centre for Free Radical Research.,the Department of Pathology and Biomedical Science
| | - Nina Dickerhof
- From the Centre for Free Radical Research.,the Department of Pathology and Biomedical Science
| | - Melanie R Hamzah
- From the Centre for Free Radical Research.,the Department of Pathology and Biomedical Science
| | | | - Lisa K Stamp
- the Department of Medicine, University of Otago Christchurch, P.O. Box 4345, Christchurch 8011, New Zealand
| | - Anthony J Kettle
- From the Centre for Free Radical Research, .,the Department of Pathology and Biomedical Science
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19
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von Stetten D, Giraud T, Bui S, Steiner RA, Fihman F, de Sanctis D, Royant A. Online Raman spectroscopy for structural biology on beamline ID29 of the ESRF. J Struct Biol 2017; 200:124-127. [DOI: 10.1016/j.jsb.2017.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/11/2017] [Accepted: 10/13/2017] [Indexed: 10/18/2022]
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20
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Wei D, Huang X, Qiao Y, Rao J, Wang L, Liao F, Zhan CG. Catalytic Mechanisms for Cofactor-Free Oxidase-Catalyzed Reactions: Reaction Pathways of Uricase-Catalyzed Oxidation and Hydration of Uric Acid. ACS Catal 2017; 7:4623-4636. [PMID: 28890842 DOI: 10.1021/acscatal.7b00901] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
First-principles quantum mechanical/molecular mechanical (QM/MM)-free energy calculations have been performed to uncover how uricase catalyzes metabolic reactions of uric acid (UA), demonstrating that the entire reaction process of UA in uricase consists of two stages-oxidation followed by hydration. The oxidation consists of four steps: (1) chemical transformation from 8-hydroxyxythine to an anionic radical via a proton transfer along with an electron transfer, which is different from the previously proposed electron-transfer mechanism that involves a dianion intermediate (UA2-) during the catalytic reaction process; (2) proton transfer to the O2- anion (radical); (3) diradical recombination to form a peroxo intermediate; (4) dissociation of H2O2 to generate the dehydrourate. Hydration, for the most favorable pathway, is initiated by the nucleophilic attack of a water molecule on dehydrourate, along with a concerted proton transfer through residue Thr69 in the catalytic site. According to the calculated free energy profile, the hydration is the rate-determining step, and the corresponding free energy barrier of 16.2 kcal/mol is consistent with that derived from experimental kinetic data, suggesting that the computational insights into the catalytic mechanisms are reasonable. The mechanistic insights not only provide a mechanistic base for future rational design of uricase mutants with improved catalytic activity against uric acid as an improved enzyme therapy, but also are valuable for understanding a variety of other cofactor-free oxidase-catalyzed reactions involving an oxygen molecule.
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Affiliation(s)
- Donghui Wei
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Xiaoqin Huang
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Center
for Theoretical Biological Physics, and Center for Research Computing, Rice University, Houston, Texas 77030, United States,
| | - Yan Qiao
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Jingjing Rao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Lu Wang
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Fei Liao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Chang-Guo Zhan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Molecular
Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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Badu-Boateng C, Pardalaki S, Wolf C, Lajnef S, Peyrot F, Naftalin RJ. Labile iron potentiates ascorbate-dependent reduction and mobilization of ferritin iron. Free Radic Biol Med 2017; 108:94-109. [PMID: 28336129 DOI: 10.1016/j.freeradbiomed.2017.03.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/29/2017] [Accepted: 03/15/2017] [Indexed: 12/18/2022]
Abstract
Ascorbate mobilizes iron from equine spleen ferritin by two separate processes. Ascorbate alone mobilizes ferritin iron with an apparent Km (ascorbate) ≈1.5mM. Labile iron >2μM, complexed with citrate (10mM), synergises ascorbate-dependent iron mobilization by decreasing the apparent Km (ascorbate) to ≈270μM and raising maximal mobilization rate by ≈5-fold. Catalase reduces the apparent Km(ascorbate) for both ascorbate and ascorbate+iron dependent mobilization by ≈80%. Iron mobilization by ascorbate alone has a higher activation energy (Ea=45.0±5.5kJ/mole) than when mediated by ascorbate with labile iron (10μM) (Ea=13.7±2.2kJ/mole); also mobilization by iron-ascorbate has a three-fold higher pH sensitivity (pH range 6.0-8.0) than with ascorbate alone. Hydrogen peroxide inhibits ascorbate's iron mobilizing action. EPR and autochemiluminescence studies show that ascorbate and labile iron within ferritin enhances radical formation, whereas ascorbate alone produces negligible radicals. These findings suggest that iron catalysed single electron transfer reactions from ascorbate, involving ascorbate or superoxide and possibly ferroxidase tyrosine radicals, accelerate iron mobilization from the ferroxidase centre more than EPR silent, bi-dentate two-electron transfers. These differing modes of electron transference from ascorbate mirror the known mono and bidentate oxidation reactions of dioxygen and hydrogen peroxide with di-ferrous iron at the ferroxidase centre. This study implies that labile iron, at physiological pH, complexed with citrate, synergises iron mobilization from ferritin by ascorbate (50-4000μM). This autocatalytic process can exacerbate oxidative stress in ferritin-containing inflamed tissue.
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Affiliation(s)
- Charles Badu-Boateng
- Cardiovascular Division, British Heart Foundation Centre of Research Excellence and Physiology Department, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Sofia Pardalaki
- Cardiovascular Division, British Heart Foundation Centre of Research Excellence and Physiology Department, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | | | - Sonia Lajnef
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (UMR CNRS 8601), Université Paris Descartes, 75006 Paris, France
| | - Fabienne Peyrot
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (UMR CNRS 8601), Université Paris Descartes, 75006 Paris, France; ESPE de l'académie de Paris, Université Paris Sorbonne, 75016 Paris, France
| | - Richard J Naftalin
- Cardiovascular Division, British Heart Foundation Centre of Research Excellence and Physiology Department, King's College London, 150 Stamford Street, London SE1 9NH, UK.
