Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.5.1.5 (urease)
7,257 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Previous studies demonstrated that two accessory proteins, HypA and HypB, play a role in nickel-dependent maturation of both hydrogenase and urease in Helicobacter pylori. Here, the two proteins were purified and characterized. HypA bound two Ni(2+) ions per dimer with positive cooperativity (Hill coefficient, approximately 2.0). The dissociation constants K(1) and K(2) for Ni(2+) were 58 and 1.3 microM, respectively. Studies on purified site-directed mutant proteins in each of the five histidine residues within HypA, revealed that only one histidine residue (His2) is vital for nickel binding. Nuclear magnetic resonance analysis showed that this purified mutant version (H2A) was similar in structure to that of the wild-type HypA protein. A chromosomal site-directed mutant of hypA (in the codon for His2) lacked hydrogenase activity and possessed only 2% of the wild-type urease activity. Purified HypB had a GTPase activity of 5 nmol of GTP hydrolyzed per nmol of HypB per min. Site-directed mutagenesis within the lysine residue in the conserved GTP-binding motif of HypB (Lys59) nearly abolished the GTPase activity of the mutant protein (K59A). In native solution, both HypA and HypB exist as homodimers with molecular masses of 25.8 and 52.4 kDa, respectively. However, a 1:1 molar mixture of HypA plus HypB gave rise to a 43.6-kDa species composed of both proteins. A 43-kDa heterodimeric HypA-HypB complex was also detected by cross-linking. The cross-linked adduct was still observed in the presence of 0.5 mM GTP or 1 microM nickel or when the mutant version of HypA (altered in His2) and HypB (altered in Lys59) were tested. Individually, HypA and HypB formed homodimeric cross-linked adducts. An interaction between HypA and the Hp0868 protein (encoded by the gene downstream of hypA) could not be detected via cross-linking, although such an interaction was predicted by yeast two-hybrid studies. In addition, the phenotype of an insertional mutation within the Hp0868 gene indicated that its presence is not critical for either the urease or the hydrogenase activity.
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PMID:Characterization of Helicobacter pylori nickel metabolism accessory proteins needed for maturation of both urease and hydrogenase. 1253 48

Five Gram-negative bacterial strains, oxidase-positive, motile by means of more than one polar flagella, facultative anaerobe, arginine dihydrolase-negative, lysine- and omithine decarboxylase-positive, sensitive to the vibriostatic agent O/129, were isolated from a flow-through rotifer culture system in Gent, Belgium, and previously characterized by fluorescent amplified fragment length polymorphism. Comparison of the 16S rDNA sequence of strain LMG 21460T indicated close relationships (approximately 99% similarity) to Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus and Vibrio parahaemolyticus. However, DNA hybridization experiments revealed similarity values below 70% with its closest species V. campbellii and V. harveyi. Additionally, the analysed strains differ from related Vibrio species by the utilization of melibiose and production of acid from L-arabinose and amygdalin. Among the strains analysed, differences were observed in some phenotypic characters, particularly susceptibility to ampicillin, polymyxin B and amikacin, and urease activity. The major fatty acids identified were 16:0, 18:1 omega7c, 14:0, 12:0 3-OH and 18:0. Vibrio rotiferianus sp. nov. is proposed, with type strain LMG 21460T (=CAIM 577T); it has a DNA G+C content of 44.5 +/- 0.01 mol%.
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PMID:Vibrio rotiferianus sp. nov., isolated from cultures of the rotifer Brachionus plicatilis. 1265 79

Isoaspartyl dipeptidase from Escherichia coli functions in protein degradation by catalyzing the hydrolysis of beta-L-isoaspartyl linkages in dipeptides. The best substrate for the enzyme reported thus far is iso-Asp-Leu. Here we report the X-ray analysis of the enzyme in its resting state and complexed with aspartate to 1.65 and 2.1 A resolution, respectively. The quaternary structure of the enzyme is octameric and can be aptly described as a tetramer of dimers. Each subunit folds into two distinct domains: the N-terminal region containing eight strands of mixed beta-sheet and the C-terminal motif that is dominated by a (beta,alpha)(8)-barrel. A binuclear zinc center is located in each subunit at the C-terminal end of the (beta,alpha)(8)-barrel. Ligands to the binuclear metal center include His 68, His 70, His 201, His 230, and Asp 285. The two zincs are bridged by a carboxylated lysine residue (Lys 162) and a solvent molecule, most likely a hydroxide ion. The product of the reaction, aspartate, binds to the enzyme by displacing the bridging solvent with its side chain functional group. From this investigation it is proposed that the reaction mechanism of the enzyme proceeds through a tetrahedral intermediate and that the bridging solvent attacks the re face of the carbonyl carbon of the scissile peptide bond. This structural analysis confirms the placement of isoaspartyl dipeptidase into the urease-related amidohydrolase superfamily.
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PMID:High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli. 1271 28

