Molecular Details of Urease Inhibition by Boric Acid:  Insights into the Catalytic Mechanism

Benini, Stefano; Rypniewski, W.; Wilson, K.S.; Mangani, T. Stefano; Ciurli, Stefano

doi:10.1021/ja049618p

Cited by 156 publications

(166 citation statements)

References 16 publications

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“…Due to its structural similarity to urea, the boric acid molecule is also considered an analog substrate. Boric acid almost exactly replaces the water molecules bonded to Ni in the center of reaction (Benini et al, 2004).…”

Section: Resultsmentioning

confidence: 99%

Nitrogen loss by volatilization of nitrogen fertilizers applied to coffee orchard

et al. 2016

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Ammonia volatilization (N-NH 3 ) is one of the main pathways of Nitrogen loss reducing nitrogen use efficiency in coffee orchard. This work aimed at quantifying ammonia volatilization (N-NH 3 ) losses from N-sources to be used in coffee plantations fertilization in Brazil. The experiment was conducted in the field on a dystrophic red latosol (Ferralsol in FAO's classification) at the Coffee Research Sector, University of Lavras, MG, Brazil. The experimental design was of complete randomized blocks with three repetitions of the following treatments: conventional urea, ammonium nitrate and urea + 0.15% Cu and 0.4% B, urea + anionic polymers, urea + elementary sulfur (S 0 ) + polymers, and urea + plastic resin. These N sources were split into three doses of 150 kg ha -1 and band applied. The N-NH 3 losses by volatilization and variations of pH (H 2 O) were measured, before and after N application. The N-sources contributed to reduce the soil pH, measured after the third nitrogen fertilization. The N-NH 3 losses by volatilization (average from three applications) was as follows: urea + anionic polymers (35.8%) > conventional urea (31.2%) = urea + S 0 + polymers (31.0%) > urea + 0.15% Cu + 0.4 % B (25.6%) > urea + plastic resin (8.6%) = ammonium nitrate (1.0%).Index terms: Coffee arabica; slow and controlled release and stabilized fertilizers; ammonium nitrate; urea. RESUMOA volatilização de amônia é uma das principais causas da redução da eficiência no uso de fertilizantes nitrogenados em lavouras cafeeiras. Neste trabalho, objetivou-se quantificar as perdas de nitrogênio por volatilização de fertilizantes nitrogenados aplicados em lavoura cafeeira. O experimento foi realizado em condições de campo, em um Latossolo Vermelho distrófico, cultivado com café, localizado no Setor de Cafeicultura/Departamento de Agricultura/UFLA, Lavras -MG. O delineamento experimental foi em blocos casualizados e os tratamentos foram: ureia; nitrato de amônio; ureia + 0,15% de Cu + 0,4% de B; ureia + polímeros; ureia + enxofre elementar (S 0 ) + polímeros e; ureia + resina plástica; distribuídos em três parcelamentos com doses iguais de 150 kg ha -1 . Foram quantificadas as perdas de nitrogênio por volatilização (N-NH 3 ) e as variações no pH em água, da camada de 0-5 cm de solo, antes e depois dos parcelamentos das adubações nitrogenadas. Os fertilizantes nitrogenados reduziram os valores do pH do solo após as três adubações de manutenção. A perda de nitrogênio por volatilização dos fertilizantes nitrogenados (média das três adubações) foi: ureia + polímeros (35,8% do total do N aplicado) > ureia (31,2%) = ureia + S 0 + polímeros (31,0%) > ureia + Cu + B (25,6%) > ureia + resina plástica (8,6%) = nitrato de amônio (1,0%).Termos para indexação: Coffee arabica; fertilizantes estabilizados e de liberação controlada; nitrato de amônio; ureia.

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Section: Resultsmentioning

confidence: 99%

Nitrogen loss by volatilization of nitrogen fertilizers applied to coffee orchard

et al. 2016

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“…Open and closed conformations of the mobile flap have been experimentally observed in urease structures from different species. 1,[19][20][21][22][23][24][25][26][27][41][42][43][44][45] The closed conformation has been reported for the K. aerogenes urease structure (KAU, pdb code 1FWJ), 24 while the open conformation has been observed in the X-ray structure of Bacillus Pasteurii urease (BPU, pdb code 2UBP). 1 For the beta-mercaptoethanol (BME, pdb code 1UBP), 20 and acetohydroxamic acid (AHA, pdb code 4UBP) 21 ) inhibited ureases, the mobile flap is found in the open conformation.…”

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confidence: 99%

Catalyzed Decomposition of Urea. Molecular Dynamics Simulations of the Binding of Urea to Urease

