Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues

P-type ion transporting ATPases are ATP-powered ion pumps that establish ion concentration gradients across biological membranes. Transfer of bound cations to the lumenal or extracellular side occurs while the ATPase is phosphorylated. Here we report at 2.3 A resolution the structure of the calcium-ATPase of skeletal muscle sarcoplasmic reticulum, a representative P-type ATPase that is crystallized in the absence of Ca2+ but in the presence of magnesium fluoride, a stable phosphate analogue. This and other crystal structures determined previously provide atomic models for all four principal states in the reaction cycle. These structures show that the three cytoplasmic domains rearrange to move six out of ten transmembrane helices, thereby changing the affinity of the Ca2+-binding sites and the gating of the ion pathway. Release of ADP triggers the opening of the lumenal gate and release of phosphate its closure, effected mainly through movement of the A-domain, the actuator of transmembrane gates.

Halomonas anticariensis sp. nov., from Fuente de Piedra, a saline-wetland wildfowl reserve in Málaga, southern Spain

Three Halomonas strains, FP34, FP35T and FP36, which were isolated from soil samples taken from Fuente de Piedra, a saline wetland in the province of Málaga in southern Spain, are described. Phylogenetic analyses based on 16S rRNA gene sequences show that the three isolates belong to the genus Halomonas in the γ-Proteobacteria and form an independent genetic line. Phenotypically, they share the characteristics of Halomonas and differ from the most closely related species, Halomonas campisalis, in the following features: they are strictly aerobic and, because of their production of exopolysaccharides, form cream-coloured, mucoid colonies; they produce phosphatase and grow within narrow pH and temperature ranges; and they are susceptible to kanamycin and streptomycin. Their G+C content varies between 60·0 and 61·4 mol%. The name Halomonas anticariensis sp. nov. is proposed for these isolates. Strain FP35T (=LMG 22089T=CECT 5854T) is the type strain. The bacterium grows best in 7·5 % (w/v) NaCl and does not require magnesium or potassium salts for growth, although they do stimulate growth somewhat when present. Its major fatty acids are 18 : 1ω7c, 16 : 0, 16 : 1ω7c, 15 : 0 iso 2-OH, 12 : 0 3-OH, 12 : 0, 10 : 0 and 19 : 0 cyclo ω8c. Its predominant respiratory lipoquinone is ubiquinone with nine isoprene units (Q-9).

Evaluation of effects of dietary carbohydrate on formation of struvite crystals in urine and macromineral balance in clinically normal cats

OBJECTIVE

To evaluate effects of dietary carbohydrate on urine volume; struvite crystal formation; and calcium, phosphorus, and magnesium balance in clinically normal cats.

ANIMALS

21 healthy adult cats (15 sexually intact males and 6 sexually intact females).

PROCEDURE

Diets containing no carbohydrate source (control diet), control plus starch, or control plus fiber were given in a 3 X 3 Latin-square design. The diets were available ad libitum in study 1 (n = 12) and given under restrictions in study 2 (9) to equalize daily intakes of crude protein among the 3 groups. Formation of struvite crystals and balance of calcium, phosphorus, and magnesium were measured.

RESULTS

Urine volume was lower in the starch group and fiber group in study 1, whereas no differences were detected among the groups in study 2. Urinary pH and struvite activity product were higher in the starch group in both studies, and the fiber group also had higher struvite activity product in study 2. In both studies, urinary concentrations of HCl-insoluble sediment were higher in the starch group and fiber group. In the fiber group, a net loss of body calcium, phosphorus, and magnesium was detected in study 2.

CONCLUSIONS AND CLINICAL RELEVANCE

Starch and fiber in diets potentially stimulate formation of struvite crystals. Hence, reducing dietary carbohydrate is desirable to prevent struvite urolith formation. In addition, a net loss of body calcium, phosphorus, and magnesium during feeding of the fiber diet suggests that dietary inclusion of insoluble fiber could increase macromineral requirements of cats.