Synthesis of active Klebsiella aerogenes urease requires four accessory proteins to generate, in a GTP-dependent process, a dinuclear nickel active site with the metal ions bridged by a carbamylated lysine residue. The UreD and UreF accessory proteins form stable complexes with urease apoprotein, comprised of UreA, UreB, and UreC. The sites of protein-protein interactions were explored by using homobifunctional amino group-specific chemical cross-linkers with reactive residues being identified by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) of tryptic peptides. On the basis of studies of the UreABCD complex, UreD is capable of cross-linking with UreB Lys(9), UreB Lys(76), and UreC Lys(401). Furthermore UreD appears to be positioned over UreC Lys(515) according to decreased reactivity of this residue compared with its reactivity in UreD-free apoprotein. Several UreB-UreC and UreC-UreC cross-links also were observed within this complex; e.g. UreB Lys(76) with the UreC amino terminus, UreB Lys(9) with UreC Lys(20), and UreC Lys(515) with UreC Lys(89). These interactions are consistent with the proximate surface locations of these residues observed in the UreABC crystal structure. MALDI-TOF MS analyses of UreABCDF are consistent with a cross-link between the UreF amino terminus and UreB Lys(76). On the basis of an unexpected cross-link between UreB Lys(76) and UreC Lys(382) (distant from each other in the UreABC structure) along with increased side chain reactivities for UreC Lys(515) and Lys(522), UreF is proposed to induce a conformational change within urease that repositions UreB and potentially could increase the accessibility of nickel ions and CO(2) to residues that form the active site.
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PMID:Chemical cross-linking and mass spectrometric identification of sites of interaction for UreD, UreF, and urease. 1474 31

Urease activation is critical to the virulence of many human and animal pathogens. Urease possesses multiple, nickel-containing active sites, and UreE, the only nickel-binding protein among the urease accessory proteins, activates urease by transporting nickel ions. We performed NMR experiments to investigate the solution structure and the nickel-binding properties of Bacillus pasteurii (Bp) UreE. The secondary structures and global folds of BpUreE were determined for its metal-free and nickel-bound forms. The results indicated that no major structural change of BpUreE arises from the nickel binding. In addition to the previously identified nickel-binding site (Gly(97)-Cys(103)), the C-terminal tail region (Lys(141)-His(147)) was confirmed for the first time to be involved in the nickel binding. The C-terminally conserved sequence ((144)GHQH(147)) was confirmed to have an inherent nickel-binding ability. Nickel addition to 1.6 mm subunit, a concentration where BpUreE predominantly forms a tetramer upon the nickel binding, induced a biphasic spectral change consistent with binding of up to at least three nickel ions per tetrameric unit. In contrast, nickel addition to 0.1 mm subunit, a concentration at which the protein is primarily a dimer, caused a monophasic spectral change consistent with more than 1 equivalent per dimeric unit. Combined with the equilibrium dialysis results, which indicated 2.5 nickel equivalents binding per dimer at a micromolar protein concentration, the nickel-binding stoichiometry of BpUreE at a physiological concentration could be three nickel ions per dimer. Altogether, the present results provide the first detailed structural data concerning the nickel-binding properties of intact, wild-type BpUreE in solution.
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PMID:Structural characterization of the nickel-binding properties of Bacillus pasteurii urease accessory protein (Ure)E in solution. 1476 2

Allantoate degradation was demonstrated in the extracts of ungerminated seeds and roots, stems and leaves in germinated seedlings of French bean (Phaseolus vulgaris L.). Activity of allantoate-degrading enzyme could only be measured when phenylhydrazine was included in the assay mixture. Partial purification of allantoate-degrading enzyme from seedlings was performed and two fractions with allantoate-degrading enzyme activity were obtained. The molecular mass of the first fraction was over 200 kD and that of the second one was 13.5 kD. The allantoate-degrading enzyme with small molecular weight contained no activity of either ureidoglycolate-degrading enzyme or urease. From the stoichiometry of the reaction catalyzed by the allantoate-degrading enzyme with small molecular weight it followed that the enzyme was allantoate amidohydrolase (EC 3.5.3.9). The optimal pH for the allantoate amidohydrolase was 8.5. Mn(2+) ions were essential for enzymatic activity. Glyoxylate and glycolate strongly inhibited the enzyme activity. The lysine and tryptophan residues were essential to the enzymatic catalysis; thiol group and tyrosyl residues were not involved in the enzyme catalysis.
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PMID:Some properties of the allantoate amidohydrolase from French bean seedlings. 1562 97