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22
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Uric acid in plants and microorganisms: Biological applications and genetics - A review. J Adv Res 2017; 8:475-486. [PMID: 28748114 PMCID: PMC5512154 DOI: 10.1016/j.jare.2017.05.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/07/2017] [Accepted: 05/08/2017] [Indexed: 11/23/2022] Open
Abstract
Uric acid increased accumulation and/or reduced excretion in human bodies is closely related to pathogenesis of gout and hyperuricemia. It is highly affected by the high intake of food rich in purine. Uric acid is present in both higher plants and microorganisms with species dependent concentration. Urate-degrading enzymes are found both in plants and microorganisms but the mechanisms by which plant degrade uric acid was found to be different among them. Higher plants produce various metabolites which could inhibit xanthine oxidase and xanthine oxidoreductase, so prohibit the oxidation of hypoxanthine to xanthine then to uric acid in the purine metabolism. However, microorganisms produce group of degrading enzymes uricase, allantoinase, allantoicase and urease, which catalyze the degradation of uric acid to the ammonia. In humans, researchers found that several mutations caused a pseudogenization (silencing) of the uricase gene in ancestral apes which exist as an insoluble crystalloid in peroxisomes. This is in contrast to microorganisms in which uricases are soluble and exist either in cytoplasm or peroxisomes. Moreover, many recombinant uricases with higher activity than the wild type uricases could be induced successfully in many microorganisms. The present review deals with the occurrence of uric acid in plants and other organisms specially microorganisms in addition to the mechanisms by which plant extracts, metabolites and enzymes could reduce uric acid in blood. The genetic and genes encoding for uric acid in plants and microorganisms are also presented.
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23
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A Therapeutic Uricase with Reduced Immunogenicity Risk and Improved Development Properties. PLoS One 2016; 11:e0167935. [PMID: 28002433 PMCID: PMC5176304 DOI: 10.1371/journal.pone.0167935] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/22/2016] [Indexed: 02/04/2023] Open
Abstract
Humans and higher primates are unique in that they lack uricase, the enzyme capable of oxidizing uric acid. As a consequence of this enzyme deficiency, humans have high serum uric acid levels. In some people, uric acid levels rise above the solubility limit resulting in crystallization in joints, acute inflammation in response to those crystals causes severe pain; a condition known as gout. Treatment for severe gout includes injection of non-human uricase to reduce serum uric acid levels. Krystexxa® is a hyper-PEGylated pig-baboon chimeric uricase indicated for chronic refractory gout that induces an immunogenic response in 91% of treated patients, including infusion reactions (26%) and anaphylaxis (6.5%). These properties limit its use and effectiveness. An innovative approach has been used to develop a therapeutic uricase with improved properties such as: soluble expression, neutral pH solubility, high E. coli expression level, thermal stability, and excellent activity. More than 200 diverse uricase sequences were aligned to guide protein engineering and reduce putative sequence liabilities. A single uricase lead candidate was identified, which showed low potential for immunogenicity in >200 human donor samples selected to represent diverse HLA haplotypes. Cysteines were engineered into the lead sequence for site specific PEGylation and studies demonstrated >95% PEGylation efficiency. PEGylated uricase retains enzymatic activity in vitro at neutral pH, in human serum and in vivo (rats and canines) and has an extended half-life. In canines, an 85% reduction in serum uric acid levels was observed with a single subcutaneous injection. This PEGylated, non-immunogenic uricase has the potential to provide meaningful benefits to patients with gout.
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New insight into cofactor-free oxygenation from combined experimental and computational approaches. Curr Opin Struct Biol 2016; 41:109-118. [DOI: 10.1016/j.sbi.2016.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 06/22/2016] [Indexed: 01/07/2023]
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Machovina MM, Usselman RJ, DuBois JL. Monooxygenase Substrates Mimic Flavin to Catalyze Cofactorless Oxygenations. J Biol Chem 2016; 291:17816-28. [PMID: 27307041 DOI: 10.1074/jbc.m116.730051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 01/16/2023] Open
Abstract
Members of the antibiotic biosynthesis monooxygenase family catalyze O2-dependent oxidations and oxygenations in the absence of any metallo- or organic cofactor. How these enzymes surmount the kinetic barrier to reactions between singlet substrates and triplet O2 is unclear, but the reactions have been proposed to occur via a flavin-like mechanism, where the substrate acts in lieu of a flavin cofactor. To test this model, we monitored the uncatalyzed and enzymatic reactions of dithranol, a substrate for the nogalamycin monooxygenase (NMO) from Streptomyces nogalater As with flavin, dithranol oxidation was faster at a higher pH, although the reaction did not appear to be base-catalyzed. Rather, conserved asparagines contributed to suppression of the substrate pKa The same residues were critical for enzymatic catalysis that, consistent with the flavoenzyme model, occurred via an O2-dependent slow step. Evidence for a superoxide/substrate radical pair intermediate came from detection of enzyme-bound superoxide during turnover. Small molecule and enzymatic superoxide traps suppressed formation of the oxygenation product under uncatalyzed conditions, whereas only the small molecule trap had an effect in the presence of NMO. This suggested that NMO both accelerated the formation and directed the recombination of a superoxide/dithranyl radical pair. These catalytic strategies are in some ways flavin-like and stand in contrast to the mechanisms of urate oxidase and (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase, both cofactor-independent enzymes that surmount the barriers to direct substrate/O2 reactivity via markedly different means.