Estiú

Merz

2006

Biochemistry

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We present the results of molecular dynamics simulations on the urea/urease system. The starting structure was prepared from the 2.0Å crystal structure of Benini et al. of DAP-inhibited urease (PDB code 3UBP), 1 and the trimeric structure (2479 residues) resulted in 180K atoms after solvation by water. The force field parameters were derived using the bonded model approach described by Hoops et al. 2 Three different systems were analyzed, each one modeling a different protonation pattern for the His320 and His219 residues. In each case, the three monomers of urease have been analyzed separately. The time averaged structures observed in the three monomers suggest that urease could follow two different competitive mechanisms. A "protein assisted proton transfer" mechanism points to Asp221 as crucial for catalysis. An "Asp mediated proton transfer" involves the transfer of a proton from the bridging OH to a NH 2 moiety of urea, assisted by Asp360 in the active site. The impact of the simulation results on our understanding of urease catalysis are discussed in detail.The reliable prediction of the mechanism involved in the selectivity and efficiency of enzyme catalyzed reactions continues to challenge both experimental and computational researchers. 3-9 Mutagenic and biochemical procedures, as well as a variety of computational methodologies have been applied with the goal of understanding the enzymatic effect on reactivity, and several working hypotheses have been proposed. Among them, there is general agreement of the role played by the reduction of the free energy of activation, 3 but the origins of the free energy lowering, which involves non-covalent and covalent effects, is the subject of ongoing debate. 10 Non-covalent factors involve transition state electrostatic stabilization, 11 ground state destabilization and desolvation, 12 reduction of reorganization energy by binding in near attack conformations, 13 entropy trapping, 14 as well as several other related effects. Covalent and non-covalent effects are not exclusive, and rate enhancement can come from both effects, as well as from others. Covalent factors are dominant, whenever present. 15 They usually occur in metalloenzymes, where the metal centers covalently bind the substrate, stabilizing the transition state complex and leading to highly proficient catalysts. 10, 16 This is the case of the metalloenzyme urease, whose proficiency is presently a matter of extensive discussion, as values of 10 17 and 10 32 have been determined by experimental and theoretical means. 17, 18Urea amidohydrolase (urease) is a nickel-containing enzyme that catalyses the hydrolysis of urea to produce ammonia and carbon dioxide in the last step of nitrogen mineralization. 1, 19-25 The mechanism of the catalyzed reaction continues to be of interest, and there is still no agreement on whether the reaction involves a carbamic acid intermediate, a cyanate * To whom correspondence should be addressed. .edu † Present address: Department of Chemistry, Quantum Theory Project, ...

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“…Esses resultados podem ser explicados em razão de o ácido bórico apresentar, de acordo com Benini et al (2004), estrutura semelhante à da ureia, fazendo com que o B iniba a enzima urease de forma competitiva; ou seja, o B compete com a urease pelo mesmo sitio ativo do substrato (ureia). A N-NH 3 volatilizada acumulada ocasionada pelo fertilizante pastilhado ureia Cu+B-1 foi de 21,8 % em relação à dose de 200 kg ha -1 de N aplicada, ou seja, 43,69 kg ha -1 de N-NH 3 foi perdida por volatilização.…”

Section: Resultsunclassified

“…De acordo com Benini et al (2004), o acido bórico atua como inibidor competitivo com a urease em relação ao substrato (ureia), uma vez que a molécula de ácido bórico apresenta conformação semelhante à da ureia, competindo assim pelos mesmos sítios enzimáticos com a enzima urease, o que confere a esse elemento maior potencial em inibir a atividade da urease. Com isso, o B pode fazer com que a ureia permaneça no solo por tempo maior sem se dissociar, aumentando assim a eficiência do fertilizante nitrogenado.…”

Section: Resultsunclassified

Volatilização de amônia oriunda de ureia pastilhada com micronutrientes em ambiente controlado

Stafanato

Goulart²,

Zonta

et al. 2013

Rev. Bras. Ciênc. Solo

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RESUMONovas tecnologias com o intuito de minimizar as perdas de N-NH 3 por volatilização devem ser desenvolvidas para aumentar a eficiência de uso do Nureia. A incorporação de boro e cobre na ureia pode reduzir esses efeitos por meio da inibição da atividade da urease. O experimento foi conduzido em casa de vegetação, onde foram aplicados diferentes fertilizantes nitrogenados (ureia pastilhada com e sem boro e cobre, sulfato de amônio, ureia com inibidor da urease NBPT, ureia granulada e ureia revestida com boro e cobre) na superfície de um Planossolo Háplico contido em bandejas (0,1 m² de área e 10 cm de profundidade), em dose equivalente a 200 kg ha -1 de N. Foram avaliadas as perdas de N-NH 3 por volatilização durante 18 dias, com o auxílio de um coletor semiaberto. A adição de cobre e boro no processo de pastilhamento da ureia reduziu as perdas de amônia por volatilização em até 54 %, quando comparado com a ureia granulada comercial, comprovando ser eficiente contra as perdas de N-NH 3 por volatilização.Termos para indexação: perdas de N-NH 3 , fertilizantes pastilhados, urease.

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Molecular Details of Urease Inhibition by Boric Acid: Insights into the Catalytic Mechanism

Cited by 156 publications

References 16 publications

Nitrogen loss by volatilization of nitrogen fertilizers applied to coffee orchard

Nitrogen loss by volatilization of nitrogen fertilizers applied to coffee orchard

Catalyzed Decomposition of Urea. Molecular Dynamics Simulations of the Binding of Urea to Urease

Volatilização de amônia oriunda de ureia pastilhada com micronutrientes em ambiente controlado

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