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1.
Microb Cell Fact ; 23(1): 168, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38858761

ABSTRACT

BACKGROUND: Microbially induced calcium carbonate precipitation has been extensively researched for geoengineering applications as well as diverse uses within the built environment. Bacteria play a crucial role in producing calcium carbonate minerals, via enzymes including carbonic anhydrase-an enzyme with the capability to hydrolyse CO2, commonly employed in carbon capture systems. This study describes previously uncharacterised carbonic anhydrase enzyme sequences capable of sequestering CO2 and subsequentially generating CaCO3 biominerals and suggests a route to produce carbon negative cementitious materials for the construction industry. RESULTS: Here, Bacillus subtilis was engineered to recombinantly express previously uncharacterised carbonic anhydrase enzymes from Bacillus megaterium and used as a whole cell catalyst allowing this novel bacterium to sequester CO2 and convert it to calcium carbonate. A significant decrease in CO2 was observed from 3800 PPM to 820 PPM upon induction of carbonic anhydrase and minerals recovered from these experiments were identified as calcite and vaterite using X-ray diffraction. Further experiments mixed the use of this enzyme (as a cell free extract) with Sporosarcina pasteurii to increase mineral production whilst maintaining a comparable level of CO2 sequestration. CONCLUSION: Recombinantly produced carbonic anhydrase successfully sequestered CO2 and converted it into calcium carbonate minerals using an engineered microbial system. Through this approach, a process to manufacture cementitious materials with carbon sequestration ability could be developed.


Subject(s)
Bacillus subtilis , Calcium Carbonate , Carbon Dioxide , Carbonic Anhydrases , Sporosarcina , Calcium Carbonate/metabolism , Calcium Carbonate/chemistry , Bacillus subtilis/metabolism , Bacillus subtilis/genetics , Bacillus subtilis/enzymology , Carbon Dioxide/metabolism , Carbonic Anhydrases/metabolism , Carbonic Anhydrases/genetics , Sporosarcina/metabolism , Sporosarcina/enzymology , Sporosarcina/genetics , Bacillus megaterium/metabolism , Bacillus megaterium/genetics , Bacillus megaterium/enzymology , Carbon Sequestration , Chemical Precipitation , Bacterial Proteins/metabolism , Bacterial Proteins/genetics
2.
Subcell Biochem ; 96: 355-372, 2021.
Article in English | MEDLINE | ID: mdl-33252736

ABSTRACT

Thermostability is a key factor in the industrial and clinical application of enzymes, and understanding mechanisms of thermostability is valuable for molecular biology and enzyme engineering. In this chapter, we focus on the thermostability of leucine dehydrogenase (LDH, EC 1.4.1.9), an amino acid-metabolizing enzyme that is an NAD+-dependent oxidoreductase which catalyzes the deamination of branched-chain l-amino acids (BCAAs). LDH from Geobacillus stearothermophilus (GstLDH) is a highly thermostable enzyme that has already been applied to quantify the concentration of BCAAs in biological specimens. However, the molecular mechanism of its thermostability had been unknown because no high-resolution structure was available. Here, we discuss the thermostability of GstLDH on the basis of its structure determined by cryo-electron microscopy. Sequence comparison with other structurally characterized LDHs (from Lysinibacillus sphaericus and Sporosarcina psychrophila) indicated that non-conserved residues in GstLDH, including Ala94, Tyr127, and the C-terminal region, are crucial for oligomeric stability through intermolecular interactions between protomers. Furthermore, NAD+ binding to GstLDH increased the thermostability of the enzyme as additional intermolecular interactions formed on cofactor binding. This knowledge is important for further applications and development of amino acid metabolizing enzymes in industrial and clinical fields.


