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Carter MS, Tuttle MJ, Mancini JA, Martineau R, Hung CS, Gupta MK. Microbially Induced Calcium Carbonate Precipitation by Sporosarcina pasteurii: a Case Study in Optimizing Biological CaCO 3 Precipitation. Appl Environ Microbiol 2023; 89:e0179422. [PMID: 37439668 PMCID: PMC10467343 DOI: 10.1128/aem.01794-22] [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] [Indexed: 07/14/2023] Open
Abstract
Current production of traditional concrete requires enormous energy investment that accounts for approximately 5 to 8% of the world's annual CO2 production. Biocement is a building material that is already in industrial use and has the potential to rival traditional concrete as a more convenient and more environmentally friendly alternative. Biocement relies on biological structures (enzymes, cells, and/or cellular superstructures) to mineralize and bind particles in aggregate materials (e.g., sand and soil particles). Sporosarcina pasteurii is a workhorse organism for biocementation, but most research to date has focused on S. pasteurii as a building material rather than a biological system. In this review, we synthesize available materials science, microbiology, biochemistry, and cell biology evidence regarding biological CaCO3 precipitation and the role of microbes in microbially induced calcium carbonate precipitation (MICP) with a focus on S. pasteurii. Based on the available information, we provide a model that describes the molecular and cellular processes involved in converting feedstock material (urea and Ca2+) into cement. The model provides a foundational framework that we use to highlight particular targets for researchers as they proceed into optimizing the biology of MICP for biocement production.
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Affiliation(s)
- Michael S. Carter
- Materials and Manufacturing Directorate Air Force Research Lab, Wright-Patterson Air Force Base, Dayton, Ohio, USA
- Biological and Nanoscale Technologies Division, UES, Inc., Dayton, Ohio, USA
| | - Matthew J. Tuttle
- Materials and Manufacturing Directorate Air Force Research Lab, Wright-Patterson Air Force Base, Dayton, Ohio, USA
- Biological and Nanoscale Technologies Division, UES, Inc., Dayton, Ohio, USA
| | - Joshua A. Mancini
- Materials and Manufacturing Directorate Air Force Research Lab, Wright-Patterson Air Force Base, Dayton, Ohio, USA
- Biological and Nanoscale Technologies Division, UES, Inc., Dayton, Ohio, USA
| | - Rhett Martineau
- Materials and Manufacturing Directorate Air Force Research Lab, Wright-Patterson Air Force Base, Dayton, Ohio, USA
- Biological and Nanoscale Technologies Division, UES, Inc., Dayton, Ohio, USA
| | - Chia-Suei Hung
- Materials and Manufacturing Directorate Air Force Research Lab, Wright-Patterson Air Force Base, Dayton, Ohio, USA
| | - Maneesh K. Gupta
- Materials and Manufacturing Directorate Air Force Research Lab, Wright-Patterson Air Force Base, Dayton, Ohio, USA
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2
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Loharch S, Berlicki Ł. Rational Development of Bacterial Ureases Inhibitors. CHEM REC 2022; 22:e202200026. [PMID: 35502852 DOI: 10.1002/tcr.202200026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/28/2022] [Indexed: 12/23/2022]
Abstract
Urease, an enzyme that catalyzes the hydrolysis of urea, is a virulence factor of various pathogenic bacteria. In particular, Helicobacter pylori, that colonizes the digestive tract and Proteus spp., that can infect the urinary tract, are related to urease activity. Therefore, urease inhibitors are considered as potential therapeutics against these infections. This review describes current knowledge of the structures, activity, and biological importance of bacterial ureases. Moreover, the structure-based design of several classes of bacterial urease inhibitors is presented and discussed. Phosphinic and phosphonic acids were applied as transition-state analogues, while Michael acceptors and ebselen derivatives were applied as covalent binders of cysteine residue. This review incorporates bacterial urease inhibitors from literature published between 2008 and 2021.
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Affiliation(s)
- Saurabh Loharch
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
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3
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Abstract
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Urease
catalyzes the hydrolysis of urea to form ammonia and carbamate,
inducing an overall pH increase that affects both human health and
agriculture. Inhibition, mutagenesis, and kinetic studies have provided
insights into its enzymatic role, but there have been debates on the
substrate binding mode as well as the reaction mechanism. In the present
study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular
mechanics molecular dynamics (QM/MM MD) calculations on urease that
mainly investigate the binding mode of urea and the mechanism of the
urease-catalyzed hydrolysis reaction. Comparison between the experimental
data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that
urea hydrolysis via a complex with bidentate-bound urea is much more
favorable than via that with monodentate-bound urea for both nucleophilic
attack and the subsequent proton transfer steps. We also indicate
that the bidentate coordination of urea fits the active site with
a closed conformation of the mobile flap and can facilitate the stabilization
of transition states and intermediates by forming multiple hydrogen
bonds with certain active site residues.