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Affiliation(s)
- Melodie M Machovina
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400
| | - Robert J Usselman
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400
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Patrício ES, Prado FM, da Silva RP, Carvalho LAC, Prates MVC, Dadamos T, Bertotti M, Di Mascio P, Kettle AJ, Meotti FC. Chemical Characterization of Urate Hydroperoxide, A Pro-oxidant Intermediate Generated by Urate Oxidation in Inflammatory and Photoinduced Processes. Chem Res Toxicol 2015. [PMID: 26207674 DOI: 10.1021/acs.chemrestox.5b00132] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Urate hydroperoxide is a strong oxidant generated by the combination of urate free radical and superoxide. The formation of urate hydroperoxide as an intermediate in urate oxidation is potentially responsible for the pro-oxidant effects of urate in inflammatory disorders, protein degradation, and food decomposition. To understand the molecular mechanisms that sustain the harmful effects of urate in inflammatory and oxidative stress related conditions, we report a detailed structural characterization and reactivity of urate hydroperoxide toward biomolecules. Urate hydroperoxide was synthesized by photo-oxidation and by a myeloperoxidase/hydrogen peroxide/superoxide system. Multiple reaction monitoring (MRM) and MS(3) ion fragmentation revealed that urate hydroperoxide from both sources has the same chemical structure. Urate hydroperoxide has a maximum absorption at 308 nm, ε308nm = 6.54 ± 0.38 × 10(3) M(-1) cm(-1). This peroxide decays spontaneously with a rate constant of k = 2.80 ± 0.18 × 10(-4) s(-1) and a half-life of 41 min at 22 °C. Urate hydroperoxide undergoes electrochemical reduction at potential values less negative than -0.5 V (versus Ag/AgCl). When incubated with taurine, histidine, tryptophan, lysine, methionine, cysteine, or glutathione, urate hydroperoxide reacted only with methionine, cysteine, and glutathione. The oxidation of these molecules occurred by a two-electron mechanism, generating the alcohol, hydroxyisourate. No adduct between cysteine or glutathione and urate hydroperoxide was detected. The second-order rate constant for the oxidation of glutathione by urate hydroperoxide was 13.7 ± 0.8 M(-1) s(-1). In conclusion, the oxidation of sulfur-containing biomolecules by urate hydroperoxide is likely to be a mechanism by which the pro-oxidant and damaging effects of urate are mediated in inflammatory and photo-oxidizing processes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Anthony J Kettle
- §Centre for Free Radical Research, Department of Pathology, University of Otago, Christchurch, 8140 Christchurch, New Zealand
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Bui S, von Stetten D, Jambrina PG, Prangé T, Colloc'h N, de Sanctis D, Royant A, Rosta E, Steiner RA. Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase. Angew Chem Int Ed Engl 2014; 53:13710-4. [PMID: 25314114 PMCID: PMC4502973 DOI: 10.1002/anie.201405485] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Indexed: 11/16/2022]
Abstract
Cofactor-free oxidases and oxygenases promote and control the reactivity of O2 with limited chemical tools at their disposal. Their mechanism of action is not completely understood and structural information is not available for any of the reaction intermediates. Near-atomic resolution crystallography supported by in crystallo Raman spectroscopy and QM/MM calculations showed unambiguously that the archetypical cofactor-free uricase catalyzes uric acid degradation via a C5(S)-(hydro)peroxide intermediate. Low X-ray doses break specifically the intermediate C5-OO(H) bond at 100 K, thus releasing O2 in situ, which is trapped above the substrate radical. The dose-dependent rate of bond rupture followed by combined crystallographic and Raman analysis indicates that ionizing radiation kick-starts both peroxide decomposition and its regeneration. Peroxidation can be explained by a mechanism in which the substrate radical recombines with superoxide transiently produced in the active site.
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Affiliation(s)
- Soi Bui
- Randall Division of Cell and Molecular Biophysics, King's College LondonNew Hunt's House, Guy's Campus, London SE1 1UL (UK)
| | - David von Stetten
- European Synchrotron Radiation FacilityCS 40220, 38043 Grenoble Cedex 9 (France)
| | - Pablo G Jambrina
- Department of Chemistry, King's College LondonBritannia House 7 Trinity Street, London, SE1 1DB (UK)
| | - Thierry Prangé
- LCRB, UMR 8015-Université Paris Descartes-CNRSFaculté de Pharmacie 75270 Paris Cedex 06 (France)
| | - Nathalie Colloc'h
- ISTCT, UMR 6301-UCBN-CNRS-CEA-Normandie UniversitéCentre Cyceron, 14074 Caen Cedex (France)
| | - Daniele de Sanctis
- European Synchrotron Radiation FacilityCS 40220, 38043 Grenoble Cedex 9 (France)
| | - Antoine Royant
- European Synchrotron Radiation FacilityCS 40220, 38043 Grenoble Cedex 9 (France)
- Institut de Biologie StructuraleUMR 5075 Université Grenoble Alpes-CNRS-CEA, CS10090, 38044 Grenoble Cedex 9 (France)
| | - Edina Rosta
- Department of Chemistry, King's College LondonBritannia House 7 Trinity Street, London, SE1 1DB (UK)
| | - Roberto A Steiner
- Randall Division of Cell and Molecular Biophysics, King's College LondonNew Hunt's House, Guy's Campus, London SE1 1UL (UK)
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Bui S, von Stetten D, Jambrina PG, Prangé T, Colloc'h N, de Sanctis D, Royant A, Rosta E, Steiner RA. Direct Evidence for a Peroxide Intermediate and a Reactive Enzyme-Substrate-Dioxygen Configuration in a Cofactor-free Oxidase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Evolutionary history and metabolic insights of ancient mammalian uricases. Proc Natl Acad Sci U S A 2014; 111:3763-8. [PMID: 24550457 DOI: 10.1073/pnas.1320393111] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Uricase is an enzyme involved in purine catabolism and is found in all three domains of life. Curiously, uricase is not functional in some organisms despite its role in converting highly insoluble uric acid into 5-hydroxyisourate. Of particular interest is the observation that apes, including humans, cannot oxidize uric acid, and it appears that multiple, independent evolutionary events led to the silencing or pseudogenization of the uricase gene in ancestral apes. Various arguments have been made to suggest why natural selection would allow the accumulation of uric acid despite the physiological consequences of crystallized monosodium urate acutely causing liver/kidney damage or chronically causing gout. We have applied evolutionary models to understand the history of primate uricases by resurrecting ancestral mammalian intermediates before the pseudogenization events of this gene family. Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history by crystallizing a mammalian uricase protein. Further, ancient and modern uricases were stably transfected into HepG2 liver cells to test one hypothesis that uricase pseudogenization allowed ancient frugivorous apes to rapidly convert fructose into fat. Finally, pharmacokinetics of an ancient uricase injected in rodents suggest that our integrated approach provides the foundation for an evolutionarily-engineered enzyme capable of treating gout and preventing tumor lysis syndrome in human patients.