Subject(s)
Leucine Dehydrogenase/chemistry , Leucine Dehydrogenase/metabolism , Bacillaceae/enzymology , Cryoelectron Microscopy , Enzyme Stability , Geobacillus stearothermophilus/enzymology , Leucine Dehydrogenase/ultrastructure , Sporosarcina/enzymology
3.
Angew Chem Int Ed Engl ; 60(11): 6029-6035, 2021 03 08.
Article in English | MEDLINE | ID: mdl-33245574

ABSTRACT

The inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by a class of six aromatic poly-hydroxylated molecules, namely mono- and dimethyl-substituted catechols, was investigated on the basis of the inhibitory efficiency of the catechol scaffold. The aim was to probe the key step of a mechanism proposed for the inhibition of SPU by catechol, namely the sulfanyl radical attack on the aromatic ring, as well as to obtain critical information on the effect of substituents of the catechol aromatic ring on the inhibition efficacy of its derivatives. The crystal structures of all six SPU-inhibitors complexes, determined at high resolution, as well as kinetic data obtained on JBU and theoretical studies of the reaction mechanism using quantum mechanical calculations, revealed the occurrence of an irreversible inactivation of urease by means of a radical-based autocatalytic multistep mechanism, and indicate that, among all tested catechols, the mono-substituted 3-methyl-catechol is the most efficient inhibitor for urease.


Subject(s)
Catechols/pharmacology , Density Functional Theory , Enzyme Inhibitors/pharmacology , Sulfhydryl Compounds/pharmacology , Urease/antagonists & inhibitors , Catechols/chemistry , Crystallography, X-Ray , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Kinetics , Models, Molecular , Molecular Structure , Sporosarcina/enzymology , Sulfhydryl Compounds/chemistry , Urease/metabolism
4.
J Biol Inorg Chem ; 25(6): 829-845, 2020 09.
Article in English | MEDLINE | ID: mdl-32809087

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.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Nickel/chemistry , Urease/chemistry , Urease/metabolism , Binding Sites , Catalysis , Crystallography, X-Ray , Enterobacter aerogenes/enzymology , Helicobacter pylori/enzymology , Protein Conformation , Signal Transduction , Sporosarcina/enzymology , Structure-Activity Relationship
5.
Bioorg Med Chem Lett ; 29(9): 1085-1089, 2019 05 01.
Article in English | MEDLINE | ID: mdl-30850166

ABSTRACT

Targeted covalent inhibitors of urease were developed on the basis of the catechol structure. Forty amide and ester derivatives of 3,4-dihydroxyphenylacetic acid, caffeic acid, ferulic acid and gallic acid were obtained and screened against Sporosarcinia pasteurii urease. The most active compound, namely propargyl ester of 3,4-dihydroxyphenylacetic acid exhibited IC50 = 518 nM andkinact/Ki = 1379 M-1 s-1. Inhibitory activity of this compound was better and toxicity lower than those obtained for the starting compound - catechol. The molecular modelling studies revealed a mode of binding consistent with structure-activity relationships.


Subject(s)
Anti-Bacterial Agents/pharmacology , Catechols/pharmacology , Sporosarcina/enzymology , Urease/antagonists & inhibitors , Anti-Bacterial Agents/chemistry , Catechols/chemistry , Enzyme Inhibitors/chemistry , Gene Expression Regulation, Bacterial/drug effects , Models, Molecular , Molecular Docking Simulation , Protein Conformation , Structure-Activity Relationship
6.
Bioorg Med Chem ; 27(6): 1009-1022, 2019 03 15.
Article in English | MEDLINE | ID: mdl-30738655

ABSTRACT

This study deals with the synthesis of benzophenone sulfonamides hybrids (1-31) and screening against urease enzyme in vitro. Studies showed that several synthetic compounds were found to have good urease enzyme inhibitory activity. Compounds 1 (N'-((4'-hydroxyphenyl)(phenyl)methylene)-4''-nitrobenzenesulfonohydrazide), 2 (N'-((4'-hydroxyphenyl)(phenyl)methylene)-3''-nitrobenzenesulfonohydrazide), 3 (N'-((4'-hydroxyphenyl)(phenyl)methylene)-4''-methoxybenzenesulfonohydrazide), 4 (3'',5''-dichloro-2''-hydroxy-N'-((4'-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide), 6 (2'',4''-dichloro-N'-((4'-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide), 8 (5-(dimethylamino)-N'-((4-hydroxyphenyl)(phenyl)methylene)naphthalene-1-sulfono hydrazide), 10 (2''-chloro-N'-((4'-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide), 12 (N'-((4'-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide) have found to be potently active having an IC50 value in the range of 3.90-17.99 µM. These compounds showed superior activity than standard acetohydroxamic acid (IC50 = 29.20 ±â€¯1.01 µM). Moreover, in silico studies on most active compounds were also performed to understand the binding interaction of most active compounds with active sites of urease enzyme. Structures of all the synthetic compounds were elucidated by 1H NMR, 13C NMR, EI-MS and FAB-MS spectroscopic techniques.