Preventing kidney stones: calcium restriction not warranted

The traditional wisdom on preventing calcium stones, the most common form of kidney stone, has been to advise patients to limit dietary calcium. Research has proved this wrong, however. Normal dietary calcium intake, along with reduced salt and protein, is now advised. This paper also summarizes the diagnosis and treatment of the less-common forms of kidney stones-struvite, uric acid, and cystine.

[Magnesium orthophosphate, a new form of reserve phosphates in the halophilic archaeon Halobacterium salinarium]

The accumulation and utilization of reserve phosphates in the extremely halophilic archaeon Halobacterium salinarium were studied. The growth of H. salinarium was found to depend on the initial concentration of inorganic phosphate (Pi) in the culture medium and its content in the inoculum. Growing cells consumed 85-95% of Pi from the medium. Unlike the reserve phosphates of many other microorganisms, which are mainly polyphosphates, the reserve phosphates of H. salinarium cells contain no more than 15% polyphosphates, the rest being magnesium orthophosphate. The excessive consumption of Pi from the medium changed cell morphology and caused the death of part of the cell population. The cells that remained viable could grow in a Pi-deficient medium, utilizing about 70% of reserve magnesium phosphate as the phosphorus source.

The structure of Ap(4)A hydrolase complexed with ATP-MgF(x) reveals the basis of substrate binding

Ap(4)A hydrolases are Nudix enzymes that regulate intracellular dinucleoside polyphosphate concentrations, implicating them in a range of biological events, including heat shock and metabolic stress. We have demonstrated that ATP x MgF(x) can be used to mimic substrates in the binding site of Ap(4)A hydrolase from Lupinus angustifolius and that, unlike previous substrate analogs, it is in slow exchange with the enzyme. The three-dimensional structure of the enzyme complexed with ATP x MgF(x) was solved and shows significant conformational changes. The substrate binding site of L. angustifolius Ap(4)A hydrolase differs markedly from the two previously published Nudix enzymes, ADP-ribose pyrophosphatase and MutT, despite their common fold and the conservation of active site residues. The majority of residues involved in substrate binding are conserved in asymmetrical Ap(4)A hydrolases from pathogenic bacteria, but are absent in their human counterparts, suggesting that it might be possible to generate compounds that target bacterial, but not human, Ap(4)A hydrolases.

Different Mg to Fe ratios in the mixed metal MgFe hydroxy-carbonate compounds and the effect on phosphate binding compared with established phosphate binders

Due to the side effects of the current oral phosphate binders, there is a need for effective alternatives. A number of mixed metal hydroxy-carbonate compounds (MMHCs) based on Mg and Fe have recently been established as effective phosphate binders. We have now carried out further studies on the MMHCs with different ratios of Mg(2+):Fe(3+) in different forms to assess for phosphate binding efficacy and ionic release in aqueous solution and food slurries. The compounds that provide the most promise are those with Mg(2+):Fe(3+) ratios of 2:1 and 4:1 in the unaged/dry form. Their phosphate binding efficacy was compared with a wide range of established phosphate binders, such as aluminum hydroxide [Al(OH)(3)], calcium carbonate (CaCO(3)), calcium acetate (CaAc(2)), magnesium hydroxide [Mg(OH)(2)], and lanthanum carbonate [La(2)(CO(3))(3)] in various food slurries. The results showed that the MgFe compounds were much more effective (on a weight for weight basis) than the established binders, and their properties were relatively pH independent. Calcium compounds (CaCO(3) and CaAc(2)) were ineffective under the experimental conditions. Mg(OH)(2) was effective at low pH but not at pHs greater than 5.0, and also released two- to threefold more magnesium than the MgFe compounds. Al(OH)(3) showed some degree of efficacy, but the binding capacity was, at best, less than 50% of the MMHCs. La(2)(CO(3))(3) required at least a 10-fold increase in weight to give comparable binding to the MMHCs. In conclusion, MgFe hydroxy-carbonate compounds are effective phosphate binders and may provide a better alternative to both existing and emerging binders for combating hyperphosphataemia.