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Oksanen E, Blakeley MP, El-Hajji M, Ryde U, Budayova-Spano M. The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation. PLoS One 2014; 9:e86651. [PMID: 24466188 PMCID: PMC3900588 DOI: 10.1371/journal.pone.0086651] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/16/2013] [Indexed: 12/02/2022] Open
Abstract
Urate oxidase transforms uric acid to 5-hydroxyisourate without the help of cofactors, but the catalytic mechanism has remained enigmatic, as the protonation state of the substrate could not be reliably deduced. We have determined the neutron structure of urate oxidase, providing unique information on the proton positions. A neutron crystal structure inhibited by a chloride anion at 2.3 Å resolution shows that the substrate is in fact 8-hydroxyxanthine, the enol tautomer of urate. We have also determined the neutron structure of the complex with the inhibitor 8-azaxanthine at 1.9 Å resolution, showing the protonation states of the K10–T57–H256 catalytic triad. Together with X-ray data and quantum chemical calculations, these structures allow us to identify the site of the initial substrate protonation and elucidate why the enzyme is inhibited by a chloride anion.
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Affiliation(s)
- Esko Oksanen
- Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives, Grenoble, France, IBS, Centre National de la Recherche Scientifique, Grenoble, France, IBS, Université Grenoble Alpes, Grenoble, France
| | | | | | - Ulf Ryde
- Department of Theoretical Chemistry Lund University, Lund, Sweden
| | - Monika Budayova-Spano
- Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives, Grenoble, France, IBS, Centre National de la Recherche Scientifique, Grenoble, France, IBS, Université Grenoble Alpes, Grenoble, France
- * E-mail:
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Thierbach S, Bui N, Zapp J, Chhabra SR, Kappl R, Fetzner S. Substrate-assisted O2 activation in a cofactor-independent dioxygenase. ACTA ACUST UNITED AC 2014; 21:217-25. [PMID: 24388758 DOI: 10.1016/j.chembiol.2013.11.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/22/2013] [Accepted: 11/27/2013] [Indexed: 11/29/2022]
Abstract
In contrast to the majority of O2-activating enzymes, which depend on an organic cofactor or a metal ion for catalysis, a particular group of structurally unrelated oxygenases is functional without any cofactor. In this study, we characterized the mechanism of O2 activation in the reaction pathway of a cofactor-independent dioxygenase with an α/β-hydrolase fold, which catalyzes the oxygenolytic cleavage of 2-alkyl-3-hydroxy-4(1H)-quinolones. Chemical analysis and electron paramagnetic resonance spectroscopic data revealed that O2 activation in the enzyme's active site is substrate-assisted, relying on single electron transfer from the bound substrate anion to O2 to form a radical pair, which recombines to a C2-peroxide intermediate. Thus, an oxygenase can function without a cofactor, if the organic substrate itself, after activation to a (carb)anion by an active-site base, is intrinsically reactive toward molecular oxygen.
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Affiliation(s)
- Sven Thierbach
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany
| | - Nguyen Bui
- Department of Biophysics, School of Medicine, Saarland University, Clinical Center, Building 76, 66421 Homburg, Germany
| | - Josef Zapp
- Pharmaceutical Biology, Saarland University, Campus, Building C2, 66123 Saarbrücken, Germany
| | - Siri Ram Chhabra
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Reinhard Kappl
- Department of Biophysics, School of Medicine, Saarland University, Clinical Center, Building 76, 66421 Homburg, Germany
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany.
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Lee IR, Yang L, Sebetso G, Allen R, Doan THN, Blundell R, Lui EYL, Morrow CA, Fraser JA. Characterization of the complete uric acid degradation pathway in the fungal pathogen Cryptococcus neoformans. PLoS One 2013; 8:e64292. [PMID: 23667704 PMCID: PMC3646786 DOI: 10.1371/journal.pone.0064292] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/10/2013] [Indexed: 01/08/2023] Open
Abstract
Degradation of purines to uric acid is generally conserved among organisms, however, the end product of uric acid degradation varies from species to species depending on the presence of active catabolic enzymes. In humans, most higher primates and birds, the urate oxidase gene is non-functional and hence uric acid is not further broken down. Uric acid in human blood plasma serves as an antioxidant and an immune enhancer; conversely, excessive amounts cause the common affliction gout. In contrast, uric acid is completely degraded to ammonia in most fungi. Currently, relatively little is known about uric acid catabolism in the fungal pathogen Cryptococcus neoformans even though this yeast is commonly isolated from uric acid-rich pigeon guano. In addition, uric acid utilization enhances the production of the cryptococcal virulence factors capsule and urease, and may potentially modulate the host immune response during infection. Based on these important observations, we employed both Agrobacterium-mediated insertional mutagenesis and bioinformatics to predict all the uric acid catabolic enzyme-encoding genes in the H99 genome. The candidate C. neoformans uric acid catabolic genes identified were named: URO1 (urate oxidase), URO2 (HIU hydrolase), URO3 (OHCU decarboxylase), DAL1 (allantoinase), DAL2,3,3 (allantoicase-ureidoglycolate hydrolase fusion protein), and URE1 (urease). All six ORFs were then deleted via homologous recombination; assaying of the deletion mutants' ability to assimilate uric acid and its pathway intermediates as the sole nitrogen source validated their enzymatic functions. While Uro1, Uro2, Uro3, Dal1 and Dal2,3,3 were demonstrated to be dispensable for virulence, the significance of using a modified animal model system of cryptococcosis for improved mimicking of human pathogenicity is discussed.