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Affiliation(s)
- Toru Saito
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194 Japan
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4
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Zhu J, Shen D, Xie J, Tang C, Jin B, Wu S. Mechanism of urea decomposition catalyzed by Sporosarcina pasteurii urease based on quantum chemical calculations. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1970156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jie Zhu
- College of Civil and Transportation Engineering, Hohai University, Nanjing, People’s Republic of China
| | - Dejian Shen
- College of Civil and Transportation Engineering, Hohai University, Nanjing, People’s Republic of China
| | - Jingjing Xie
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, People’s Republic of China
| | - Chunmei Tang
- College of Science, Hohai University, Nanjing, People’s Republic of China
| | - Baosheng Jin
- School of Energy and Environment, Southeast University, Nanjing, People’s Republic of China
| | - Shengxing Wu
- College of Civil and Transportation Engineering, Hohai University, Nanjing, People’s Republic of China
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5
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Trinuclear nickel(II) amino acid Schiff base complex containing phenolato and acetato bridges: Structural and functional resemblance of urease. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Cunha ES, Chen X, Sanz-Gaitero M, Mills DJ, Luecke H. Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 Å resolution. Nat Commun 2021; 12:230. [PMID: 33431861 PMCID: PMC7801526 DOI: 10.1038/s41467-020-20485-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/04/2020] [Indexed: 02/08/2023] Open
Abstract
Infection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of the world population will continue to be infected with this gastric pathogen. Current eradication, called triple therapy, entails a proton-pump inhibitor and two broadband antibiotics, however resistance to either clarithromycin or metronidazole is greater than 25% and rising. Therefore, there is an urgent need for a targeted, high-specificity eradication drug. Gastric infection by H. pylori depends on the expression of a nickel-dependent urease in the cytoplasm of the bacteria. Here, we report the 2.0 Å resolution structure of the 1.1 MDa urease in complex with an inhibitor by cryo-electron microscopy and compare it to a β-mercaptoethanol-inhibited structure at 2.5 Å resolution. The structural information is of sufficient detail to aid in the development of inhibitors with high specificity and affinity.
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Affiliation(s)
- Eva S. Cunha
- grid.5510.10000 0004 1936 8921Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Xiaorui Chen
- grid.266093.80000 0001 0668 7243Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 USA ,grid.506938.10000 0004 0633 8088Present Address: Genomics Research Center, Academia Sinica, 128 Academia Road, Sect. 2, Nankang District, Taipei, Taiwan
| | - Marta Sanz-Gaitero
- grid.5510.10000 0004 1936 8921Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Deryck J. Mills
- grid.419494.50000 0001 1018 9466Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Hartmut Luecke
- Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318, Oslo, Norway. .,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA. .,Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway. .,Department of Physiology and Biophysics, University of California, Irvine, CA, 92697, USA.
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7
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The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate. J Biol Inorg Chem 2020; 25:829-845. [PMID: 32809087 PMCID: PMC7433671 DOI: 10.1007/s00775-020-01808-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/29/2020] [Indexed: 01/22/2023]
Abstract
This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.
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8
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Kataria R, Khatkar A. Lead Molecules for Targeted Urease Inhibition: An Updated Review from 2010 -2018. Curr Protein Pept Sci 2020; 20:1158-1188. [PMID: 30894105 DOI: 10.2174/1389203720666190320170215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/01/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022]
Abstract
The field of enzyme inhibition is a tremendous and quickly growing territory of research. Urease a nickel containing metalloenzyme found in bacteria, algae, fungi, and plants brings hydrolysis of urea and plays important role in environmental nitrogen cycle. Apart from this it was found to be responsible for many pathological conditions due to its presence in many microorganisms such as H. Pylori, a ureolytic bacteria having urease which elevates pH of gastric medium by hydrolyzing urea present in alimentary canal and help the bacteria to colonize and spread infection. Due to the infections caused by the various bacterial ureases such as Bacillus pasteurii, Brucella abortus, H. pylori, H. mustelae, Klebsiella aerogenes, Klebsiella tuberculosis, Mycobacterium tuberculosis, Pseudomonas putida, Sporosarcina pasteurii and Yersinia enterocolitica, it has been the current topic of today's research. About a wide range of compounds from the exhaustive literature survey has been discussed in this review which is enveloped into two expansive classes, as Inhibitors from synthetic origin and Inhibitors from natural origin. Moreover active site details of enzyme, mechanism of catalysis of substrate by enzyme, uses of plant urease and its pathogenic behavior has been included in the current review. So, overall, this review article diagrams the current landscape of the developments in the improvements in the thriving field of urease inhibitory movement in medicinal chemistry from year 2010 to 2018, with an emphasis on mechanism of action of inhibitors that may be used for more development of recent and strong urease inhibitors and open up new doors for assist examinations in a standout amongst the most lively and promising regions of research.
