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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A patient suspected of an inborn error of metabolism will commonly have urine organic acid analysis performed as part of their workup. The traditional urine organic acid method involves extraction of the acidic fraction from urine samples using an organic solvent, derivatization of extracted compounds, and identification using gas chromatography-mass spectrometry (GC-MS). Unfortunately, the extraction step results in the loss of many neutral and positively charged compounds, which may be of interest to metabolic physicians and biochemical geneticists. By replacing the traditional extraction step with an enzymatic treatment of the sample with urease, an abundance of organic molecules are available for separation and quantitation by GC-MS. The urease method is a useful adjunct to newborn screening follow-up and it has the additional benefit of being able to identify many classes of biochemical compounds, such as amino acids, acylglycines, neurotransmitters, and carbohydrates. The method below describes the urease treatment, derivatization, and the organic acids, and other biochemical metabolites that can be identified.
Methods Mol Biol 2010
PMID:Identification of urine organic acids for the detection of inborn errors of metabolism using urease and gas chromatography-mass spectrometry (GC-MS). 2007 95

The measurement of urinary orotic acid excretion is an important test for establishing a diagnosis of hereditary orotic aciduria, a genetic defect of pyrimidine biosynthesis. Measurement of secondary urinary orotic acid elevation is also an important clinical test for the differential diagnosis of hyperammonemia due to some of the primary disorders of the urea cycle including ornithine transcarbamylase (OTC) deficiency, and the hyperornithinemia-hyperammonemia-homocitrullinemia (HHH) syndrome. Low levels of orotic acid are observed in carbamylphosphate synthetase (CPS) defects. This method utilizes a stable-isotope labeled internal standard (1, 3-(15)N-orotic acid), which is added to the standards, controls, and patient samples prior to extraction. Interference from urea is removed by incubation of samples with urease and the orotic acid is derivatized by trimethylsilylation. Quantitation is made against an eight-point standard curve using specific selected ions from both the labeled and unlabeled orotic acid.
Methods Mol Biol 2010
PMID:Quantitation of orotic acid in urine using isotope dilution-selected ion gas chromatography-mass spectrometry. 2007 96

Arginase of the Helicobacter pylori hydrolyzes l-arginine to l-ornithine and urea. H. pylori urease hydrolyzes urea to carbon dioxide and ammonium, which neutralizes acid. Both enzymes are involved in H. pylori nitrogen metabolism. The role of arginase in the physiology of H. pylori is metabolically upstream of urease which contributes in pathogeneses of this bacterium, so arginase could be potential drug target for H. pylori infection. We performed homology modeling of H. pylori arginase using the crystal structure of Bacillus caldovelox arginase as a template, and then refined the model through molecular dynamics (MD) simulations. Different criteria measured by PROCHECK, VERIFY-3D and PROSA were indicative of the proper fold for the predicted structural model of H. pylori arginase. Further evaluation on the model quality was performed by investigating the interaction of some arginase inhibitors with the modeled enzyme. Such interactions were determined employing Autodock 3.0.5 program. Our results are compatible with the published data on contribution of four aspartic acids: D116, D120, D234, D236 and three histidines: H91, H118, H133 for catalysis and stability of binuclear metal center of arginase that have important role in binding and catalytic activity in active site. In the absence of the experimental structure of H. pylori arginase we hope that our model will be useful to provide rational design of novel anti-H. pylori drugs.
J Mol Graph Model 2010 Apr
PMID:Molecular modeling of Helicobacter pylori arginase and the inhibitor coordination interactions. 2008 52

For mass production of urease B subunit (UreB) and heat shock protein A subunit (HspA) of Helicobacter pylori with Bombyx mori nuclear polyhedrosis virus (BmNPV) baculovirus expression system (BES) and to determine whether they could be used as an oral vaccine against H. pylori, besides, to determine the time course of expressed recombinant protein and the optimum acquisition time directly through green fluorescence, HspA and enhanced green fluorescence protein (EGFP) genes were cloned into vector pFastBacDual to form donor vector pFastBacDual-(EGFP) (HspA), UreB gene was cloned into vector pFastBacDual to form donor vector pFastBacDual-UreB,then they were transformed into E. coli BmDH10Bac to obtain the recombinant Bacmid-(EGFP) (HspA) and Bacmid-UreB respectively. They were used to transfect BmN cells and generated the recombinant baculovirus BmNPV-(EGFP) (HspA) and BmNPV-UreB. Using these recombinant baculovirus BmNPV-(EGFP) (HspA) and BmNPV-UreB inoculated the silkworm pupae, a recombinant HspA and UreB protein were expressed in silkworm pupae, which were around 13 and 62 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blot analysis. After oral immunization of mice, serum specific IgG antibodies against HspA and UreB in vaccine group were much higher than that in mock and native silkworm powder control groups. The results indicated that the expressed recombinant HspA and UreB in silkworm pupae would possess good immunogenicity. In addition, when EGFP and HspA proteins were expressed, a direct correlation between the increase in intensity of fluorescence and HspA concentration.
Mol Biol Rep 2011 Jun
PMID:Expression of UreB and HspA of Helicobacter pylori in silkworm pupae and identification of its immunogenicity. 2012 14