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Affiliation(s)
- I. Russel Lee
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Liting Yang
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gaseene Sebetso
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Rebecca Allen
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Thi H. N. Doan
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Ross Blundell
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Edmund Y. L. Lui
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Carl A. Morrow
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Feng J, Liu H, Yang X, Gao A, Liao J, Feng L, Pu J, Xie Y, Long G, Li Y, Liao F. Comparison of activity indexes for recognizing enzyme mutants of higher activity with uricase as model. Chem Cent J 2013; 7:69. [PMID: 23594729 PMCID: PMC3637054 DOI: 10.1186/1752-153x-7-69] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/06/2013] [Indexed: 11/13/2022] Open
Abstract
Background For screening a library of enzyme mutants, an efficient and cost-effective method for reliable assay of enzyme activity and a decision method for safe recognition of mutants of higher activity are needed. The comparison of activity concentrations of mutants in lysates of transformed Escherichia coli cells against a threshold is unsafe to recognize mutants of higher activity due to variations of both expression levels of mutant proteins and lysis efficiency of transformed cells. Hence, by a spectrophotometric method after verification to measure uricase activity, specific activity calculated from the level of total proteins in a lysate was tested for recognizing a mutant of higher activity. Results During uricase reaction, the intermediate 5-hydroxyisourate interferes with the assay of uric acid absorbance, but the measurement of absorbance at 293 nm in alkaline borate buffer was reliable for measuring uricase initial rates within a reasonable range. The level of total proteins in a lysate was determined by the Bradford assay. Polyacrylamide gel electrophoresis analysis supported different relative abundance of uricase mutant proteins in their lysates; activity concentrations of uricase in such lysates positively correlated with levels of total proteins. Receiver-operation-curve analysis of activity concentration or specific activity yielded area-under-the-curve close to 1.00 for recognizing a mutant with > 200% improvement of activity. For a mutant with just about 80% improvement of activity, receiver-operation-curve analysis of specific activity gave area-under-the-curve close to 1.00 while the analysis of activity concentration gave smaller area-under-the-curve. With the mean plus 1.4-fold of the standard deviation of specific activity of a starting material as the threshold, uricase mutants whose activities were improved by more than 80% were recognized with higher sensitivity and specificity. Conclusion Specific activity calculated from the level of total proteins is a favorable index for recognizing an enzyme mutant with small improvement of activity.
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Affiliation(s)
- Juan Feng
- Unit for Analytical Probes and Protein Biotechnology, Key Laboratory of Clinical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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Identification and bioactivity analysis of transthyretin-like protein in amphioxus: A case demonstrating divergent evolution from an enzyme to a hormone distributor. Comp Biochem Physiol B Biochem Mol Biol 2013; 164:143-50. [DOI: 10.1016/j.cbpb.2012.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 12/30/2022]
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Hennebry SC, Sait LC, Mantena R, Humphrey TJ, Yang J, Scott T, Kupz A, Richardson SJ, Strugnell RA. Salmonella typhimurium's transthyretin-like protein is a host-specific factor important in fecal survival in chickens. PLoS One 2012; 7:e46675. [PMID: 23284609 PMCID: PMC3528726 DOI: 10.1371/journal.pone.0046675] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 09/03/2012] [Indexed: 01/30/2023] Open
Abstract
The transthyretin-like protein (TLP) from Salmonella enterica subspecies I is a periplasmic protein with high level structural similarity to a protein found in mammals and fish. In humans, the protein homologue, transthyretin, binds and carries retinol and thyroxine, and a series of other, unrelated aromatic compounds. Here we show that the amino acid sequence of the TLP from different species, subspecies and serovars of the Salmonella genus is highly conserved and demonstrate that the TLP gene is constitutively expressed in S. Typhimurium and that copper and other divalent metal ions severely inhibit enzyme activity of the TLP, a cyclic amidohydrolase that hydrolyses 5-hydroxyisourate (5-HIU). In order to determine the in vivo role of the S. Typhimurium TLP, we constructed a strain of mouse-virulent S. Typhimurium SL1344 bearing a mutation in the TLP gene (SL1344 ΔyedX). We assessed the virulence of this strain via oral inoculation of mice and chickens. Whilst SL1344 ΔyedX induced a systemic infection in both organisms, the bacterial load detected in the faeces of infected chickens was significantly reduced when compared to the load of S. Typhimurium SL1344. These data demonstrate that the TLP gene is required for survival of S. Typhimurium in a high uric acid environment such as chicken faeces, and that metabolic traits of Salmonellae in natural and contrived hosts may be fundamentally different. Our data also highlight the importance of using appropriate animal models for the study of bacterial pathogenesis especially where host-specific virulence factors or traits are the subject of the study.
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Affiliation(s)
- Sarah C Hennebry
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia.
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Zhang C, Fan K, Ma X, Wei D. Impact of large aggregated uricases and PEG diol on accelerated blood clearance of PEGylated canine uricase. PLoS One 2012; 7:e39659. [PMID: 22745806 PMCID: PMC3383732 DOI: 10.1371/journal.pone.0039659] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 05/28/2012] [Indexed: 11/18/2022] Open
Abstract
Background Uricase has proven therapeutic value in treating hyperuricemia but sufficient reduction of its immunogenicity may be the largest obstacle to its chronic use. In this study, canine uricase was modified with 5 kDa mPEG-SPA and the impact of large aggregated uricases and cross-linked conjugates induced by difunctional PEG diol on immunogenicity was investigated. Methods and Findings Recombinant canine uricase was first expressed and purified to homogeneity. Source 15Q anion-exchange chromatography was used to separate tetrameric and aggregated uricase prior to pegylation, while DEAE anion-exchange chromatography was used to remove Di-acid PEG (precursor of PEG diol) from unfractionated 5 kDa mPEG-propionic acid. Tetrameric and aggregated uricases were separately modified with the purified mPEG-SPA. In addition, tetrameric uricases was modified with unfractionated mPEG-SPA, resulting in three types of 5 kDa mPEG-SPA modified uricase. The conjugate size was evaluated by dynamic light scattering and transmission electron microscope. The influence of differently PEGylated uricases on pharmacokinetics and immunogenicity were evaluated in vivo. The accelerated blood clearance (ABC) phenomenon previously identified for PEGylated liposomes occurred in rats injected with PEGylated uricase aggregates. Anti-PEG IgM antibodies, rather than neutralizing antibodies, were found to mediate the ABC. Conclusions The size of conjugates is important for triggering such phenomena and we speculate that 40–60 nm is the lower size limit that can trigger ABC. Removal of the uricase aggregates and the PEG diol contaminant and modifying with small PEG reagents enabled ABC to be successfully avoided and sufficient reduction in the immunogenicity of 5 kDa mPEG-modified tetrameric canine uricase.