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Affiliation(s)
- Ritu Kataria
- International Institute of Pharmaceutical Sciences, Sonepat, Haryana, India
| | - Anurag Khatkar
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, India
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9
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Mazzei L, Cianci M, Benini S, Ciurli S. The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease, a Nickel Enzyme. Chemistry 2019; 25:12145-12158. [DOI: 10.1002/chem.201902320] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/01/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography LaboratoryFaculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Bologna Italy
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10
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Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
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11
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Fernandes HS, Teixeira CSS, Sousa SF, Cerqueira NMFSA. Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:E2462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [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] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
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Affiliation(s)
- Henrique S Fernandes
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
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12
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019; 58:7415-7419. [DOI: 10.1002/anie.201903565] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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13
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Mazzei L, Cianci M, Benini S, Ciurli S. The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marche Ancona Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl)Faculty of Science and TechnologyFree University of Bolzano Bolzano Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartement of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40138 Bologna Italy
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14
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Fopase R, Nayak S, Mohanta M, Kale P, Balasubramanian P. Inhibition Assays of Urease for Detecting Trivalent Chromium in Drinking Water. SPRINGER TRANSACTIONS IN CIVIL AND ENVIRONMENTAL ENGINEERING 2019. [DOI: 10.1007/978-981-13-1202-1_27] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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15
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Liu Q, Yao X, Liang Q, Li J, Fang F, Du G, Kang Z. Molecular Engineering of Bacillus paralicheniformis Acid Urease To Degrade Urea and Ethyl Carbamate in Model Chinese Rice Wine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:13011-13019. [PMID: 30450906 DOI: 10.1021/acs.jafc.8b04566] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacillus paralicheniformis urease (BpUrease) has been shown to be a promising biocatalyst for degrading the carcinogenic chemical ethyl carbamate (EC or urethane) in rice wine. However, low EC affinity and catalytic efficiency limit the practical application of BpUrease. In this study, we improved the EC degradation capability of BpUrease by site-saturation mutagenesis (SSM). The best variant L253P/L287N showed a 49% increase in EC affinity, 1027% increase in catalytic efficiency ( kcat/ Km), and 583% increase in half-life ( t1/2) at 70 °C. Homology modeling analysis suggest that mutation of Leu253 to Pro increased the BpUrease EC specificity by affecting the interaction between Arg339 with the catalytic residue His323, while Leu287Asn mutation benefits EC specificity and affinity by changing the interaction networks among the residues in the catalytic pocket. Our results show that the L253P/L287N variant efficiently degraded urea and EC in a model rice wine, making it a good candidate for practical application in the food industry.
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16
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Sangeeta S, Ahmad K, Noorussabah N, Bharti S, Mishra M, Sharma S, Choudhary M. Synthesis, crystal structures, molecular docking and urease inhibition studies of Ni(II) and Cu(II) Schiff base complexes. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.062] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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17
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Design, synthesis, in vitro Evaluation and docking studies on dihydropyrimidine-based urease inhibitors. Bioorg Chem 2017; 74:53-65. [DOI: 10.1016/j.bioorg.2017.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/11/2017] [Accepted: 07/11/2017] [Indexed: 12/28/2022]
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18
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The synthesis and characterization of new nickel complexes with unusual coordination modes. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Hassan STS, Žemlička M. Plant-Derived Urease Inhibitors as Alternative Chemotherapeutic Agents. Arch Pharm (Weinheim) 2016; 349:507-22. [DOI: 10.1002/ardp.201500019] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Sherif T. S. Hassan
- Faculty of Pharmacy; Department of Natural Drugs; University of Veterinary and Pharmaceutical Sciences Brno; Brno Czech Republic
| | - Milan Žemlička
- Department of Pharmacognosy and Botany; University of Veterinary Medicine and Pharmacy in Košice; Košice Slovak Republic
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20
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Boer JL, Mulrooney SB, Hausinger RP. Nickel-dependent metalloenzymes. Arch Biochem Biophys 2014; 544:142-52. [PMID: 24036122 PMCID: PMC3946514 DOI: 10.1016/j.abb.2013.09.002] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/31/2013] [Accepted: 09/03/2013] [Indexed: 11/29/2022]
Abstract
This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.