Subject(s)
Benzophenones/chemistry , Benzophenones/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Sporosarcina/enzymology , Urease/antagonists & inhibitors , Benzophenones/chemical synthesis , Enzyme Inhibitors/chemical synthesis , Inhibitory Concentration 50 , Molecular Docking Simulation , Sporosarcina/drug effects , Structure-Activity Relationship , Sulfonamides/chemical synthesis , Sulfonamides/chemistry , Sulfonamides/pharmacology , Urease/metabolism
7.
Bioorg Chem ; 82: 6-16, 2019 02.
Article in English | MEDLINE | ID: mdl-30267972

ABSTRACT

Urease is a bacterial enzyme that is responsible for virulence of various pathogenic bacteria such as Staphylococcus aureus, Proteus mirabilis, Klebsiella pneumoniae, Ureaplasma urealyticum, Helicobacter pylori and Mycobacterium tuberculosis. Increased urease activity aids in survival and colonization of pathogenic bacteria causing several disorders especially gastric ulceration. Hence, urease inhibitors are used for treatment of such diseases. In search of new molecules with better urease inhibitory activity, herein we report a series of acridine derived (thio)semicarbazones (4a-4e, 6a-6l) that were found to be active against urease enzyme. Molecular docking studies were carried out to better comprehend the preferential mode of binding of these compounds against urease enzyme. Docking against urease from pathogenic bacterium S. pasteurii was also carried out with favorable results. In silico ADME evaluation was done to determine drug likeness of synthesized compounds.


Subject(s)
Acridines/chemistry , Enzyme Inhibitors/chemistry , Hydrazones/chemistry , Semicarbazones/chemistry , Urease/antagonists & inhibitors , Acridines/chemical synthesis , Acridines/pharmacokinetics , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacokinetics , Catalytic Domain , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/pharmacokinetics , Hydrazones/chemical synthesis , Hydrazones/pharmacokinetics , Molecular Docking Simulation , Molecular Structure , Semicarbazones/chemical synthesis , Semicarbazones/pharmacokinetics , Sporosarcina/enzymology , Structure-Activity Relationship , Urease/chemistry
8.
Angew Chem Int Ed Engl ; 58(22): 7415-7419, 2019 05 27.
Article in English | MEDLINE | ID: mdl-30969470

ABSTRACT

Urease, the most efficient enzyme known, contains an essential dinuclear NiII cluster in the active site. It catalyzes the hydrolysis of urea, inducing a rapid pH increase that has negative effects on human health and agriculture. Thus, the control of urease activity is of utmost importance in medical, pharmaceutical, and agro-environmental applications. All known urease inhibitors are either toxic or inefficient. The development of new and efficient chemicals able to inhibit urease relies on the knowledge of all steps of the catalytic mechanism. The short (microseconds) lifetime of the urease-urea complex has hampered the determination of its structure. The present study uses fluoride to substitute the hydroxide acting as the co-substrate in the reaction, preventing the occurrence of the catalytic steps that follow substrate binding. The 1.42 Šcrystal structure of the urease-urea complex, reported here, resolves the enduring debate on the mechanism of this metalloenzyme.


Subject(s)
Nickel/chemistry , Sporosarcina/enzymology , Urea/metabolism , Urease/chemistry , Urease/metabolism , Binding Sites , Catalysis , Catalytic Domain , Crystallography, X-Ray , Hydrolysis , Kinetics , Models, Molecular , Protein Conformation
9.
Pak J Pharm Sci ; 32(3 (Supplementary)): 1179-1183, 2019 May.
Article in English | MEDLINE | ID: mdl-31303588

ABSTRACT

The current article discusses the activities of several synthesized metal heterochelates in in-vitro as anti-ulcer agents followed by their docking study. For this purpose, two important ligands like 8-hydroxyquinoline and DL-methionine were used in synthesis of heterochelates of metal including Cr (III), Mn (II), Fe (III), Co (II), Ni (II), Cu (II), Zn (II), Cd (II) and Pb (II). It was observed that these complexes showed excellent urease inhibition activities in which thiourea was the standard having IC50 value 21.6 ± 0.12µM. The Cu (II) complex showed potent inhibitory activity (22.6 ± 0.72 µM) when compared with the standard thiourea (21.6±0.12µM) among the nine synthesized complexes while Mn (II), Fe (III), Cd (II) and Pb (II) also showed better inhibitory activities. The urease inhibitory activities of hetercochelates also tested and validated by docking analysis.