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Affiliation(s)
- Chun Zhang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, People’s Republic of China
- Modern TCM Institute, Linyi University, Linyi, Shandong, People’s Republic of China
| | - Kai Fan
- Fagen Biomedical Inc., Chongqing, People’s Republic of China
| | - Xuefeng Ma
- Fagen Biomedical Inc., Chongqing, People’s Republic of China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, People’s Republic of China
- * E-mail:
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Delineation of the caffeine C-8 oxidation pathway in Pseudomonas sp. strain CBB1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism. J Bacteriol 2012; 194:3872-82. [PMID: 22609920 DOI: 10.1128/jb.00597-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The molecular basis of the ability of bacteria to live on caffeine via the C-8 oxidation pathway is unknown. The first step of this pathway, caffeine to trimethyluric acid (TMU), has been attributed to poorly characterized caffeine oxidases and a novel quinone-dependent caffeine dehydrogenase. Here, we report the detailed characterization of the second enzyme, a novel NADH-dependent trimethyluric acid monooxygenase (TmuM), a flavoprotein that catalyzes the conversion of TMU to 1,3,7-trimethyl-5-hydroxyisourate (TM-HIU). This product spontaneously decomposes to racemic 3,6,8-trimethylallantoin (TMA). TmuM prefers trimethyluric acids and, to a lesser extent, dimethyluric acids as substrates, but it exhibits no activity on uric acid. Homology models of TmuM against uric acid oxidase HpxO (which catalyzes uric acid to 5-hydroxyisourate) reveal a much bigger and hydrophobic cavity to accommodate the larger substrates. Genes involved in the caffeine C-8 oxidation pathway are located in a 25.2-kb genomic DNA fragment of CBB1, including cdhABC (coding for caffeine dehydrogenase) and tmuM (coding for TmuM). Comparison of this gene cluster to the uric acid-metabolizing gene cluster and pathway of Klebsiella pneumoniae revealed two major open reading frames coding for the conversion of TM-HIU to S-(+)-trimethylallantoin [S-(+)-TMA]. The first one, designated tmuH, codes for a putative TM-HIU hydrolase, which catalyzes the conversion of TM-HIU to 3,6,8-trimethyl-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (TM-OHCU). The second one, designated tmuD, codes for a putative TM-OHCU decarboxylase which catalyzes the conversion of TM-OHCU to S-(+)-TMA. Based on a combination of enzymology and gene-analysis, a new degradative pathway for caffeine has been proposed via TMU, TM-HIU, TM-OHCU to S-(+)-TMA.
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Siitonen V, Blauenburg B, Kallio P, Mäntsälä P, Metsä-Ketelä M. Discovery of a Two-Component Monooxygenase SnoaW/SnoaL2 Involved in Nogalamycin Biosynthesis. ACTA ACUST UNITED AC 2012; 19:638-46. [DOI: 10.1016/j.chembiol.2012.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/16/2012] [Accepted: 04/04/2012] [Indexed: 11/30/2022]
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Zhang C, Fan K, Zhang W, Zhu R, Zhang L, Wei D. Structure-based characterization of canine-human chimeric uricases and its evolutionary implications. Biochimie 2012; 94:1412-20. [PMID: 22481018 DOI: 10.1016/j.biochi.2012.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 03/21/2012] [Indexed: 02/04/2023]
Abstract
Uricase was lost in hominoids during primate evolution, but the inactivation mechanism remains controversial. To investigate the inactivation process of hominoid uricase, chimeric constructions between canine and human uricase were employed to screen the target regions that may contain labile or inactivated mutations in deduced human uricase. Four chimeric uricases were constructed and showed different enzymatic characteristics. Homology modeling, rational site-directed mutagenesis and DNA alignment were used to analyze the changes. Arg119 is conserved in functional mammalian uricases and its side-chains are crucial in maintaining the stability of the β-barrel core. A single CGT (Arg) to CAT (His) mutation at codon 119 that is shared by the human and great ape clade greatly reduces this stability and could cause the loss of uricase activity. We speculate that this missense mutation occurred first and inactivated the uricase protein in humans and great apes and that later the known nonsense mutation at codon 33 occurred and silenced the uricase gene. A single GTC (Val) to GCC (Ala) mutation at codon 296 in canine uricase is regarded as deleterious structural mutation, but such kinds of deleterious mutations have been widely accumulated in extant mammalian uricases. We speculate that a reduction in uricase activity has been an evolutionary tendency in mammals. Moreover, from structure-activity analysis of helix 2 in ancestral primate uricase, we suggest that before the inactivation of hominoid uricase, deleterious structural evolutionary changes had occurred in ancestral primates. The loss of hominoid uricase should be caused by progressive multistep mutations rather than a single mutation event.
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Affiliation(s)
- Chun Zhang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, PR China
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40
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Gerola AP, Semensato J, Pellosi DS, Batistela VR, Rabello BR, Hioka N, Caetano W. Chemical determination of singlet oxygen from photosensitizers illuminated with LED: New calculation methodology considering the influence of photobleaching. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.01.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Yang X, Yuan Y, Zhan CG, Liao F. Uricases as therapeutic agents to treat refractory gout: Current states and future directions. Drug Dev Res 2011; 73:66-72. [PMID: 22665944 DOI: 10.1002/ddr.20493] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Treatment of refractory gout remains a challenge on drug development. While pegloticase, a recombinant mammalian uricase modified with monomethoxyl-poly(ethylene glycol) (mPEG) is effective in treating refractory gout, after continued treatment for three months biweekly at a therapeutic dose of 0.14 mg/kg body weight, it elicits an immune response against mPEG in nearly 20% of patients. For continued treatment of refractory gout PEGylated uricases at monthly therapeutic doses below 4 μg/kg body weight have promise. To formulate uricases to achieve monthly therapeutic regimens requires pharmacodynamics simulation and experimentation including: (a) molecular engineering of uricases based on rational design and evolution biotechnology in combination to improve their inherent catalytic efficiency, thermostability and selectivity for urate over xanthine and; (b) optimization of the number and distribution of accessible reactive amino acid residues in native uricases for site-specific PEGylation with PEG derivatives with lower of immunogenicity than mPEG to retain activity, minimize immunogenicity and enhance the pharmacokinetics of the PEGylated uricase. These issues are briefly reviewed as a means to stimulate the development of safer uricase formulations for continued treatment of refractory gout.