The nutritional and physiological characteristics of 15 isolates from four species of the Azolla fern were determined. Although some minor variation existed in levels of urease activity, ability to utilize xylose, and formation of N(2) gas from NO(3), all 15 isolates were rather similar and believed to represent a single species. These eubacteria exhibited aminopeptidase activity and became viscous when treated with KOH, similar to gram-negative organisms; however, the absence of lipopolysaccharide and 2-keto-3-deoxyoctonate in cell walls indicated that they are truly gram-positive organisms. They are unusual because peptidoglycan could not be detected during most of their growth cycle. The presence of lysine as the major diamino acid in cell wall hydrolysates, the inability to hydrolyze cellulose, and the distinctive developmental pattern with rods and "V" forms present during log phase, becoming progressively shorter until cocci dominated during stationary and death phases, indicated that these organisms belong to the genus Arthrobacter Conn and Dimmick. With the exception of the inability to hydrolyze gelatin, their characteristics are consistent with those of the type species, Arthrobacter globiformis Conn and Dimmick.
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PMID:Identification of eubacteria isolated from leaf cavities of four species of the N-fixing azolla fern as arthrobacter conn and dimmick. 1634 44

Strain CP2CT was isolated from biological soil crusts in the Colorado Plateau, USA. The isolate was aerobic, facultatively fermentative, Gram-negative, non-motile and red-pigmented (due to the presence of carotenoids), but did not contain bacteriochlorophyll a. The strain tested positive for catalase, oxidase and urease and was negative for lysine and ornithine decarboxylases and arginine dihydrolase. The major fatty acids present were C(18 : 1)omega7c and C(16 : 0). It had a high DNA G+C content of 75 mol%. Comparisons of 16S rRNA gene sequences identified bacteriochlorophyll a-producing strains of Paracraurococcus ruber (94.9 %), Craurococcus roseus (92.2 %) and Roseococcus thiosulfatophilus (92.3 %), as well as non-bacteriochlorophyll a-producing bacteria Muricoccus roseus (94.9 %), Roseomonas gilardii (94.2 %) and Roseomonas mucosa (93.8 %), as the bacteria most closely related to strain CP2CT. Phylogenetically, CP2CT was placed roughly equidistantly from the above organisms. Based on its phylogenetic placement and morphological and physiological characteristics, strain CP2CT is assigned to a new genus in the alpha-1 subgroup of the Proteobacteria, for which the name Belnapia gen. nov. is proposed. Strain CP2CT (= ATCC BAA-1043T = DSM 16746T) is proposed as the type strain of the type species of this genus, with the name Belnapia moabensis gen. nov., sp. nov.
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PMID:Belnapia moabensis gen. nov., sp. nov., an alphaproteobacterium from biological soil crusts in the Colorado Plateau, USA. 1640 66

Short peptides resembling the Helicobacter pylori urease antigen (UreB F8 Ser-Ile-Lys-Glu-Asp-Val-Gln-Phe) with deleted aspartic acid and glutamic acid residues, anchored through a triazine linker via the N-terminal moiety to cellulose plate were prepared. The peptides were used for binding of antibodies from sera of patients with medically confirmed atherosclerosis. Recognition of the peptides was also tested with anti-Jack beans urease antibodies. The important role of a Gly-Gly spacer separating the peptides from the cellulose support was shown. Different patterns of binding of antibodies from H. pylori infected patients and anti-Jack bean urease antibodies were observed only in the case of pentapeptides. The peptide Gly-Gly-Leu-Val-Phe-Lys-Thr was recognized by most of the tested sera.
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PMID:Synthetic peptides mimicking antigenic epitope of Helicobacter pylori urease. 1649 40

Using succinic anhydride, a succinylated derivative of anti-urease IgG having 49 +/- 6% modification was prepared and its physicochemical and immunological properties were studied. IgG undergoes substantial changes in its native conformation on succinylation, which was mainly attributed to electrostatic destabilization of the native protein conformation. The modified IgG exhibited a decrease in its cross-reactivity with urease. This decrease is attributed to the conformational change in IgG upon succinylation and/or is due to the disruption of the lysine residues in the antigen-binding site of IgG upon succinylation, which may be involved in binding the antigen. IgG was able to bind to the specific antigen although its conformation was partially modified. Therefore, partial modification of the conformation of the antigen-binding site of IgG is permissible in order to bind to the antigen.
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PMID:Effect of succinylation of antibodies on their conformation and interaction with the antigen. 1722 86


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