Subject(s)
Chelating Agents/chemistry , Enzyme Inhibitors/pharmacology , Urease/antagonists & inhibitors , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Catalytic Domain , Chelating Agents/pharmacology , Drug Evaluation, Preclinical , Enzyme Inhibitors/chemistry , Molecular Docking Simulation , Sporosarcina/enzymology , Urease/chemistry , Urease/metabolism
10.
Biochemistry ; 56(40): 5391-5404, 2017 10 10.
Article in English | MEDLINE | ID: mdl-28857549

ABSTRACT

The nickel-dependent enzyme urease is a virulence factor for a large number of pathogenic and antibiotic-resistant bacteria, as well as a negative factor for the efficiency of soil nitrogen fertilization for crop production. The use of urease inhibitors to offset these effects requires knowledge, at a molecular level, of their mode of action. The 1.28 Å resolution structure of the enzyme-inhibitor complex obtained upon incubation of Sporosarcina pasteurii urease with N-(n-butyl)thiophosphoric triamide (NBPT), a molecule largely utilized in agriculture, reveals the presence of the monoamidothiophosphoric acid (MATP) moiety, obtained upon enzymatic hydrolysis of the diamide derivative of NBPT (NBPD) to yield n-butyl amine. MATP is bound to the two Ni(II) ions in the active site of urease using a µ2-bridging O atom and terminally bound O and NH2 groups, with the S atom of the thiophosphoric amide pointing away from the metal center. The mobile flap modulating the size of the active site cavity is found in the closed conformation. Docking calculations suggest that the interaction between urease in the open flap conformation and NBPD involves a role for the conserved αArg339 in capturing and orienting the inhibitor prior to flap closure. Calorimetric and spectrophotometric determinations of the kinetic parameters of this inhibition indicate the occurrence of a reversible slow inhibition mode of action, characterized, for both bacterial and plant ureases, by a very small value of the dissociation constant of the urease-MATP complex. No need to convert NBPT to its oxo derivative NBPTO, as previously proposed, is necessary for urease inhibition.


Subject(s)
Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacology , Organophosphorus Compounds/metabolism , Organophosphorus Compounds/pharmacology , Urease/antagonists & inhibitors , Urease/metabolism , Catalytic Domain , Hydrolysis , Kinetics , Molecular Docking Simulation , Sporosarcina/enzymology , Urea/metabolism , Urease/chemistry
11.
Biochim Biophys Acta ; 1844(9): 1662-74, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24982029

ABSTRACT

Urease, the most efficient enzyme so far discovered, depends on the presence of nickel ions in the catalytic site for its activity. The transformation of inactive apo-urease into active holo-urease requires the insertion of two Ni(II) ions in the substrate binding site, a process that involves the interaction of four accessory proteins named UreD, UreF, UreG and UreE. This study, carried out using calorimetric and NMR-based structural analysis, is focused on the interaction between UreE and UreG from Sporosarcina pasteurii, a highly ureolytic bacterium. Isothermal calorimetric protein-protein titrations revealed the occurrence of a binding event between SpUreE and SpUreG, entailing two independent steps with positive cooperativity (Kd1=42±9µM; Kd2=1.7±0.3µM). This was interpreted as indicating the formation of the (UreE)2(UreG)2 hetero-oligomer upon binding of two UreG monomers onto the pre-formed UreE dimer. The molecular details of this interaction were elucidated using high-resolution NMR spectroscopy. The occurrence of SpUreE chemical shift perturbations upon addition of SpUreG was investigated and analyzed to establish the protein-protein interaction site. The latter appears to involve the Ni(II) binding site as well as mobile portions on the C-terminal and the N-terminal domains. Docking calculations based on the information obtained from NMR provided a structural basis for the protein-protein contact site. The high sequence and structural similarity within these protein classes suggests a generality of the interaction mode among homologous proteins. The implications of these results on the molecular details of the urease activation process are considered and analyzed.