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Affiliation(s)
- Xiaolan Yang
- Unit for Analytical Probes and Protein Biotechnology, Key Laboratory of Medical Laboratory Diagnosis of the Education Ministry of China, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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French JB, Ealick SE. Structural and kinetic insights into the mechanism of 5-hydroxyisourate hydrolase from Klebsiella pneumoniae. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:671-7. [PMID: 21795808 PMCID: PMC3144850 DOI: 10.1107/s090744491101746x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/09/2011] [Indexed: 11/10/2022]
Abstract
The stereospecific oxidative degradation of uric acid to (S)-allantoin has recently been demonstrated to proceed via two unstable intermediates and requires three separate enzymatic reactions. The second step of this reaction, the conversion of 5-hydroxyisourate (HIU) to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, is catalyzed by HIU hydrolase (HIUH). The high-resolution crystal structure of HIUH from the opportunistic pathogen Klebsiella pneumoniae (KpHIUH) has been determined. KpHIUH is a homotetrameric protein that, based on sequence and structural similarity, belongs to the transthyretin-related protein family. In addition, the steady-state kinetic parameters for this enzyme and four active-site mutants have been measured. These data provide valuable insight into the functional roles of the active-site residues. Based upon the structural and kinetic data, a mechanism is proposed for the KpHIUH-catalyzed reaction.
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Affiliation(s)
- Jarrod B. French
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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Werner AK, Witte CP. The biochemistry of nitrogen mobilization: purine ring catabolism. TRENDS IN PLANT SCIENCE 2011; 16:381-7. [PMID: 21482173 DOI: 10.1016/j.tplants.2011.03.012] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/10/2011] [Accepted: 03/11/2011] [Indexed: 05/20/2023]
Abstract
The enzymatic route of purine ring catabolism has recently been completed by the discovery of several novel enzymes identified through comparative genome analyses. Here, we review these recent discoveries and present an overview of purine ring catabolism in plants. Xanthine is oxidized to urate in the cytosol, followed by three enzymatic steps taking place in the peroxisome and four reactions in the endoplasmic reticulum releasing the four ring nitrogen as ammonia. Although the main physiological function of purine degradation might lie in the remobilization of nitrogen resources, it has also emerged that catabolic intermediates, the ureides allantoin and allantoate, are likely to be involved in protecting plants against abiotic stress. Conserved alternative splicing mediating the peroxisomal as well as cytosolic localization of allantoin synthase potentially links purine ring catabolism to brassinosteroid signaling.
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Affiliation(s)
- Andrea K Werner
- Department of Plant Biochemistry, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Germany
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44
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Pipolo S, Percudani R, Cammi R. Absolute stereochemistry and preferred conformations of urate degradation intermediates from computed and experimental circular dichroism spectra. Org Biomol Chem 2011; 9:5149-55. [PMID: 21647520 DOI: 10.1039/c1ob05433c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The enzymatic oxidation of urate leads to the sequential formation of optically active intermediates with unknown stereochemistry: (-)-5-hydroxyisourate (HIU) and (-)-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU). In accordance with the observation that a defect in HIU hydrolase causes hepatocarcinoma in mouse, a detoxification role has been proposed for the enzymes accelerating the conversion of HIU and OHCU into optically active (+)-allantoin. The enzymatic products of urate oxidation are normally not present in humans, but are formed in patients treated with urate oxidase. We used time-dependent density functional theory (TDDFT) to compute the electronic circular dichroism (ECD) spectra of the chiral compounds of urate degradation (HIU, OHCU, allantoin) and we compared the results with experimentally measured ECD spectra. The calculated ECD spectra for (S)-HIU and (S)-OHCU reproduced well the experimental spectra obtained through the enzymatic degradation of urate. Less conclusive results were obtained with allantoin, although the computed optical rotations in the transparent region supported the original assignment of the (+)-S configuration. These absolute configuration assignments can facilitate the study of the enzymes involved in urate metabolism and help us to understand the mechanism leading to the toxicity of urate oxidation products.
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Affiliation(s)
- Silvio Pipolo
- Dipartimento di Chimica G.I.A.F, Universitá di Parma, 43100, Parma, Italy
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Cendron L, Ramazzina I, Percudani R, Rasore C, Zanotti G, Berni R. Probing the evolution of hydroxyisourate hydrolase into transthyretin through active-site redesign. J Mol Biol 2011; 409:504-12. [PMID: 21515285 DOI: 10.1016/j.jmb.2011.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 04/08/2011] [Accepted: 04/10/2011] [Indexed: 12/18/2022]
Abstract
5-Hydroxyisourate hydrolase (HIUase) and transthyretin (TTR) are closely related phylogenetically and structurally, while performing quite different functions. The former catalyzes the hydrolysis of 5-hydroxyisourate within the urate degradation pathway, and the latter is a carrier protein involved in the extracellular transport of thyroid hormones and in the cotransport of retinol. The evolution of HIUase into TTR represents a remarkable example of adaptation of a new function by active-site modification of an enzyme. On the basis of phylogenetic reconstructions and structural comparison of HIUase and TTR, two mutations (Y116T and I16A) were likely to be crucial events in order to induce, after a gene duplication event, the conversion of the enzyme into a binding protein. By rational reshaping of the active sites of HIUase and functional analyses of its mutant forms, we have provided insights into how its neofunctionalization could be achieved. We show here that the two mutations at the active sites of HIUase open up the two ends of the channel that transverses the entire tetrameric protein, generating two cavities accessible to the thyroxine molecule and abrogating, at the same time, the enzymatic activity. Our data indicate that a small number of critical mutations affecting the active site of an enzyme may be sufficient to generate a drastically different function, while a large number of additional mutations may be required for the fine-tuning of the structural and functional features of new proteins.
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Affiliation(s)
- Laura Cendron
- Department of Biological Chemistry, University of Padua, Viale Colombo 3, 35121 Padua, Italy
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Gabison L, Chopard C, Colloc'h N, Peyrot F, Castro B, Hajji ME, Altarsha M, Monard G, Chiadmi M, Prangé T. X-ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor-less urate oxidase. Proteins 2011; 79:1964-76. [DOI: 10.1002/prot.23022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 02/09/2011] [Accepted: 02/11/2011] [Indexed: 11/11/2022]
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47
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French JB, Ealick SE. Structural and mechanistic studies on Klebsiella pneumoniae 2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase. J Biol Chem 2010; 285:35446-54. [PMID: 20826786 PMCID: PMC2975168 DOI: 10.1074/jbc.m110.156034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 08/31/2010] [Indexed: 11/06/2022] Open
Abstract
The stereospecific oxidative degradation of uric acid to (S)-allantoin was recently shown to proceed via three enzymatic steps. The final conversion is a decarboxylation of the unstable intermediate 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) and is catalyzed by OHCU decarboxylase. Here we present the structures of Klebsiella pneumoniae OHCU decarboxylase in unliganded form and with bound allantoin. These structures provide evidence that ligand binding organizes the active site residues for catalysis. Modeling of the substrate and intermediates provides additional support for this hypothesis. In addition we characterize the steady state kinetics of this enzyme and report the first OHCU decarboxylase inhibitor, allopurinol, a structural isomer of hypoxanthine. This molecule is a competitive inhibitor of K. pneumoniae OHCU decarboxylase with a K(i) of 30 ± 2 μM. Circular dichroism measurements confirm structural observations that this inhibitor disrupts the necessary organization of the active site. Our structural and biochemical studies also provide further insights into the mechanism of catalysis of OHCU decarboxylation.