Chemolysis of struvite stones by acidification of artificial urine--an in vitro study

OBJECTIVE

The aim of the study was to look for strategies that improve the clinical outcome of struvite stones. An in vitro experimental set up with artificial stones made of struvite (BON(N)-STONES) was chosen to perform standardized and reproducible analyses on various artificial urines with pH-values that may be reached by acidification with oral methionine treatment.

MATERIALS AND METHODS

Artificial ball-shaped stones made of struvite (BON(N)-STONES) with a diameter of 0.8 cm were used. The investigations on chemolysis were performed using a dissolution device which simulates the physiological conditions in the upper urinary tract with computer-assisted on line measurement of data. For chemolysis of struvite BON(N)-STONES artificial urines according to Griffith at four different pH-values (pH 5.75, pH 6.0, pH 6.25, pH 6.5) were used. Furthermore natural and struvite BON(N)-STONES were treated with Suby G-solution (pH = 4.0).

RESULTS

Comparing natural and artificial struvite stones after treatment with Suby G there was no significant difference regarding their dissolution rate. The dissolution rate of struvite stones in artificial urine rose with a decreasing pH-value. The diminution of the pH-value from 6.5 to 5.75 lead to an increase of the dissolution rate of more than 35%. This increase in the dissolution rate decreased with falling pH-value.

CONCLUSIONS

The acidification of urine accelerated the dissolution rate of struvite stones in vitro. Considering in vivo conditions the intake of 1,500-3,000 mg L-methionine may lead to a sufficient acidification for a good dissolution of struvite stones.

Gastric patch pyeloplasty: development of an animal model to produce upper tract urinary acidification for treating struvite urinary calculi

PURPOSE

Struvite calculi form in an alkaline environment created by urease producing uropathogens. We developed a viable upper tract urinary acidification model by performing gastric patch pyeloplasty in the rabbit. This model produces urinary acidification sufficient for the treatment and prevention of struvite renal calculi. We evaluated the physiological, metabolic and surgical outcomes.

MATERIALS AND METHODS

gastric segment was harvested based on branches of the left gastro-epiploic artery. The flap was folded along the transverse axis and the adjacent edges were closed. The mouth of this reconfigured pouch provided optimal dimensions for anastomosis with the diminutive renal pelvis. Half of the rabbits were treated with internal stenting and H-2 blockade. Urinary pH was assessed by weekly cage collection and direct collection from the cannulated ureters. Urine culture was done, and serum gastrin and electrolytes were assessed at regular intervals. The rabbits were sacrificed at 3 to 26 weeks. Histological examination was routinely performed.

RESULTS

A total of 15 rabbits were available for complete assessment. Sustained urinary acidification was produced in 7 animals (47%) with a mean pH decrease of 2.27. In another 2 rabbits (13%) the urine was initially acidic but subsequently became alkaline due to ureteral obstruction. Electrolytes and gastrin were unchanged in these rabbits and urine culture was positive in 2. Histological testing revealed nonspecific inflammatory changes of the renal pelvis. Anastomotic complications were the most common surgical complication and the most common cause of failed acidification. The cohort treated without stents and H-2 blockade was at significantly greater risk for anastomotic leakage.

CONCLUSIONS

Gastric patch pyeloplasty may significantly increase urinary acidity in the rabbit model without altering the serum electrolyte balance or gastrin level. The procedure utilizes common techniques of reconstructive urology and may be possible with laparoscopy. Further study is required to assess the in vivo effect of this procedure for treating and preventing upper tract struvite calculi.

Surreptitious abuse of magnesium laxatives as a cause of chronic diarrhoea

Surreptitious laxative abuse is increasingly considered as a possible cause of unexplained chronic diarrhoea. Laboratory services for detection of colonic stimulant laxatives are widely available; however, laboratory facilities for identifying patients with magnesium-induced diarrhoea are not commonly provided, making diagnosis difficult. We describe three patients who surreptitiously abused magnesium laxatives, and whose diagnoses were delayed, leading in each case to extensive investigations and lengthy in-patient stays. In all three cases, the diagnosis was eventually made by the simple measurement of magnesium in a random faecal sample. We would like to increase the awareness of surreptitious magnesium laxative abuse as a cause of chronic diarrhoea so that costly and unnecessary investigations may be minimized.