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Affiliation(s)
- Jodi L Boer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Scott B Mulrooney
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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21
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Affiliation(s)
- Michael J Maroney
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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22
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Rashid U, Batool I, Wadood A, Khan A, ul-Haq Z, Chaudhary MI, Ansari FL. Structure based virtual screening-driven identification of monastrol as a potent urease inhibitor. J Mol Graph Model 2013; 43:47-57. [DOI: 10.1016/j.jmgm.2013.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 02/26/2013] [Accepted: 04/23/2013] [Indexed: 11/26/2022]
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23
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Ibrar A, Khan I, Abbas N. Structurally Diversified Heterocycles and Related Privileged Scaffolds as Potential Urease Inhibitors: A Brief Overview. Arch Pharm (Weinheim) 2013; 346:423-46. [DOI: 10.1002/ardp.201300041] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/29/2013] [Accepted: 04/03/2013] [Indexed: 12/31/2022]
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Ramos JM, de M Cruz MT, Costa AC, Ondar GF, Ferreira GB, Raniero L, Martin AA, Versiane O, Téllez Soto CA. Molecular structure, natural bond analysis, vibrational, and electronic spectra of aspartateguanidoacetatenickel(II), [Ni(Asp)(GAA)]·H₂O: DFT quantum mechanical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 97:1041-1051. [PMID: 22925980 DOI: 10.1016/j.saa.2012.07.087] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/24/2012] [Accepted: 07/05/2012] [Indexed: 06/01/2023]
Abstract
The aspartateguanidoacetatenickel (II) complex, [Ni(Asp)(GAA)], was synthesized and structural analysis was performed by means of the experimental methods: determination of the C, H, N and O contents, thermogravimetry, infrared and Raman spectroscopy. DFT:B3LYP/6-311G(d, p) calculations have been performed giving optimized structure and harmonic vibrational wavenumbers. Second derivative of the FT-infrared, FT-Raman and Surface Raman Enhanced Scattering (SERS) spectra, and band deconvolution analysis were also performed. Features of the FT-infrared, FT-Raman and SERS confirmed theoretical structure prediction. Full assignment of the vibrational spectrum was also supported by a carefully analysis of the distorted geometries generated by the normal modes. The Natural Bond Orbital analysis (NBO) was also carried out as a way to study the Ni (II) hybridization leading to the pseudo planar geometry of the framework, and the extension of the atomic N and O hybrid orbital of the different amino acids in the bond formation. Bands of charge transfer and d-d transitions were assigned in the UV-Vis spectrum.
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Affiliation(s)
- J M Ramos
- IQ-UFF, Departamento de Química Inorgânica, Morro de Valonguinho s/n. - Centro, 24210-150 Niterói, RJ, Brazil
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25
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Valdez CE, Alexandrova AN. Why Urease Is a Di-Nickel Enzyme whereas the CcrA β-Lactamase Is a Di-Zinc Enzyme. J Phys Chem B 2012; 116:10649-56. [DOI: 10.1021/jp302771n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Crystal E. Valdez
- Department of Chemistry
and Biochemistry, University of California, Los Angeles, Los Angeles,
California 90095-1569, United States
| | - Anastassia N. Alexandrova
- Department of Chemistry
and Biochemistry, University of California, Los Angeles, Los Angeles,
California 90095-1569, United States
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Abstract
Substrate ingress and product egress from the active site of urease is tightly controlled by an active-site flap. Molecular dynamics simulations of urease have revealed a previously unobserved wide-open flap state that, unlike the well-characterized closed and open states, allows ready access to the metal cluster in the active site. This state is easily reached from the open state via low free energy barriers. Additionally, we have found that even when the flap is closed, a region of the binding pocket is solvent-exposed, leading to the hypothesis that it may act as a substrate/product reservoir. The newly identified wide-open state offers further opportunities for small-molecule drug discovery by defining a more extensive active-site pocket than has been previously described.
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Witkowska D, Rowinska-Zyrek M, Valensin G, Kozlowski H. Specific poly-histidyl and poly-cysteil protein sites involved in Ni2+ homeostasis in Helicobacter pylori. Impact of Bi3+ ions on Ni2+ binding to proteins. Structural and thermodynamic aspects. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.06.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Carter EL, Flugga N, Boer JL, Mulrooney SB, Hausinger RP. Interplay of metal ions and urease. Metallomics 2011; 1:207-21. [PMID: 20046957 DOI: 10.1039/b903311d] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Urease, the first enzyme to be crystallized, contains a dinuclear nickel metallocenter that catalyzes the decomposition of urea to produce ammonia, a reaction of great agricultural and medical importance. Several mechanisms of urease catalysis have been proposed on the basis of enzyme crystal structures, model complexes, and computational efforts, but the precise steps in catalysis and the requirement of nickel versus other metals remain unclear. Purified bacterial urease is partially activated via incubation with carbon dioxide plus nickel ions; however, in vitro activation also has been achieved with manganese and cobalt. In vivo activation of most ureases requires accessory proteins that function as nickel metallochaperones and GTP-dependent molecular chaperones or play other roles in the maturation process. In addition, some microorganisms control their levels of urease by metal ion-dependent regulatory mechanisms.
