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1.
The 3D structure of the methionyl-tRNA synthetase from E. coli has been investigated using X-ray analysis1,2 at a resolution 1.8Å. 90% of the molecule is now well defined and the zinc atom has been identified in a buried region of the molecule, close to the active site. At the same time, the refinement of the complex ATP-MetRS at 2.5 Å has been carried out. The crystallographic R factor has been assigned a value of 25% at 2.5Å with an overall temperature factor of 9Å2 and 22% when the individual temperature factors are refined. A Fourier difference map clearly reveals the electron density of the bound ATP, showing the phosphate groups deeply plunging into the active site. In parallel, the synthetase gene has been used to probe some of the enzyme structure-activity relationships. A series of 60 modified enzymes truncated at the C-terminus have been constructed in vitro and assayed for activity. In agreement with the graphics model, the results show that a minimum of 534 residues is necessary to sustain the aminoacylation reaction. A programme of site-directed mutagenesis is in progress: residues thought to be important for the catalytic activity, the metal coordination and tRNA interaction are being modified. Preliminary results are discussed in the light of the crystallographic model.  相似文献   

2.
Binding of 1,N6-ethanoadenosine triphosphate to actin   总被引:3,自引:0,他引:3  
G-actin is known to bind one molecule of ATP. Its polymerization to F-actin is accompanied by the splitting off of the terminal phosphate of the bound nucleotide. We have found that the fluorescent 1,N6-ethanoadenosine triphosphate (?ATP) can substitute for ATP in G-actin and that G-actin containing bound ?ATP possesses essentially full polymerizability. The binding of this ATP analog has been studied by following the inactivation of the ?ATP·G-actin complex. The binding constant (4?5.7 × 106 M?1) obtained in the absence of EDTA is about 50% of that for ATP, while the binding constant obtained in the presence of EDTA (0.9?3.0 × 105 M?1) is comparable to those for ATP and ADP. These findings suggest that ?ATP can be used as a structural probe for actin. The fluorescence lifetime of ?ATP bound to G·actin is 36 nsec. The rotational relaxation time of ?ATP·G-actin is near 60 nsec. at 20°C.  相似文献   

3.
Extracellular nucleoside triphosphate diphosphohydrolases (NTPDases) are enzymes that hydrolyze extracellular nucleotides to the respective monophosphate nucleotides. In the past 20 years, NTPDases belonging to mammalian, parasitic and prokaryotic domains of life have been discovered, cloned and characterized. We reveal the first structures of NTPDases from the legume plant species Trifolium repens (7WC) and Vigna unguiculata subsp. cylindrica (DbLNP). Four crystal structures of 7WC and DbLNP were determined at resolutions between 1.9 and 2.6 Å. For 7WC, structures were determined for an ‐apo form (1.89 Å) and with the product AMP (2.15 Å) and adenine and phosphate (1.76 Å) bound. For DbLNP, a structure was solved with phosphate and manganese bound (2.60 Å). Thorough kinetic data and analysis is presented. The structure of 7WC and DbLNP reveals that these NTPDases can adopt two conformations depending on the molecule and co‐factor bound in the active site. A central hinge region creates a “butterfly‐like” motion of the domains that reduces the width of the inter‐domain active site cleft upon molecule binding. This phenomenon has been previously described in Rattus norvegicus and Legionella pneumophila NTPDaseI and Toxoplasma gondii NTPDaseIII suggesting a common catalytic mechanism across the domains of life.  相似文献   