Subject(s)
Bacterial Proteins/chemistry , Carrier Proteins/chemistry , Nickel/chemistry , Sporosarcina/chemistry , Urease/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Calorimetry , Carrier Proteins/genetics , Carrier Proteins/metabolism , Cations, Divalent , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Kinetics , Magnetic Resonance Spectroscopy , Molecular Docking Simulation , Nickel/metabolism , Phosphate-Binding Proteins , Protein Binding , Protein Interaction Domains and Motifs , Protein Multimerization , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sporosarcina/enzymology , Thermodynamics , Urease/genetics , Urease/metabolism
12.
J Appl Microbiol ; 118(6): 1321-32, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25809221

ABSTRACT

AIMS: Ureolysis drives microbially induced calcium carbonate precipitation (MICP). MICP models typically employ simplified urea hydrolysis kinetics that do not account for cell density, pH effect or product inhibition. Here, ureolysis rate studies with whole cells of Sporosarcina pasteurii aimed to determine the relationship between ureolysis rate and concentrations of (i) urea, (ii) cells, (iii) NH4+ and (iv) pH (H(+) activity). METHODS AND RESULTS: Batch ureolysis rate experiments were performed with suspended cells of S. pasteurii and one parameter was varied in each set of experiments. A Michaelis-Menten model for urea dependence was fitted to the rate data (R(2)  = 0·95) using a nonlinear mixed effects statistical model. The resulting half-saturation coefficient, Km , was 305 mmol l(-1) and maximum rate constant, Vmax , was 200 mmol l(-1)  h(-1) . However, a first-order model with k1  = 0·35 h(-1) fit the data better (R(2)  = 0·99) for urea concentrations up to 330 mmol l(-1) . Cell concentrations in the range tested (1 × 10(7) -2 × 10(8)  CFU ml(-1) ) were linearly correlated with ureolysis rate (cell dependent Vmax' = 6·4 × 10(-9)  mmol CFU(-1)  h(-1) ). CONCLUSIONS: Neither pH (6-9) nor ammonium concentrations up to 0·19 mol l(-1)  had significant effects on the ureolysis rate and are not necessary in kinetic modelling of ureolysis. Thus, we conclude that first-order kinetics with respect to urea and cell concentrations are likely sufficient to describe urea hydrolysis rates at most relevant concentrations. SIGNIFICANCE AND IMPACT OF THE STUDY: These results can be used in simulations of ureolysis driven processes such as microbially induced mineral precipitation and they verify that under the stated conditions, a simplified first-order rate for ureolysis can be employed. The study shows that the kinetic models developed for enzyme kinetics of urease do not apply to whole cells of S. pasteurii.


Subject(s)
Sporosarcina/metabolism , Urea/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Calcium Carbonate/chemistry , Calcium Carbonate/metabolism , Hydrolysis , Kinetics , Sporosarcina/chemistry , Sporosarcina/enzymology , Urea/chemistry , Urease/chemistry , Urease/metabolism
13.
An Acad Bras Cienc ; 87(1): 109-19, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25806979

ABSTRACT

Two psychrophilic bacterial samples were isolated from King George Island soil, in Antarctica. The phylogenetic analysis based on the 16S rRNA (rrs) gene led to the correlation with the closest related isolates as Sporosarcina aquimarina (99%) and Algoriphagus antarcticus (99%), with query coverage of 99% and 98%, respectively. The spent culture media from both isolates displayed proteolytic activities detected by sodium dodecyl sulfate polyacrylamide gel electrophoresis containing gelatin as protein substrate. Under the employed conditions, S. aquimarina showed a 55 kDa protease with the best activity detected at pH 7.0 and at 27°C. A. antarcticus also showed a single extracellular protease, however its molecular mass was around 90kDa and its best activity was detected at pH 9.0 and at 37°C. The proteases from both isolates were inhibited by 1,10-phenanthroline and EDTA, two metalloprotease inhibitors. This is the first record of protease detection in both species, and our results may contribute to broaden the basic knowledge of proteases from the Antarctica environment and may help prospecting future biotechnological applications of these enzymes.