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Affiliation(s)
- Eric L Carter
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
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Sakiyama H, Tone K, Yamasaki M, Mikuriya M. Electronic spectrum and magnetic properties of a dinuclear nickel(II) complex with two nickel(II) ions of C2-twisted octahedral geometry. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2010.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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An active site water network in the plasminogen activator pla from Yersinia pestis. Structure 2010; 18:809-18. [PMID: 20637417 DOI: 10.1016/j.str.2010.03.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/22/2010] [Accepted: 03/31/2010] [Indexed: 01/28/2023]
Abstract
The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 A. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.
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31
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Marlier JF, Robins LI, Tucker KA, Rawlings J, Anderson MA, Cleland WW. A kinetic and isotope effect investigation of the urease-catalyzed hydrolysis of hydroxyurea. Biochemistry 2010; 49:8213-9. [PMID: 20695482 DOI: 10.1021/bi100890v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The urease-catalyzed hydrolysis of hydroxyurea is known to exhibit biphasic kinetics, showing a rapid burst phase followed by a slow plateau phase. Kinetic isotope effects for both phases of this reaction were measured at pH 6.0 and 25 °C. The observed nitrogen isotope effects for the ammonia leaving group [(15)(V/K)(NH(3))] were 1.0016 ± 0.0005 during the burst phase and 1.0019 ± 0.0007 during the plateau phase, while those for the hydroxylamine leaving group [(15)(V/K)(NH(2)OH)] were 1.0013 ± 0.0005 for the burst phase and 1.0022 ± 0.0003 for the plateau phase. These isotope effects are consistent with a rate-determining step that occurs prior to breaking either of the two possible C-N bonds. The observed carbonyl carbon isotope effects [(13)(V/K)] were 1.0135 ± 0.0003 during the burst phase and 1.0178 ± 0.0003 during the plateau phase. The similarity of the magnitude of the carbon isotope effects argues for formation of a common intermediate during both phases.
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Affiliation(s)
- John F Marlier
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, USA.
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32
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Computational modeling of the mechanism of urease. Bioinorg Chem Appl 2010. [PMID: 20886006 PMCID: PMC2945649 DOI: 10.1155/2010/364891] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 05/31/2010] [Indexed: 12/02/2022] Open
Abstract
In order to elucidate aspects of the mechanism of the hydrolytic enzyme urease, theoretical calculations were undertaken on a model of the active site, using density functional theory. The bridging oxygen donor that has been found in the crystal structures was determined to be a hydroxide ion. The initial coordination of urea at the active site occurs most likely through the urea oxygen to the nickel ion with the lowest coordination number. This coordination can be made without much gain in energy. The calculations also showed that weak coordination of one of the urea amine nitrogen atoms to the second nickel atom is energetically feasible. Furthermore, a proposed mechanism including a tetrahedral intermediate generated by hydrolytic attack on the urea carbon by the bridging hydroxide was modeled, and the tetrahedral intermediate was found to be energetically unfavorable relative to terminal coordination of the substrate (urea).
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33
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Cui YM, Yan WX, Cai YJ, Chen W, Zhu HL. Synthesis, molecular docking, and inhibitory activity of a Ni Schiff-base complex against urease. J COORD CHEM 2010. [DOI: 10.1080/00958972.2010.517268] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yong Ming Cui
- a Engineering Research Center for Clean Production of Textile Printing, Ministry of Education, Wuhan Textile University , Wuhan 430073, P.R. China
- b State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, P.R. China
| | - Wen Xuan Yan
- c Library of Wuhan Textile University , Wuhan 430073, P.R. China
| | - Ying Jie Cai
- a Engineering Research Center for Clean Production of Textile Printing, Ministry of Education, Wuhan Textile University , Wuhan 430073, P.R. China
| | - Wu Chen
- a Engineering Research Center for Clean Production of Textile Printing, Ministry of Education, Wuhan Textile University , Wuhan 430073, P.R. China
| | - Hai Liang Zhu
- a Engineering Research Center for Clean Production of Textile Printing, Ministry of Education, Wuhan Textile University , Wuhan 430073, P.R. China
- b State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, P.R. China
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Lee WZ, Tseng HS, Wang TL, Tsai HL, Kuo TS. Bioinspired Catalytic Conjugate Additions of Thiophenols to α,β-Enones by a Disubstituted Benzoate-Bridged Nickel Mimic for the Active Site of Urease. Organometallics 2010. [DOI: 10.1021/om100103u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Way-Zen Lee
- Department of Chemistry, National Taiwan Normal University, Taipei 11650, Taiwan
| | - Huan-Sheng Tseng
- Department of Chemistry, National Taiwan Normal University, Taipei 11650, Taiwan
| | - Tzu-Li Wang
- Department of Chemistry, National Taiwan Normal University, Taipei 11650, Taiwan
| | - Hui-Lien Tsai
- Department of Chemistry, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ting-Shen Kuo
- Instrumentation Center, Department of Chemistry, National Taiwan Normal University, Taipei 11650, Taiwan
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35