4.
We report here results of crystallographic studies at 3.0 Å resolution of complexes of phosphate ligands with aspartate carbamoyltransferase from Escherichia coli. Specifically, we interpret the binding of CTP, ATP, 5-bromo-CTP, 8-bromo-GTP. formycin A 5′-triphosphate. 3,N6-etheno-ATP. phosphate/carbamoyl-d.l-aspartate and pyrophosphate to the catalytic and regulatory chains of the enzyme.We observed two modes of binding of ligands to the phosphate crevice of the catalytic chain. Pyrophosphate and phosphate penetrate deeply into the cleft between the two domains of a catalytic monomer. In contrast. ATP, CTP. formycin A 5′-triphosphate and 3,N6-etheno-ATP bind to an exposed region of this cleft through their β and γ phosphates. Although the β and γ phosphates of 8-bromo-GTP bind to the same region as do the non-brominated nucleotides. 8-bromo-GTP interacts with the protein through all three of its phosphates and its ribose.Ser52, Arg54. Thr55, Arg105, His134. Gln137 and Arg167 are residues of the catalytic chain near density corresponding to phosphate ligands. The interactions of phosphate ligands are consistent with results of nuclear magnetic resonance, kinetics and equilibrium binding studies.Nucleoside triphosphates also bind to the regulatory chain in two modes. ATP and CTP bind in similar conformations to nearly the same site of the allosteric domain. The effector 8-bromo-GTP interacts at a location that does not overlap with the ATP-CTP site. The phosphates are in an extended conformation for all effectors. Furthermore, ATP. 5-bromo-CTP and 8-bromo-GTP bind to the protein in the anti conformation.Interactions of ATP and CTP with the protein are essentially consistent with the proposals put forward by London &; Schmidt (1972). We suggest, however, a modification of the London &; Schmidt model on the basis of our results with 8-bromo-GTP. In addition, we propose that the allosteric binding sites of nucleoside triphosphates are coupled to each other through the N-terminal segments of monomers of a regulatory dimer.  相似文献   

5.
PII constitutes a family of signal transduction proteins that act as nitrogen sensors in microorganisms and plants. Mycobacterium tuberculosis (Mtb) has a single homologue of PII whose precise role has as yet not been explored. We have solved the crystal structures of the Mtb PII protein in its apo and ATP bound forms to 1.4 and 2.4 Å resolutions, respectively. The protein forms a trimeric assembly in the crystal lattice and folds similarly to the other PII family proteins. The Mtb PII:ATP binary complex structure reveals three ATP molecules per trimer, each bound between the base of the T‐loop of one subunit and the C‐loop of the neighboring subunit. In contrast to the apo structure, at least one subunit of the binary complex structure contains a completely ordered T‐loop indicating that ATP binding plays a role in orienting this loop region towards target proteins like the ammonium transporter, AmtB. Arg38 of the T‐loop makes direct contact with the γ‐phosphate of the ATP molecule replacing the Mg2+ position seen in the Methanococcus jannaschii GlnK1 structure. The C‐loop of a neighboring subunit encloses the other side of the ATP molecule, placing the GlnK specific C‐terminal 310 helix in the vicinity. Homology modeling studies with the E. coli GlnK:AmtB complex reveal that Mtb PII could form a complex similar to the complex in E. coli. The structural conservation and operon organization suggests that the Mtb PII gene encodes for a GlnK protein and might play a key role in the nitrogen regulatory pathway.  相似文献   

6.
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mn2+ Ap5A, and Mg2+ Ap5A have been determined by X-ray crystallography to resolutions of 1.6 Å, 1.85 Å, and 1.96 Å, respectively. The protein's lid domain is partially open, being both rotated and translated away from bound Ap5A. The flexibility of the lid domain in the ternary state and its ability to transfer force directly to the the active site is discussed in light of our proposed entropic mechanism for catalytic turnover. The bound Zn2+ atom is demonstrably structural in nature, with no contacts other than its ligating cysteine residues within 5 Å. The B. stearothermophilus adenylate kinase lid appears to be a truncated zinc finger domain, lacking the DNA binding finger, which we have termed a zinc knuckle domain. In the Mg2+ Ap5A and Mn2+ Ap5A structures, Mg2+ and Mn2+ demonstrate six coordinate octahedral geometry. The interactions of the Mg2+-coordinated water molecules with the protein and Ap5A phosphate chain demonstrate their involvement in catalyzing phosphate transfer. The protein selects for β-γ (preferred by Mg2+) rather than α-γ (preferred by Mn2+) metal ion coordination by forcing the ATP phosphate chain to have an extended conformation. Proteins 32:276–288, 1998. © 1998 Wiley-Liss, Inc.  相似文献   