This paper shows analysis of the association of the 802C>T polymorphism of the NOD2/CARD15 gene with the occurrence of the chronic inflammation of the gastric mucosa associated with the Helicobacter pylori infections, development of intestinal metaplasia and dysplasia and, in the result of this, gastric cancer. Genomic DNA samples were extracted from paraffin blocks of gastric mucosal biopsies and from peripheral blood. H. pylori infection was confirmed by histological analysis and urease test. Pyrosequencing of 802C>T polymorphism of the NOD2/CARD15 gene was performed for H. pylori infected patients (131) and population group (100). Analysis of the NOD2/CARD15 gene showed that frequency of the T allele was significantly higher (32.8%) in the group of patients in comparison with the population group (18.1%), with the relative risk of 1.8. In the patient group, the frequency of the CC genotype was 51.1%, CT 32.1% and TT 16.8% (relative risk: 0.7, 1.1 and 4.2, respectively), while in the population group it was 69.0%, 25.7% and 5.3% (relative risk: 1.0, 0.9 and 1.3, respectively). The increasing frequency of the T allele and CT and TT genotypes in the patients with increasingly deeper changes in the gastric mucosa becomes apparent. Our findings suggest that polymorphism 802C>T is associated with changes in gastric mucosa and plays a significant role in the initiation and the progression of carcinogenesis. The number of observed mutations in gastric mucosa correlated with severity of disease.
Exp Mol Pathol 2010 Jun
PMID:Association of c.802C>T polymorphism of NOD2/CARD15 gene with the chronic gastritis and predisposition to cancer in H. pylori infected patients. 2023 Aug 16

Polymorphisms in cytokine genes may contribute to increased susceptibility to different cancers. The aim of this paper is to investigate the association of IL-8-251A/T polymorphism and Helicobacter pylori (H. pylori) infection with the risk of developing gastric cardiac adenocarcinoma (GCA) in the south of Taihang Mountain, a high-incidence area of esophageal cancer in China. The IL-8-251 A/T polymorphism was genotyped in 519 cases of GCA and 504 healthy controls. The H. pylori infection in GCA patients and controls was detected by rapid urease test (RUT), histopathology or (14)C-urea breath test ((14)C-UBT). The results showed that family history of upper gastrointestinal cancer (UGIC) and H. pylori infection significantly increased the risk of developing GCA. The overall genotype and allelotype distributions of IL-8 promoter SNPs in GCA patients were significantly different from those in healthy controls. Compared with TT genotype, AA genotype significantly elevated the risk of developing GCA. The stratification analysis revealed that, compared with the TT genotype, the AA genotype significantly elevated the risk of developing GCA in both positive family history of UGIC and H. pylori infection subgroups. This study provides evidence to support a relationship of increased susceptibility to GCA in individuals of the south Taihang Mountain region with IL-8 251 AA genotype, especially for those individuals who have family history of UGIC or H. pylori infection.
Mol Biol Rep 2010 Dec
PMID:Interleukin-8-251A/T polymorphism and Helicobacter pylori infection influence risk for the development of gastric cardiac adenocarcinoma in a high-incidence area of China. 2030 Aug 63

A pharmacophore model was developed based on three structurally diverse urease inhibitors by using the GASP program. This model comprises the positions and tolerance for two acceptor atoms (AA1 and AA2), one donor atom (DA1), and one hydrophobic center (HYP1). This derived phamacophore model was employed to screen an in-house database of organic compounds. Hits obtained were evaluated by molecular docking using GOLD software. On the basis of ligand- and structural-based predictions, an in vitro testing of short-listed compounds was conducted and a novel class of urease inhibitors (2-aminothiophines) was identified. The potent in vitro activity and selectivity of these compounds, along with their non-toxic nature against the plant cells indicated that they can serve as leads for solving urease-associated health and agriculture problems.
J Mol Graph Model 2010 Jun
PMID:Identification of potent urease inhibitors via ligand- and structure-based virtual screening and in vitro assays. 2033 93