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Eltayeb AZ, Nimir HI, Brown DA, Lan Y, Anson CE, Powell AK. Magnetic and structural studies of novel tetranickel hydroxamates. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2009.12.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Zhang S, Li D, Tian K, Bai Y, Zhang H, Song C, Qiao M, Kong D, Yu Y. Development of a Recombinant UreolyticLactococcus Lactisfor Urea Removal. ACTA ACUST UNITED AC 2009; 37:227-34. [DOI: 10.3109/10731190903356420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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37
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Mao WJ, Lv PC, Shi L, Li HQ, Zhu HL. Synthesis, molecular docking and biological evaluation of metronidazole derivatives as potent Helicobacter pylori urease inhibitors. Bioorg Med Chem 2009; 17:7531-6. [DOI: 10.1016/j.bmc.2009.09.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 09/08/2009] [Accepted: 09/10/2009] [Indexed: 12/01/2022]
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38
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Tikhonenko SA, Saburova EA, Durdenko EN, Sukhorukov BI. Enzyme-polyelectrolyte complex: Salt effects on the reaction of urease with polyallylamine. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2009. [DOI: 10.1134/s0036024409100276] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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40
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41
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SAKIYAMA H, OSHIMA M, SUZUKI S, NISHIDA Y. Several Molecular Orbital Computations for a Dinuclear Nickel(II) Complex. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2009. [DOI: 10.2477/jccj.h2029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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42
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Marlier JF, Fogle EJ, Cleland WW. A heavy-atom isotope effect and kinetic investigation of the hydrolysis of semicarbazide by urease from jack bean (Canavalia ensiformis). Biochemistry 2008; 47:11158-63. [PMID: 18817416 DOI: 10.1021/bi801338c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A kinetic investigation of the hydrolysis of semicarbazide by urease gives a relatively flat log V/ K versus pH plot between pH 5 and 8. A log V m versus pH plot shows a shift of the optimum V m toward lower pH when compared to urea. These results are explained in terms of the binding of the outer N of the NHNH 2 group in semicarbazide to an active site residue with a relatively low p K a ( approximately 6). Heavy-atom isotope effects for both leaving groups have been determined. For the NHNH 2 side, (15) k obs = 1.0045, whereas for the NH 2 side, (15) k obs = 1.0010. This is evidence that the NHNH 2 group leaves prior to the NH 2 group. Using previously published data from the urease-catalyzed hydrolysis of formamide, the commitment factors for semicarbazide and urea hydrolysis are estimated to be 2.7 and 1.2, respectively. The carbonyl-C isotope effect ( (13) k obs) equals 1.0357, which is consistent with the transition state occurring during either formation or breakdown of the tetrahedral intermediate.
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Affiliation(s)
- John F Marlier
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California 93407, USA.
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43
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Contreras-Rodriguez A, Quiroz-Limon J, Martins AM, Peralta H, Avila-Calderon E, Sriranganathan N, Boyle SM, Lopez-Merino A. Enzymatic, immunological and phylogenetic characterization of Brucella suis urease. BMC Microbiol 2008; 8:121. [PMID: 18638408 PMCID: PMC2492869 DOI: 10.1186/1471-2180-8-121] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 07/19/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The sequenced genomes of the Brucella spp. have two urease operons, ure-1 and ure-2, but there is evidence that only one is responsible for encoding an active urease. The present work describes the purification and the enzymatic and phylogenomic characterization of urease from Brucella suis strain 1330. Additionally, the urease reactivity of sera from patients diagnosed with brucellosis was examined. RESULTS Urease encoded by the ure-1 operon of Brucella suis strain 1330 was purified to homogeneity using ion exchange and hydrophobic interaction chromatographies. The urease was purified 51-fold with a recovery of 12% of the enzyme activity and 0.24% of the total protein. The enzyme had an isoelectric point of 5, and showed optimal activity at pH 7.0 and 28-35 degrees C. The purified enzyme exhibited a Michaelis-Menten saturation kinetics with a Km of 5.60 +/- 0.69 mM. Hydroxyurea and thiourea are competitive inhibitors of the enzyme with Ki of 1.04 +/- 0.31 mM and 26.12 +/- 2.30 mM, respectively. Acetohydroxamic acid also inhibits the enzyme in a competitive way. The molecular weight estimated for the native enzyme was between 130-135 kDa by gel filtration chromatography and 157 +/- 7 kDa using 5-10% polyacrylamide gradient non-denaturing gel. Only three subunits in SDS-PAGE were identified: two small subunits of 14,000 Da and 15,500 Da, and a major subunit of 66,000 Da. The amino terminal sequence of the purified large subunit corresponded to the predicted amino acid sequence encoded by ureC1. The UreC1 subunit was recognized by sera from patients with acute and chronic brucellosis. By phylogenetic and cluster structure analyses, ureC1 was related to the ureC typically present in the Rhizobiales; in contrast, the ureC2 encoded in the ure-2 operon is more related to distant species. CONCLUSION We have for the first time purified and characterized an active urease from B. suis. The enzyme was characterized at the kinetic, immunological and phylogenetic levels. Our results confirm that the active urease of B. suis is a product of ure-1 operon.