7.
Comparisons among evolutionarily related enzymes offer opportunities to reveal how structural differences produce different catalytic activities. Two structurally related enzymes, Escherichia coli alkaline phosphatase (AP) and Xanthomonas axonopodis nucleotide pyrophosphatase/phosphodiesterase (NPP), have nearly identical binuclear Zn2+ catalytic centers but show tremendous differential specificity for hydrolysis of phosphate monoesters or phosphate diesters. To determine if there are differences in Zn2+ coordination in the two enzymes that might contribute to catalytic specificity, we analyzed both x-ray absorption spectroscopic and x-ray crystallographic data. We report a 1.29-Å crystal structure of AP with bound phosphate, allowing evaluation of interactions at the AP metal site with high resolution. To make systematic comparisons between AP and NPP, we measured zinc extended x-ray absorption fine structure for AP and NPP in the free-enzyme forms, with AMP and inorganic phosphate ground-state analogs and with vanadate transition-state analogs. These studies yielded average zinc–ligand distances in AP and NPP free-enzyme forms and ground-state analog forms that were identical within error, suggesting little difference in metal ion coordination among these forms. Upon binding of vanadate to both enzymes, small increases in average metal–ligand distances were observed, consistent with an increased coordination number. Slightly longer increases were observed in NPP relative to AP, which could arise from subtle rearrangements of the active site or differences in the geometry of the bound vanadyl species. Overall, the results suggest that the binuclear Zn2+ catalytic site remains very similar between AP and NPP during the course of a reaction cycle.  相似文献   

8.
N10‐formyltetrahydrofolate synthetase (FTHFS) is a folate enzyme that catalyzes the formylation of tetrahydrofolate (THF) in an ATP dependent manner. Structures of FTHFS from the thermophilic homoacetogen, Moorella thermoacetica, complexed with (1) a catalytic intermediate—formylphosphate (XPO) and product—ADP; (2) with an inhibitory substrate analog–folate; (3) with XPO and an inhibitory THF analog, ZD9331, were used to analyze the enzyme mechanism. Nucleophilic attack of the formate ion on the gamma phosphate of ATP leads to the formation of XPO and the first product ADP. A channel that leads to the putative formate binding pocket allows for the binding of ATP and formate in random order. Formate binding is due to interactions with the gamma‐phosphate moiety of ATP and additionally to two hydrogen bonds from the backbone nitrogen of Ala276 and the side chain of Arg97. Upon ADP dissociation, XPO reorients and moves to the position previously occupied by the beta‐phosphate of ATP. Conformational changes that occur due to the XPO presence apparently allow for the recruitment of the third substrate, THF, with its pterin moiety positioned between Phe384 and Trp412. This position overlaps with that of the bound nucleoside, which is consistent with a catalytic mechanism hypothesis that FTHFS works via a sequential ping‐pong mechanism. More specifically, a random bi uni uni bi ping‐pong ter ter mechanism is proposed. Additionally, the native structure originally reported at a 2.5 Å resolution was redetermined at a 2.2 Å resolution.  相似文献   

9.
Members of the universal stress protein (USP) family are conserved in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants and confer abilities to respond to a wide range of environmental stresses. Arabidopsis thaliana contains 44 USP domain‐containing proteins, and USP domain is found either in a small protein with unknown physiological function or in an N‐terminal portion of a multi‐domain protein, usually a protein kinase. Here, we report the first crystal structure of a eukaryotic USP‐like protein encoded from the gene At3g01520. The crystal structure of the protein At3g01520 was determined by the single‐wavelength anomalous dispersion method and refined to an R factor of 21.8% (Rfree = 26.1%) at 2.5 Å resolution. The crystal structure includes three At3g01520 protein dimers with one AMP molecule bound to each protomer, comprising a Rossmann‐like α/β overall fold. The bound AMP and conservation of residues in the ATP‐binding loop suggest that the protein At3g01520 also belongs to the ATP‐binding USP subfamily members. Proteins 2015; 83:1368–1373. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.  相似文献   