Struvite precipitation potential for nutrient recovery from anaerobically treated wastes

Geochemical equilibrium speciation modeling was used to determine optimum conditions for precipitation of magnesium ammonium phosphate, or struvite, for the recovery of nutrients from anaerobically digested wastes. Despite a wide range of pH values with the potential to precipitate struvite, the optimum pH was determined to be 9.0. Bench experiments conducted on effluent from an anaerobic sequencing batch reactor (ASBR) treating swine wastes achieved a maximum of 88% ammonia removal at a pH of 9.5 with added magnesium and phosphate to achieve an ammonium: magnesium: phosphate molar ratio of 1:1.25:1. Struvite precipitation was performed on a continuous basis in a pilot-scale ASBR treating swine wastes. Through the addition of supplemental magnesium and phosphate, the ammonia concentration was reduced from 1500 mg/L as nitrogen to less than 10 mg/L. The supenatant from the struvite precipitation clarifier was recycled to the feed of the ASBR without adverse impact, simulating on-farm effluent reuse as flush water.

Solution structure of myosin-ADP-MgFn ternary complex by fluorescent probes and small-angle synchrotron X-ray scattering

In the presence of excess amounts of fluorine, a physiological divalent cation, magnesium (Mg(2+)), forms a novel phosphate analogue, magnesium fluoride (MgFn). Park et al. [Biochim. Biophys. Acta 1430, 127-140 (1999)] previously demonstrated that MgADP. MgFn forms a complex with myosin subfragment-1 (S-1), and the S-1.ADP. MgFn ternary complex mimics a transient state in the activity cycle of ATPase. In the present study, localized conformations in the regions of highly reactive cysteine and lysine residues, Cys 707 (SH1), Cys 697 (SH2), and Lys 83 (RLR), which change their conformations markedly during ATP hydrolysis, were studied using fluorescent probes and chemical modification. The global shape of the complex was also studied using small angle X-ray solution scattering and compared it with other previously reported myosin.ADP. fluorometal ternary complexes. The results suggest that the overall conformation and localized functional regions of the complex are quite similar to those in the presence of ATP, indicating that the complex mimics the M(**).ADP.P(i) steady state.

Struvite stones

Struvite stones constitute only about 2-3% of the stones reaching the laboratory for analysis, but the clinical problems they create including sepsis and even renal demise are greater than with any other stone type. This article reviews the evidence that bacterial urease, usually from a Proteus species, is responsible for the chemical changes in urine which result in struvite formation. Available urease inhibitors and other forms of medical management of patients with these stones are discussed. A patient with struvite stones should be assumed to have a progressive disease which cannot be ignored. Even after seemingly successful elimination of stones with lithotripsy and/or percutaneous nephrolithotomy, careful medical follow-up is critical. The medical profession is probably underutilizing postprocedure hemiacidrin irrigation because of shortsighted financial considerations. Primary-care physicians need to be educated in the importance of aggressive management of Proteus and other urea-splitting infections.

Effect of culture conditions on the formation of struvite by Myxococcus xanthus

The amount of struvite (MgNH4PO4 x 6H2O) produced by Myxococcus xanthus as well as the culture parameter values (pH, total phosphorus, total Kjeldahl nitrogen) were dependent on the culture medium used. Struvite formation started during the exponential phase and the maximum concentration was observed at the beginning of stationary growth phase. The addition of each medium component to the liquid culture influenced the amount of crystal produced. This amount did not depend on the pH increase during the culture period. The moment of the bacterial growth phase, at which each medium component was added, influenced the struvite formation.