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Affiliation(s)
- Araceli Contreras-Rodriguez
- Escuela Nacional de Ciencias Biológicas, I,P,N, México, Prol, Carpio y Plan de Ayala s/n, Col, Sto. Tomas, CP 11340, Mexico.
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44
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Sun H, Pan Y, Zhao Y, Jackson WA, Nuckles LM, Malkina IL, Arteaga VE, Mitloehner FM. Effects of sodium bisulfate on alcohol, amine, and ammonia emissions from dairy slurry. JOURNAL OF ENVIRONMENTAL QUALITY 2008; 37:608-614. [PMID: 18396547 DOI: 10.2134/jeq2006.0446] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Sodium bisulfate (SBS) is extensively used in the poultry industry to reduce ammonia and bacterial levels in litter. It is also used in the dairy industry to reduce bacterial counts in bedding and ammonia emissions, preventing environmental mastitis and calf respiratory stress. The present study measured the effect of SBS on the air emission of ammonia, amine, and alcohol from a dairy slurry mix. Amine flux was undetectable (<5 ng L(-1)) across treatments. Application of SBS decreased ammonia, methanol, and ethanol emissions from fresh dairy slurry. Ammonia emissions decreased with increasing levels of SBS treatment. The 3-d average ammonia flux from the control (no SBS applied) and the three different SBS surface application levels of 0.125, 0.250, and 0.375 kg m(-2) were 513.4, 407.2, 294.8, and 204.5 mg h(-1) m(-2), respectively. The ammonia emission reduction potentials were 0, 21, 43, and 60%, respectively. Methanol and ethanol emissions decreased with an increase in the amount of SBS applied. The 3-d average methanol emissions were 223.7, 178.0, 131.6, and 87.0 mg h(-1) m(-2) for SBS surface application level of 0, 0.125, 0.250, and 0.375 kg m(-2), with corresponding reduction potentials of 0, 20, 41, and 61, respectively. Similar emission reduction potentials of 0, 18, 35, and 58% were obtained for ethanol. Sodium bisulfate was shown to be effective in the mitigation of ammonia and alcohol emissions from fresh dairy slurry.
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Affiliation(s)
- Huawei Sun
- Dep. of Biological & Agricultural Engineering, Univ. of California Davis, Davis, CA 95616, USA
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45
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Follmer C. Insights into the role and structure of plant ureases. PHYTOCHEMISTRY 2008; 69:18-28. [PMID: 17706733 DOI: 10.1016/j.phytochem.2007.06.034] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/11/2007] [Accepted: 06/28/2007] [Indexed: 05/11/2023]
Abstract
The broad distribution of ureases in leguminous seeds, as well as the accumulation pattern of the protein during seed maturation, are suggestive of an important physiological role for this enzyme. Since the isolation and characterization of jack bean urease by Sumner in 1926, many investigations have been dedicated to the structural and biological features of this enzyme; nevertheless, many questions still remain. It has been reported that ureases from plants (jack bean and soybean seeds) display biological properties unrelated to their ureolytic activity, notably a high insecticidal activity against Coleoptera (beetles) and Hemiptera (bugs), suggesting that ureases might be involved in plant defense. Besides the insecticidal activity, canatoxin, a jack bean urease isoform, causes convulsions and death in mice and rats, induces indirect hemagglutination (hemilectin activity) and promotes exocytosis in several cell types. Not only plant ureases but also some microbial ureases (found in Bacillus pasteurii and Helicobacter pylori) are able to induce activation of platelets in a process mediated by lipoxygenase-derived metabolites. This review summarizes the biological and structural properties of plant ureases, compares them with those displayed by bacterial ureases, and discusses the significance of these findings.
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Affiliation(s)
- Cristian Follmer
- Departamento de Físico-Química, Instituto de Química, Universidade Federal do Rio de Janeiro, CT, Bloco A S410, Rio de Janeiro 21941-909, Brazil.