Subject(s)
Bacteroidetes/enzymology , Peptide Hydrolases/isolation & purification , Sporosarcina/enzymology , Antarctic Regions , Bacterial Typing Techniques , Bacteroidetes/classification , Electrophoresis, Polyacrylamide Gel , Molecular Weight , Peptide Hydrolases/genetics , Phylogeny , Soil Microbiology , Sporosarcina/classification
14.
J Biol Inorg Chem ; 19(8): 1243-61, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25113581

ABSTRACT

Urease is a nickel-dependent enzyme and a virulence factor for ureolytic bacterial human pathogens, but it is also necessary to convert urea, the most worldwide used fertilizer, into forms of nitrogen that can be taken up by crop plants. A strategy to control the activity of urease for medical and agricultural applications is to use enzyme inhibitors. Fluoride is a known urease inhibitor, but the structural basis of its mode of inhibition is still undetermined. Here, kinetic studies on the fluoride-induced inhibition of urease from Sporosarcina pasteurii, a widespread and highly ureolytic soil bacterium, were performed using isothermal titration calorimetry and revealed a mixed competitive and uncompetitive mechanism. The pH dependence of the inhibition constants, investigated in the 6.5-8.0 range, reveals a predominant uncompetitive mechanism that increases by increasing the pH, and a lesser competitive inhibition that increases by lowering the pH. Ten crystal structures of the enzyme were independently determined using five crystals of the native form and five crystals of the protein crystallized in the presence of fluoride. The analysis of these structures revealed the presence of two fluoride anions coordinated to the Ni(II) ions in the active site, in terminal and bridging positions. The present study consistently supports an interaction of fluoride with the nickel centers in the urease active site in which one fluoride competitively binds to the Ni(II) ion proposed to coordinate urea in the initial step of the catalytic mechanism, while another fluoride uncompetitively substitutes the Ni(II)-bridging hydroxide, blocking its nucleophilic attack on urea.


Subject(s)
Enzyme Inhibitors/pharmacology , Fluorides/pharmacology , Sporosarcina/enzymology , Thermodynamics , Urease/antagonists & inhibitors , Enzyme Inhibitors/chemistry , Fluorides/chemistry , Models, Molecular , Molecular Conformation , Urease/metabolism
15.
J Biol Inorg Chem ; 19(8): 1341-54, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25200810

ABSTRACT

Urease is an essential Ni(II) enzyme involved in the nitrogen metabolism of bacteria, plants and fungi. Ni(II) delivery into the enzyme active site requires the presence of four accessory proteins, named UreD, UreF, UreG and UreE, acting through a complex protein network regulated by metal binding and GTP hydrolysis. The GTPase activity is catalyzed by UreG, which couples this function to a non-enzymatic role as a molecular chaperone. This moonlighting activity is reflected in a flexible fold that makes UreG the first discovered intrinsically disordered enzyme. UreG binds Ni(II) and Zn(II),which in turn modulate the interactions with other urease chaperones. The aim of this study is to understand the structural implications of metal binding to Sporosarcina pasteurii UreG (SpUreG). A combination of light scattering, calorimetry, mass spectrometry, and NMR spectroscopy revealed that SpUreG exists in monomer-dimer equilibrium (K(d)= 45 µM), sampling three distinct folding populations with different degrees of compactness. Binding of Zn(II) ions, occurring in two distinct sites (K(d1) = 3 nM, K(d2) = 0.53 µM), shifts the protein conformational landscape toward the more compact population, while maintaining the overall protein structural plasticity. Differently, binding of Ni(II) ions occurs in three binding sites (K(d1(= 14 µM; K(d2) = 270 µM; K(d3)= 160 µM), with much weaker influence on the protein conformational equilibrium. These distinct conformational responses of SpUreG to Ni(II) and Zn(II) binding suggest that selective metal binding modulates protein plasticity, possibly having an impact on the protein-protein interactions and the enzymatic activity of UreG.