10.
Conformation of coenzyme fragments when bound to lactate dehydrogenase   总被引:7,自引:0,他引:7  
The conformations of adenosine, 5′-AMP and 5′-ADP when bound to dogfish M4 lactate dehydrogenase at pH 7.8 or greater have been determined at 2.8 Å resolution to investigate the events on coenzyme binding. The coenzyme fragments AMP and ADP induce a conformational change in lactate dehydrogenase at pH values less than 6.0 in the same way as do NAD+, NADH or ADPR at any pH value. The structure of NAD+ when bound to lactate dehydrogenase had previously been determined at 5.0 Å resolution. The structures of the bound adenosine, AMP, ADP and NAD+ are compared with the preliminary structure of NAD in a 3.0 Å resolution map of the ternary complex LDH-NAD—pyruvate. Small but significant changes in the binding of the phosphates could be important in the folding of the protein loop over the substrate binding pocket.  相似文献   

11.
31P-NMR has been used to quantify inorganic phosphate (Pi) and high-energy phosphates in the isolated, functioning perfused rat kidney, while monitoring oxygen consumption, glomerular filtration rate and sodium reabsorption. Compared with enzymatic analysis, 100% of ATP, but only 25% of ADP and 27% of Pi are visible to NMR. This is indicative that a large proportion of both ADP and Pi are bound in the intact kidney. NMR is measuring free, and therefore probably cytosolic concentrations of these metabolites. ATP synthesis rate, measured by saturation transfer NMR shows the P:O ratio of 2.45 for the intact kidney. This is close to the theoretical value, suggesting the NMR visible pool is that which is involved in oxidative phosphorylation. The energy cost of Na transport, calculated from the theoretical Na:ATP of 3.0 exceeded the measured rate of ATP synthesis. Instead, Na:ATP for active transport in the perfused kidney was 12. Since the phosphorylation potential ([ATP][ADP]×[Pi]) by NMR was 10 000 M?1, the free-energy of ATP hydrolysis was 52 kJ/mol. Using this figure, the rate of ATP hydrolysis observed could fully account for the observed rate of sodium reabsorption.  相似文献   

12.
Five analogues of ATP and six other non-nucleotide compounds with phosphate groups were tested as gorging stimulants for second-instar larvae of Rhodnius prolixus to determine the importance of the phosphate chain. Only molecules with terminal phosphate groups were potent. Insertion of an imido group (5′-Adenylylimidodiphosphate, AMP-PNP) or a methylene group (β, γ-Methylene adenosine 5′-triphosphate, AMP-PCP) between the β and γ phosphates of ATP reduced the potency compared to ATP by ratios of 1.8 and 25.5, respectively. Substituting ribose (Adenosine 5′-diphosphoribose, AMP-PR) for the γ phosphate group or an amidate or a sulphate group (Adenosine 5′-phosphoramidate, AMP-N; Adenosine 5′-phosphosulphate, AMP-S) for the β and γ phosphate groups of ATP resulted in a complete loss of stimulatory activity.Some non-nucleotide phosphate compounds were potent phagostimulants. Pyrophosphate with an ED50 of 64 μM had a potency ratio compared with ATP of 1:17. Methylene diphosphonic acid (ED50 680 μM) and even single phosphate ions (ED50 2.5 mM) had substantial potency. Two isomers of phosphoglyceric acid differ greatly in their ability to stimulate gorging; 2-PGA was active (ED50 160 μM) whereas 3-PGA had almost no activity.A summary of known phagostimulants to R. prolixus supports the hypothesis that ATP-like gorging stimulants act by forming a temporary binding to 3 sites on a receptor protein in the membrane of the chemosensory cell. The amino group on C6 of adenine, the OH group on C2 of ribose and the terminal phosphate group(s) determine potency, presumably by determining binding affinity. However, only the phosphate group appears essential to the chemosensory process.  相似文献   

13.
1. The chemical shifts (delta) of the phosphates of 2,3-diphosphoglycerate and adenosine triphosphate (ATP) were determined by phosphorus nuclear magnetic resonance (31P NMR) spectroscopy and were found to be displaced downfield following the addition of hemoglobin (3 mM) to a solution of either diphosphoglycerate (5 mM) or ATP (1 mM). 2. The binding of these compounds to hemoglobin was also determined by membrane ultrafiltration. A direct relationship was observed between the change in chemical shift ((delta delta) of the 2-P and 3-P of diphosphoglycerate and the percent diphosphoglycerate bound, when the latter was varied by altering pH, oxygenation state, or total diphosphoglycerate concentration. 3. In comparable studies with ATP binding, a linear relationship between the delta delta values of the gamma-, beta-, and alpha-P of ATP and the percent of ATP bound was not observed when the data from all of the experiments were plotted. NMR signals were not detectible in deoxyhemoglobin solutions containing 1 mM ATP but were seen in solutions containing 3.8 mM ATP. 4. The results indicate that 31P NMR spectroscopy is a promising tool for investigating organic phosphate interactions with hemoglobin.  相似文献   