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46
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Lee WZ, Tseng HS, Ku MY, Kuo TS. Dinickel complexes of disubstituted benzoate polydentate ligands: mimics for the active site of urease. Dalton Trans 2008:2538-41. [DOI: 10.1039/b803094b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Salomone-Stagni M, Zambelli B, Musiani F, Ciurli S. A model-based proposal for the role of UreF as a GTPase-activating protein in the urease active site biosynthesis. Proteins 2007; 68:749-61. [PMID: 17510959 DOI: 10.1002/prot.21472] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UreF is a protein that plays a role in the in vivo urease activation as a chaperone involved in the insertion of two Ni(2+) ions in the apo-urease active site. The molecular details of this process are unknown. In the absence of any molecular information on the UreF protein class, and as a step toward the comprehension of the relationships between UreF function and structure, we applied a structural modeling approach to infer useful biochemical knowledge on Bacillus pasteurii UreF (BpUreF). Similarity searches and multiple alignment of UreF protein sequences indicated that this class of proteins has a low homology with proteins of known structure. Fold recognition methods were therefore used to identify useful protein structural templates to model the structure of BpUreF. In particular, the templates belong to the class of GTPase-activating proteins. Modeling of BpUreF based on these templates was performed using the program MODELLER. The structure validation yielded good statistics, indicating that the model is plausible. This result suggests a role for UreF in urease active site biosynthesis as a regulator of the activity of UreG, a small G protein involved in the in vivo apo-urease activation process and established to catalyze GTP hydrolysis.
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Affiliation(s)
- Marco Salomone-Stagni
- Laboratory of Bioinorganic Chemistry, Department of Agro-Environmental Science and Technology, University of Bologna, I-40127 Bologna, Italy
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48
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Estiu G, Suárez D, Merz KM. Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. J Comput Chem 2007; 27:1240-62. [PMID: 16773613 DOI: 10.1002/jcc.20411] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Herein we briefly review theoretical contributions that have increased our understanding of the structure and function of metallo-beta-lactamases and ureases. Both are bimetallic metalloenzymes, with the former containing two zinc ions and the latter containing two nickel ions. We describe the use of several different methodologies, including quantum chemical calculations, molecular dynamic simulations, as well as mixed QM/MM approaches and how they have impacted our understanding of the structure and function of metallo-beta-lactamases and ureases.
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Affiliation(s)
- Guillermina Estiu
- Department of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, P.O. Box 118435, Gainesville, Florida 32611-8435, USA
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49
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Estiu G, Merz KM. Competitive Hydrolytic and Elimination Mechanisms in the Urease Catalyzed Decomposition of Urea. J Phys Chem B 2007; 111:10263-74. [PMID: 17676790 DOI: 10.1021/jp072323o] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a high-level quantum chemical study of possible elimination reaction mechanisms associated with the catalytic decomposition of urea at the binuclear nickel active site cluster of urease. Stable intermediates and transition state structures have been identified along several possible reaction pathways. The computed results are compared with those reported by Suarez et al. for the hydrolytic catalyzed decomposition. On the basis of these comparative studies, we propose a monodentate coordination of urea in the active site from which both the elimination and hydrolytic pathways can decompose urea into CO2 and NH3. This observation is counter to what has been experimentally suggested based on the exogenous observation of carbamic acid (the reaction product from the hydrolysis pathway). However, this does not address what has occurred at the active site of urease prior to product release. On the basis of our computed results, the observation that urea prefers the elimination channel in aqueous solution and on the observation of Lippard and co-workers of an elimination reaction channel in a urease biomimetic model, we propose that the elimination channel needs to be re-examined as a viable reaction channel in urease.
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Affiliation(s)
- Guillermina Estiu
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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50
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Nazari K, Mahmoudi A, Esmaeili N, Sadeghian L, Moosavi-Movahedi AA, Khodafarin R. Denaturation of jack-bean urease by sodium n-dodecyl sulphate: A kinetic study below the critical micelle concentration. Colloids Surf B Biointerfaces 2006; 53:139-48. [PMID: 17010576 DOI: 10.1016/j.colsurfb.2006.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 08/03/2006] [Accepted: 08/03/2006] [Indexed: 10/24/2022]
Abstract
Kinetics of urease denaturation by anionic surfactant (sodium n-dodecyl sulphate, SDS) at concentrations below the critical micelle concentration (CMC) is investigated spectrophotometrically at neutral pH and the corresponding two-phase kinetic parameters of the process are estimated from a three-state reversible process using a binomial exponential relation based on the relaxation time method as: Using a prepared computer program, the experimental data are properly fitted into a binomial exponential relation, considering a two-phase denaturation pathway including a kinetically stable folded intermediate formed at SDS concentration of 1.1 mM. Forward and backward rate constants are estimated as: k(1)=0.2141+/-4.5 x 10(-3), k(2)=5.173 x 10(-3)+/-8.3 x 10(-5), k(-1)=0.09432+/-3.6 x 10(-4) and k(-2)=2.079 x 10(-3)+/-5.6 x 10(-5)s(-1) for the proposed mechanism. The rate-limiting step as well as the reaction coordinates in the denaturation mechanism are established. The mechanism involves formation of a kinetically stable folded native like intermediate through the electrostatic interactions. The intermediate was found to be more stable even than the native form (by about 9 kJmol(-1)) and still hexamer, because no loss of amplitude was observed. Electrophoresis experiments on the native and surfactant/urease complexes indicated a higher mobility for the kinetically folded native like intermediate.
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Affiliation(s)
- K Nazari
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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