A study of struvite precipitation and urease activity in bacteria isolated from patients with urinary infections and their possible involvement in the formation of renal calculi

Struvite precipitation and urease activity were studied in 72 bacterial strains isolated from patients with an urinary infection. The results revealed struvite precipitation by urease-positive, urease-negative and weakly urealitic bacteria. However, in some strains of each of these groups, no precipitation was observed. Variations in pH within the cultures were also investigated as were the mineralogy and morphology of the crystals precipitated using X-ray diffraction and scanning electron microscopy, respectively. The role of urease activity and alkalinization of the medium in struvite precipitation is discussed, as is the possible involvement of bacteria in nucleation processes. We concluded that urease-negative bacteria or those with weak urease activity may also be involved in the formation of struvite renal calculi although urease-positive bacteria seem to make a greater contribution.

Mechanism of Ca2+-induced inhibition of Escherichia coli inorganic pyrophosphatase

The causes of inhibition of Escherichia coli inorganic pyrophosphatase (PPase) by Ca2+ were investigated. The interactions of several mutant pyrophosphatases with Ca2+ in the absence of substrate were analyzed by equilibrium dialysis. The kinetics of Ca2+ inhibition of hydrolysis of the substrates MgPPi and LaPPi by the native PPase and three mutant enzymes (Asp-42-Asn, Ala, and Glu) were studied. X-Ray data on E. coli PPase complexed with Ca2+ or CaPPi solved at atomic resolution were analyzed. It was shown that, in the course of the catalytic reaction, Ca2+ replaces Mg2+ at the M2 site, which shows higher affinity for Ca2+ than for Mg2+. Different properties of these cations account for active site deformation. Our findings indicate that the filling of the M2 site with Ca2+ is sufficient for PPase inhibition. This fact proves that Ca2+ is incapable of properly activating the H2O molecule for nucleophilic attack on PPi. It was also demonstrated that Ca2+, as a constituent of the non-hydrolyzable substrate analog CaPPi, competes with MgPPi at the M3 binding site. As a result, Ca2+ is a powerful inhibitor of all known PPases. Other possible reasons for the inhibitory effect of Ca2+ on the enzyme activity are also considered.

Role of bacteria in the development of kidney stones

Currently, only struvite stones are regarded as deriving from bacteria. Recent work has suggested that calcium-based stones might also have an infectious origin. Nanobacteria, small intracellular bacteria found in human kidney stones, are capable of forming a calcium phosphate shell, and thus could serve as crystallization centres for renal calculi formation. Until now, however, all trials performed to confirm the presence of nanobacteria in human calculi, serum or urine have failed. In a hyperoxaluric rat model, tissue-residing macrophages were able to remove interstitial crystals and thus may not be primarily engaged in defending against micro-organisms, if present.

Magnesium fluoride-dependent binding of small G proteins to their GTPase-activating proteins

GTPase-activating proteins (GAPs) enhance the intrinsic GTPase activity of small G proteins, such as Ras and Rho, by contributing a catalytic arginine to the active site. An intramolecular arginine plays a similar role in heterotrimeric G proteins. Aluminum fluoride activates the GDP form of heterotrimeric G proteins, and enhances binding of the GDP form of small G proteins to their GAPs. The resultant complexes have been interpreted as analogues of the transition state of the hydrolytic reaction. Here, equilibrium binding has been measured using scintillation proximity assays to provide quantitative information on the fluoride-mediated interaction of Ras and Rho proteins with their respective GAPs, neurofibromin (NF1) and RhoGAP. High-affinity fluoride-mediated complex formation between Rho.GDP and RhoGAP occurred in the absence of aluminum; however, under these conditions, magnesium was required. Additionally, the novel observation was made of magnesium-dependent, fluoride-mediated binding of Ras.GDP to NF1 in the absence of aluminum. Aluminum was required for complex formation when the concentration of magnesium was low. Thus, either aluminum fluoride or magnesium fluoride can mediate the high-affinity binding of Rho. GDP or Ras.GDP to GAPs. It has been reported that magnesium fluoride can activate heterotrimeric G proteins. Thus, magnesium-dependent fluoride effects might be a general phenomenon with G proteins. Moreover, these data suggest that some protein.nucleotide complexes previously reported to contain aluminum fluoride may in fact contain magnesium fluoride.