14.
Shigella dysentriae and other Gram‐negative human pathogens are able to use iron from heme bound to hemoglobin for growing. We solved at 2.6 Å resolution the 3D structure of the TonB‐dependent heme/hemoglobin outer membrane receptor ShuA from S. dysenteriae. ShuA binds to hemoglobin and transports heme across the outer membrane. The structure consists of a C‐terminal domain that folds into a 22‐stranded transmembrane β‐barrel, which is filled by the N‐terminal plug domain. One distal histidine ligand of heme is located at the apex of the plug, exposed to the solvent. His86 is situated 9.86 Å apart from His420, the second histidine involved in the heme binding. His420 is in the extracellular loop L7. The heme coordination by His86 and His420 involves conformational changes. The comparisons with the hemophore receptor HasR of Serratia marcescens bound to HasA‐Heme suggest an extracellular induced fit mechanism for the heme binding. The loop L7 contains hydrophobic residues which could interact with the hydrophobic porphyring ring of heme. The energy required for the transport by ShuA is derived from the proton motive force after interactions between the periplasmic N‐terminal TonB‐box of ShuA and the inner membrane protein, TonB. In ShuA, the TonB‐box is buried and cannot interact with TonB. The structural comparisons with HasR suggest its conformational change upon the heme binding for interacting with TonB. The signaling of the heme binding could involve a hydrogen bond network going from His86 to the TonB‐box. Proteins 2010. © 2009 Wiley‐Liss, Inc.  相似文献   

15.
The biological and chemical basis of vanadium action in fungi is relatively poorly understood. In the present study, we investigate the influence of vanadate (V5+) on phosphate metabolism of Phycomyces blakesleeanus. Addition of V5+ caused increase of sugar phosphates signal intensities in 31P NMR spectra in vivo. HPLC analysis of mycelial phosphate extracts demonstrated increased concentrations of glucose 6 phosphate, fructose 6 phosphate, fructose 1, 6 phosphate and glucose 1 phosphate after V5+ treatment. Influence of V5+ on the levels of fructose 2, 6 phosphate, glucosamine 6 phosphate and glucose 1, 6 phosphate (HPLC), and polyphosphates, UDPG and ATP (31P NMR) was also established. Increase of sugar phosphates content was not observed after addition of vanadyl (V4+), indicating that only vanadate influences its metabolism. Obtained results from in vivo experiments indicate catalytic/inhibitory vanadate action on enzymes involved in reactions of glycolysis and glycogenesis i.e., phosphoglucomutase, phosphofructokinase and glycogen phosphorylase in filamentous fungi.  相似文献   

16.
BackgroundThe paper presents a study on the influence of different lithium carbonate and lithium citrate concentration on proteolytic enzymes, namely pepsin and trypsin, in vitro. Lithium can directly affect enzyme activity. Its influence on many bodily functions in both ill and healthy people has been proven.MethodsTo assess the influence of Li+ ions concentration and the substrate/enzyme ratio on pepsin and trypsin activity in vitro, 60 factorial experiments were conducted (each repeated 30 times).Main findingsFor both enzymes, statistically significant changes in their activity under the influence of lihium carbonate and lithium citrate were observed. The biggest increase in enzyme activity reached even 198.6 % and the largest decrease in enzyme activity reached about 50 %.ConclusionsThe study shows that both organic and inorganic forms of lithium salts cause changes in the activity of digestive enzymes. Different concentrations of lithium carbonate and lithium citrate stimulate or inhibit the activity of trypsin and pepsin.  相似文献   