Subject(s)
Molecular Conformation/drug effects , Nickel/pharmacology , Sporosarcina/enzymology , Urease/chemistry , Urease/metabolism , Zinc/pharmacology , Binding Sites , Nickel/metabolism , Zinc/metabolism
16.
J Biol Inorg Chem ; 18(8): 1005-17, 2013 Dec.
Article in English | MEDLINE | ID: mdl-24126709

ABSTRACT

Urease is a nickel-dependent enzyme that plays a critical role in the biogeochemical nitrogen cycle by catalyzing the hydrolysis of urea to ammonia and carbamate. This enzyme, initially synthesized in the apo form, needs to be activated by incorporation of two nickel ions into the active site, a process driven by the dimeric metallochaperone UreE. Previous studies reported that this protein can bind different metal ions in vitro, beside the cognate Ni(II). This study explores the metal selectivity and affinity of UreE from Sporosarcina pasteurii (Sp, formerly known as Bacillus pasteurii) for cognate [Ni(II)] and noncognate [Zn(II)] metal ions. In particular, the thermodynamic parameters of SpUreE Ni(II) and Zn(II) binding have been determined using isothermal titration calorimetry. These experiments show that two Ni(II) ions bind to the protein dimer with positive cooperativity. The high-affinity site involves the conserved solvent-exposed His(100) and the C-terminal His(145), whereas the low-affinity site comprises also the C-terminal His(147). Zn(II) binding to the protein, occurring in the same protein regions and with similar affinity as compared to Ni(II), causes metal-driven dimerization of the protein dimer. The crystal structure of the protein obtained in the presence of equimolar amounts of both metal ions indicates that the high-affinity metal binding site binds Ni(II) preferentially over Zn(II). The ability of the protein to select Ni(II) over Zn(II) was confirmed by competition experiments in solution as well as by analysis of X-ray anomalous dispersion data. Overall, the thermodynamics and structural parameters that modulate the metal ion specificity of the different binding sites on the protein surface of SpUreE have been established.


Subject(s)
Bacterial Proteins/metabolism , Carrier Proteins/metabolism , Nickel/metabolism , Sporosarcina/enzymology , Urease/metabolism , Zinc/metabolism , Bacterial Proteins/chemistry , Binding Sites , Carrier Proteins/chemistry , Crystallography, X-Ray , Models, Molecular , Protein Conformation , Protein Multimerization , Sporosarcina/metabolism , Urease/chemistry
17.
J Biol Inorg Chem ; 18(3): 391-9, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23412551

ABSTRACT

Urease, the enzyme that catalyses the hydrolysis of urea, is a virulence factor for a large number of ureolytic bacterial human pathogens. The increasing resistance of these pathogens to common antibiotics as well as the need to control urease activity to improve the yield of soil nitrogen fertilization in agricultural applications has stimulated the development of novel classes of molecules that target urease as enzyme inhibitors. We report on the crystal structure at 1.50-Å resolution of a complex formed between citrate and urease from Sporosarcina pasteurii, a widespread and highly ureolytic soil bacterium. The fit of the ligand to the active site involves stabilizing interactions, such as a carboxylate group that binds the nickel ions at the active site and several hydrogen bonds with the surrounding residues. The citrate ligand has a significantly extended structure compared with previously reported ligands co-crystallized with urease and thus represents a unique and promising scaffold for the design of new, highly active, stable, selective inhibitors.


Subject(s)
Citric Acid/metabolism , Drug Design , Sporosarcina/enzymology , Urease/antagonists & inhibitors , Urease/chemistry , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Bacterial Infections/drug therapy , Catalytic Domain , Citric Acid/chemistry , Crystallography, X-Ray , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Humans , Models, Molecular , Nickel/chemistry , Nickel/metabolism , Sporosarcina/chemistry , Urease/metabolism
18.
Biosci Biotechnol Biochem ; 76(9): 1721-7, 2012.
Article in English | MEDLINE | ID: mdl-22972336

ABSTRACT

A novel esterase showing activity specific for esters of aryl-carboxylic acids was discovered in Sporosarcina sp. nov., which was identified by the 16S rDNA sequencing method in addition to morphological and physiological analyses. The aryl-carboxylesterase (named EstAC) was purified 780-fold from crude cell extracts by a 5-step procedure. EstAC was characterized as a monomeric protein with a molecular weight of 43,000, an optimum pH of around 9.0, and an optimum temperature of 40 °C. The pH optimum and the effects of inhibitors together with an internal amino acid sequence suggested that EstAC is a member of family VIII esterases. EstAC was found to be highly active on a wide variety of substrates such as alkyl benzoates, alkyl phenylacetates, ethyl α- or ß-substituted phenylpropionates, dialkyl terephthalates, dimethyl isophthalate, and ethylene glycol dibenzoate. However, monomethyl terephthalate was not hydrolyzed. It was suggested that EstAC had 4-hydroxybenzoyl and cinnamoyl esterase activities as well.