Urease, a nickel-dependent metalloenzyme, is synthesized by plants, some bacteria, and fungi. It catalyzes the hydrolysis of urea into ammonia and carbon dioxide. Although the amino acid sequences of plant and bacterial ureases are closely related, some biological activities differ significantly. Plant ureases but not bacterial ureases possess insecticidal properties independent of its ureolytic activity. To date, the structural information is available only for bacterial ureases although the jack bean urease (Canavalia ensiformis; JBU), the best-studied plant urease, was the first enzyme to be crystallized in 1926. To better understand the biological properties of plant ureases including the mechanism of insecticidal activity, we initiated the structural studies on some of them. Here, we report the crystal structure of JBU, the first plant urease structure, at 2.05 A resolution. The active-site architecture of JBU is similar to that of bacterial ureases containing a bi-nickel center. JBU has a bound phosphate and covalently modified residue (Cys592) by beta-mercaptoethanol at its active site, and the concomitant binding of multiple inhibitors (phosphate and beta-mercaptoethanol) is not observed so far in bacterial ureases. By correlating the structural information of JBU with the available biophysical and biochemical data on insecticidal properties of plant ureases, we hypothesize that the amphipathic beta-hairpin located in the entomotoxic peptide region of plant ureases might form a membrane insertion beta-barrel as found in beta-pore-forming toxins.
J Mol Biol 2010 Jul 16
PMID:Crystal structure of the first plant urease from jack bean: 83 years of journey from its first crystal to molecular structure. 2047 1

The oligopeptide transport systems Opp belong to the nickel/peptide/opine PepT subfamily of ABC-transporters. The opportunist pathogen Staphylococcus aureus encodes four putative Opps and one orphean substrate binding protein Opp5A. Here, we report that the Opp2 permease complex (Opp2BCDF) and Opp5A are involved in nickel uptake and then renamed them NikBCDE and NikA respectively. S. aureus carries also a high-affinity nickel transporter NixA belonging to the NiCoT family of secondary transporters. The activity of these two nickel transporters determine that of urease, a multimeric nickel-dependent enzyme mainly involved in the neutralization of acidic environments. However, only the Nik system was responsible for the neutralization and deposit of pH-dependent crystals in human urine. Inactivation of the nik genes affected bacterial colonization of mouse urinary tract, as well as the 50% infective dose levels compared with the parental and nixA strains. Finally, complementation of the nik mutations restored bacterial colonization. Together, our results suggest a role for the Nik system in the urinary tract infection by S. aureus, probably due to the urease-mediated pH increase of the urine.
Mol Microbiol 2010 Sep
PMID:A nickel ABC-transporter of Staphylococcus aureus is involved in urinary tract infection. 2066 75

Jack bean (Canavalia ensiformis) seeds are toxic for insects and the toxicity is due in part to an entomotoxic peptide enzymatically released from ureases in the midgut of susceptible insects. To characterize expression of urease isoforms in jack bean seed, particularly the more abundant urease isoform (JBU), quantitative proteomics was performed. Quiescent through 5-day germinating seeds were analyzed at 1-day intervals using a total proteomics approach (TPA) and also after co-immunoprecipitation (co-IP) with anti-JBU monoclonal antibodies. Jack bean proteins for TPA and co-IP were pre-fractionated by SDS-PAGE, segmented for in-gel trypsin digestion, and analyzed by liquid chromatography coupled to nanospray ionization tandem mass spectrometry (LC-MS/MS). Acquired MS(2) data were searched against a comprehensive plant database and the MEROPS peptidase database, in the absence of a jack bean EST database. Proteins detected in TPA were quantified by label-free spectral counting. A total of 234 and 106 non-redundant proteins were detected in TPA and co-IP, respectively. Mobilization of JBU was observed beginning 3-days after imbibition indicating that the entomotoxic peptide was not formed before this stage. A predicted urease isoform, JBURE-IIb, was detected in the co-IP study. Additionally, 46 plastid proteins, including RuBisCO and plastid ATPase were pulled down with JBU antibodies. These data shed new light on the behavior of urease isoforms during the early stages of plant development.
Plant Mol Biol 2011 Jan
PMID:Global and targeted proteomics in developing jack bean (Canavalia ensiformis) seedlings: an investigation of urease isoforms mobilization in early stages of development. 2097 23


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