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Affiliation(s)
- Jarrod B. French
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Steven E. Ealick
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
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48
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Puehringer S, RoseFigura J, Metlitzky M, Toyama H, Klinman JP, Schwarzenbacher R. Structural studies of mutant forms of the PQQ-forming enzyme PqqC in the presence of product and substrate. Proteins 2010; 78:2554-62. [PMID: 20602352 DOI: 10.1002/prot.22769] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Pyrroloquinoline quinone [4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid (PQQ)] is a bacterial cofactor in numerous alcohol dehydrogenases including methanol dehydrogenase and glucose dehydrogenase. Its biosynthesis in Klebsiella pneumoniae is facilitated by six genes, pqqABCDEF and proceeds by an unknown pathway. PqqC is one of two metal free oxidases of known structure and catalyzes the last step of PQQ biogenesis which involves a ring closure and an eight-electron oxidation of the substrate [3a-(2-amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline-7,9-dicarboxylic acid (AHQQ)]. PqqC has 14 conserved active site residues, which have previously been shown to be in close contact with bound PQQ. Herein, we describe the structures of three PqqC active site variants, H154S, Y175F, and the double mutant R179S/Y175S. The H154S crystal structure shows that, even with PQQ bound, the enzyme is still in the "open" conformation with helices alpha5b and alpha6 unfolded and the active site solvent accessible. The Y175F PQQ complex crystal structure reveals the closed conformation indicating that Y175 is not required for the conformational change. The R179S/Y175S AHQQ complex crystal structure is the most mechanistically informative, indicating an open conformation with a reaction intermediate trapped in the active site. The intermediate seen in R179S/Y175S is tricyclic but nonplanar, implying that it has not undergone oxidation. These studies implicate a stepwise process in which substrate binding leads to the generation of the closed protein conformation, with the latter playing a critical role in O(2) binding and catalysis.
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Affiliation(s)
- Sandra Puehringer
- Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
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49
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Girard E, Marchal S, Perez J, Finet S, Kahn R, Fourme R, Marassio G, Dhaussy AC, Prangé T, Giffard M, Dulin F, Bonneté F, Lange R, Abraini JH, Mezouar M, Colloc'h N. Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure. Biophys J 2010; 98:2365-73. [PMID: 20483346 DOI: 10.1016/j.bpj.2010.01.058] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 01/26/2010] [Accepted: 01/28/2010] [Indexed: 10/19/2022] Open
Abstract
Structure-function relationships in the tetrameric enzyme urate oxidase were investigated using pressure perturbation. As the active sites are located at the interfaces between monomers, enzyme activity is directly related to the integrity of the tetramer. The effect of hydrostatic pressure on the enzyme was investigated by x-ray crystallography, small-angle x-ray scattering, and fluorescence spectroscopy. Enzymatic activity was also measured under pressure and after decompression. A global model, consistent with all measurements, discloses structural and functional details of the pressure-induced dissociation of the tetramer. Before dissociating, the pressurized protein adopts a conformational substate characterized by an expansion of its substrate binding pocket at the expense of a large neighboring hydrophobic cavity. This substate should be adopted by the enzyme during its catalytic mechanism, where the active site has to accommodate larger intermediates and product. The approach, combining several high-pressure techniques, offers a new (to our knowledge) means of exploring structural and functional properties of transient states relevant to protein mechanisms.
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Affiliation(s)
- Eric Girard
- Institut de Biologie Structurale J.-P. Ebel UMR 5075 CEA CNRS UJF, Grenoble, France
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50
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Lash TD, Mani UN, Keck ASIM, Jones MA. Normal and abnormal heme biosynthesis. 6. Synthesis and metabolism of a series of monovinylporphyrinogens related to harderoporphyrinogen. Further insights into the oxidative decarboxylation of porphyrinogen substrates by coproporphyrinogen oxidase. J Org Chem 2010; 75:3183-92. [PMID: 20387847 DOI: 10.1021/jo100083t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of vinylporphyrinogens were prepared to probe the enzyme coproporphyrinogen oxidase (CPO). Six (2-chloroethyl)porphyrins were synthesized from a common dipyrrylmethane via a,c-biladiene intermediates in excellent yields. Subsequent dehydrohalogenation with DBU in refluxing DMF then gave the required vinylporphyrin methyl esters, including harderoporphyrin-I, harderoporphyrin-III, and isoharderoporphyrin. The corresponding porphyrinogen carboxylic acids were incubated with chicken red cell hemolysates, which contain the enzyme CPO, and the products analyzed. The 17-ethyl analogue of harderoporphyrinogen-III, but not its 13-ethyl isomer, was shown to be an excellent substrate for CPO in accord with a proposed model for the active site of this enzyme. In addition, harderoporphyrinogen-VII, the monovinyl intermediate in the metabolism of coproporphyrinogen-IV, was shown to be an equally good substrate for this enzyme. However, isoharderoporphyrinogen, which lacks the correct ordering of peripheral substituents, was also a substrate for CPO. Furthermore, a nonnatural type I isomer of harderoporphyrinogen was shown to be acted on by CPO, but in this case further metabolism was noted and this afforded an unprecedented trivinyl porphyrinogen product. The corresponding porphyrin methyl ester was isolated and characterized by FAB MS and proton NMR spectroscopy. The results from these studies allow the binding requirements of CPO to be further assessed and provide a series of substrates to investigate this poorly understood enzyme.
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Affiliation(s)
- Timothy D Lash
- Department of Chemistry, Illinois State University, Normal, Illinois 61790-4160, USA.
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