Subject(s)
Bacterial Proteins/metabolism , Carboxylesterase/metabolism , Carboxylic Acids/metabolism , Sporosarcina/enzymology , Bacterial Proteins/chemistry , Bacterial Proteins/isolation & purification , Biocatalysis , Carboxylesterase/chemistry , Carboxylesterase/classification , Carboxylesterase/isolation & purification , Carboxylic Acids/chemistry , DNA, Ribosomal/genetics , Esters , Hydrogen-Ion Concentration , Hydrolysis , Kinetics , Molecular Weight , Phylogeny , RNA, Ribosomal, 16S/genetics , Sporosarcina/chemistry , Substrate Specificity , Temperature
19.
Biometals ; 24(2): 301-9, 2011 Apr.
Article in English | MEDLINE | ID: mdl-21181488

ABSTRACT

Mercuric reductase (MerA) enzyme plays an important role in biogeochemical cycling and detoxification of Hg and recently, has also been shown to be useful in clean up of Hg-contaminated effluents. Present study describes isolation of a heavy metal-resistant isolate of Sporosarcina, which could tolerate up to 40, 525, 210, 2900 and 370 µM of Cd, Co, Zn, Cr and Hg respectively. It was found to reduce and detoxify redox-active metals like Cr and Hg. The chromate reductase and MerA activities in the crude cell extract of the culture were 1.5 and 0.044 units/mg protein respectively. The study also describes designing of a new set of highly degenerate primers based on a dataset of 23 Firmicute merA genes. As the primers encompass the known diversity of merA genes within the phylum Firmicutes, they can be very useful for functional diversity analysis. They were successfully used to amplify a 787 bp merA fragment from the current isolate. A 1174 bp merA fragment was further cloned by designing an additional downstream primer. It was found to show 92% similarity to the putative merA gene from Bacillus cereus AH820. To the best of our knowledge, this is the first report of mercury resistance and merA gene sequence from Sporosarcina.


Subject(s)
Sporosarcina/drug effects , Bacillus cereus/enzymology , Base Sequence , Cadmium/pharmacology , Chromium/pharmacology , Cobalt/pharmacology , Mercury , Molecular Sequence Data , Oxidoreductases/chemistry , Oxidoreductases/classification , Oxidoreductases/genetics , Sequence Homology, Nucleic Acid , Sporosarcina/enzymology , Sporosarcina/metabolism , Zinc/pharmacology
20.
Int J Biol Macromol ; 181: 263-274, 2021 Jun 30.
Article in English | MEDLINE | ID: mdl-33775759

ABSTRACT

The study of enzymes from extremophiles arouses interest in Protein Science because of the amazing solutions these proteins adopt to cope with extreme conditions. Recently solved, the structure of the psychrophilic acyl aminoacyl peptidase from Sporosarcina psychrophila (SpAAP) pinpoints a mechanism of dimerization unusual for this class of enzymes. The quaternary structure of SpAAP relies on a domain-swapping mechanism involving the N-terminal A1 helix. The A1 helix is conserved among homologous mesophilic and psychrophilic proteins and its deletion causes the formation of a monomeric enzyme, which is inactive and prone to aggregate. Here, we investigate the dimerization mechanism of SpAAP through the analysis of chimeric heterodimers where a protomer lacking the A1 helix combines with a protomer carrying the inactivated catalytic site. Our results indicate that the two active sites are independent, and that a single A1 helix is sufficient to partially recover the quaternary structure and the activity of chimeric heterodimers. Since catalytically competent protomers are unstable and inactive unless they dimerize, SpAAP reveals as an "obligomer" for both structural and functional reasons.


Subject(s)
Cold Temperature , Peptide Hydrolases/chemistry , Peptide Hydrolases/metabolism , Protein Multimerization , Sporosarcina/enzymology , Amino Acid Sequence , Catalytic Domain , Enzyme Stability , Models, Molecular , Mutation/genetics , Peptide Hydrolases/genetics , Peptide Hydrolases/isolation & purification , Phylogeny , Protein Domains , Protein Structure, Secondary , Protein Structure, Tertiary , Time Factors
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