Struvite stones: diagnosis and current treatment concepts

Effective management of struvite calculi requires a comprehensive approach to eliminate the stone burden and prevent stone recurrence. These stones occur more frequently in women, infants, and the elderly, as these patients are at greater risk for urinary tract infections. All patients should have routine laboratory testing as well as an excretory urogram. Appropriate urine cultures should be completed. Definitive management should promptly follow diagnosis. Percutaneous nephrolithotomy with or without SWL is the usual treatment. Appropriate antibiotic use is helpful; magnesium and phosphorus restriction and administration of urease inhibitors are less valuable.

Historical perspectives and current advancements in the bacteriology and medical therapy of struvite urinary stone disease

Struvite calculi have afflicted man for thousands of years. Despite recent advances in surgical technology to treat these disabling stones, high recurrence rates and inability to remove all stone fragments remain significant problems. Previous non-surgical alternatives have been disappointing because of low success rates, increased side effects or poor tolerability. New research in this area continues to provide insight into origins of lithogenesis and non-invasive therapy for calculi caused by infection.

Biomineralization of carbonates by Marinococcus albus and Marinococcus halophilus isolated from the Salar de Atacama (Chile)

We studied the precipitation of carbonates in 17 strains of moderately halophilic, Gram-positive cocci belonging to two species: Marinococcus halophilus and Marinococcus albus, isolated from the Salar de Atacama (Chile). They were cultivated in solid and liquid laboratory media for 42 days at salt concentrations (wt/vol) of 3%, 7.5%, 15%, and 20%. The bioliths precipitated were studied by X-ray diffraction and scanning electron microscopy. M. halophilus formed crystals at each of the salt concentrations, with a maximum number of strains capable of precipitating carbonates at 7.5% and 15% salt concentrations. M. albus did not precipitate at 20% and showed a maximum at 7.5%. This behavior is similar to that of other gram-positive bacteria and differs from that found in gram-negative bacteria. The bioliths precipitated were spherical, generally isolated, with a size of 10-100 microm, varying with salinity. They were of magnesium calcite (CO3 Ca1-x Mgx) with Mg content increasing with increasing salinity and Mg/Ca molar ratio of the culture medium. These results demonstrate the active role played by M. halophilus and M. albus in the precipitation of carbonates.

The 2.0 A structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with a transition-state analog inhibitor

The structure of human HGPRT bound to the transition-state analog immucillinGP and Mg2+-pyrophosphate has been determined to 2.0 A resolution. ImmucillinGP was designed as a stable analog with the stereoelectronic features of the transition state. Bound inhibitor at the catalytic site indicates that the oxocarbenium ion of the transition state is stabilized by neighboring-group participation from MgPPi and O5'. A short hydrogen bond forms between Asp 137 and the purine ring analog. Two Mg2+ ions sandwich the pyrophosphate and contact both hydroxyls of the ribosyl analog. The transition-state analog is shielded from bulk solvent by a catalytic loop that moves approximately 25 A to cover the active site and becomes an ordered antiparallel beta-sheet.

Transition-state analogs as inhibitors of human and malarial hypoxanthine-guanine phosphoribosyltransferases

The proposed transition state for hypoxanthine-guanine phosphoribosyltransferases (HGPRTs) has been used to design and synthesize powerful inhibitors that contain features of the transition state. The iminoribitols (1S)-1-(9-deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol 5-phosphate (immucillinHP) and (1S)-1-(9-deazaguanin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol 5-phosphate (immucillinGP) are the most powerful inhibitors yet reported for both human and malarial HGPRTs. Equilibrium binding constants are >1,000-fold tighter than the binding of the nucleotide substrate. The NMR spectrum of malaria HGXPRT in the Michaelis complex reveals downfield hydrogen-bonded protons. The chemical shifts move farther downfield with bound inhibitor. The inhibitors are lead compounds for species-specific antibiotics against parasitic protozoa. The high-resolution crystal structure of human HGPRT with immucillinGP is reported in the companion paper.