17.
The interaction of a series of phosphate diesters and triesters (1=diphenyl phosphate, 2=dimethyl phosphate, 3=bis(2-ethylhexyl) phosphate, 4=trimethyl phosphate, 5=methyldiphenyl phosphate, 6=triphenyl phosphate) with [Mg(15-crown-5)]2+ (15-crown-5=1,4,7,10,13-pentaoxocyclopentadecane) was studied as a simplified model for the interaction of aqueous Mg2+ ion with phosphate-containing biomolecules such as RNA. Using electrospray mass spectrometry, we confirm the formation of 1:1 adducts in the gas phase. Proton and 31P NMR titration data were used to construct binding isotherms, and a 1:1 binding equilibrium was fit to the isotherms at room temperature to estimate the binding affinities. The binding affinity data are consistent with ditopic coordination of neutral dialkyl phosphate ligands to the [Mg(15-crown-5)]2+ unit. This involves inner-sphere coordination to the Mg2+ via an oxygen atom, which is complemented by a weak hydrogen-bonding interaction with the crown ether ligand. Ditopic interaction is consistent with low-temperature NMR spectra showing four different configurations for 1 coordinated to [Mg(15-crown-5)]2+, which are interpreted in terms of hindered rotation around the Mg–Ophos bond. Thermochemical analysis of the binding affinity data suggests that the second-shell interaction contributes only about 1 kcal/mol to the binding free energy, so additional factors, such as steric constraints, must be operative to give a preferred phosphate orientation in this system. However, the experimental data do suggest that second-shell interactions contribute as much as 40% of the total binding energy, consistent with the pronounced ability of aqueous Mg2+ to form salt-bridges linking secondary and tertiary elements of RNA structure.Abbreviations OTf trifluoromethanesulfonate - ESI-MS electrospray mass spectrometry  相似文献   

18.
31P-NMR techniques offer a useful method of studying changes in the metabolism of intact parasitic worms. The liver flukes, Fasciola hepatica, provide good quality 31P high resolution NMR spectra for at least 6 h under anaerobic conditions. The levels of ATP remain constant throughout this period. There is no signal for phosphocreatine or phosphoarginine. In contrast to the findings in mammalian tissues, there is a distinct peak for the terminal phosphate of ADP. A number of signals are observed in the phosphodiester region of the spectrum the largest of which is identified as l-α-glycerophosphoryl choline. Serotonin (5-hydroxytryptamine) causes an appreciable increase in the levels of sugar phosphates when the flukes are incubated in the absence of glucose. The addition of glucose also causes a marked increase in the signals for the hexose phosphate.  相似文献   

19.
31P-NMR techniques offer a useful method of studying changes in the metabolism of intact parasitic worms. The liver flukes, Fasciola hepatica, provide good quality 31P high resolution NMR spectra for at least 6 h under anaerobic conditions. The levels of ATP remain constant throughout this period. There is no signal for phosphocreatine or phosphoarginine. In contrast to the findings in mammalian tissues, there is a distinct peak for the terminal phosphate of ADP. A number of signals are observed in the phosphodiester region of the spectrum the largest of which is identified as l-α-glycerophosphoryl choline. Serotonin (5-hydroxytryptamine) causes an appreciable increase in the levels of sugar phosphates when the flukes are incubated in the absence of glucose. The addition of glucose also causes a marked increase in the signals for the hexose phosphate.  相似文献   

20.
The title compound, Co(NH3)5PO4, prepared by a modified literature procedure, was used to study the inhibition of Na+-K+ ATPase and to serve as a structural model for ML4(nucleotide) complexes. The structure was determined by single crystal X-ray diffraction techniques. The crystals are monoclinic, space group P21/n, a = 8.638(3), b = 14.517(2), c = 9.145(2) Å, and β = 112.71(2)°. The structure, solved by the heavy atom method to an R value of 3.3% for 1924 reflections, consists of a slightly distorted octahedron with the cobalt bound to the five amines and a monodentate phosphate. Solution structural data is taken from 31P NMR measurements. From comparison with other metal phosphate complexes it is concluded that multiple monodentate coordination of a di- or triphosphate closely resembles the coordination of a monophosphate This is based on the similarity of the MO bond angle which is 129.6° in the present example.  相似文献   

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