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1.
The enzymes of the shikimate pathway represent potential molecular targets for the development of non-toxic antimicrobial agents and anti-parasite drugs. One of the most promising of these enzymes is shikimate kinase (EC 2.7.1.71), which is responsible for the fifth step in the shikimate pathway. This enzyme phosphorylates shikimic acid to yield shikimate-3-phosphate, using ATP as a substrate. In this work, the conformational dynamics of the shikimate kinase from Mycobacterium tuberculosis was investigated in its apostate in solution. For this study, the enzyme was subjected to a gradient of temperatures from 15°C to 45°C in the presence or absence of deuterium oxide, and the amide H/D exchange was monitored using ESI-mass spectrometry. We observed: i) the phosphate binding domain in the apo-enzyme is fairly rigid and largely protected from solvent access, even at relatively high temperatures; ii) the shikimate binding domain is highly flexible, as indicated by the tendency of the apo-enzyme to exhibit large conformational changes to permit LID closure after the shikimate binding; iii) the nucleotide binding domain is initially conformationally rigid, which seems to favour the initial orientation of ADP/ATP, but becomes highly flexible at temperatures above 30°C, which may permit domain rotation; iv) part of the LID domain, including the phosphate binding site, is partially rigid, while another part is highly flexible and accessible to the solvent.  相似文献   

2.
L-beta-(2,3-epoxycyclohexanono-4)-alanine, an active fragment of the antibiotic tetaine, identical to the antimetabolite anticapsin, is a powerful inhibitor of partially purified glucosamine-6-phosphate synthetase (2-amino-2-deoxy-D-glucose-6-phosphate ketol isomerase, aminotransferring, EC 5.3.1.19) from pathogenic fungus Candida albicans. Anticapsin was demonstrated to be a competitive inhibitor of this enzyme with respect to L-glutamine and uncompetitive with respect to D-fructose-6-phosphate. Incubation of anticapsin with glucosamine-6-phosphate synthetase in the absence of glutamine led to the formation of an inactive enzyme, irreversibly modified. The inactivation obeyed saturation kinetics; the determined Kinact was 9.5 X 10(-6) M. Addition of glutamine protected the enzyme against inactivation by anticapsin. Reaction of anticapsin with the enzyme exhibited characteristics of affinity labelling of the glutamine binding site. Probably the inactivation proceeds via an alkylation of cysteine residue at the glutamine binding site.  相似文献   

3.
Adenosine kinase (AK) is an enzyme responsible for converting endogenous adenosine (ADO) to adenosine monophosphate (AMP) in an adenosine triphosphate- (ATP-) dependent manner. The structure of AK consists of two domains, the first a large alpha/beta Rossmann-like nucleotide binding domain that forms the ATP binding site, and a smaller mixed alpha/beta domain, which, in combination with the larger domain, forms the ADO binding site and the site of phosphoryl transfer. AK inhibitors have been under investigation as antinociceptive, antiinflammatory, and anticonvulsant as well as antiinfective agents. In this work, we report the structures of AK in complex with two classes of inhibitors: the first, ADO-like, and the second, a novel alkynylpyrimidine series. The two classes of structures, which contain structurally similar substituents, reveal distinct binding modes in which the AK structure accommodates the inhibitor classes by a 30 degrees rotation of the small domain relative to the large domain. This change in binding mode stabilizes an open and a closed intermediate structural state and provide structural insight into the transition required for catalysis. This results in a significant rearrangement of both the protein active site and the orientation of the alkynylpyrimidine ligand when compared to the observed orientation of nucleosidic inhibitors or substrates.  相似文献   

4.
3-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) is the phosphorylated precursor of KDO, an essential sugar of the lipopolysaccharide of Gram negative bacteria. KDO8P is produced by a specific synthase (KDO8PS) by condensing arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP), with release of inorganic phosphate. As KDO8PS is present in bacteria and plants, but not in mammalian cells, and mutations that inactivate KDO8PS also block cell replication, KDO8PS is a promising target for the design of new antimicrobials that act by blocking lipopolysaccharide biosynthesis. Previous studies have shown that a compound mimicking an intermediate of the condensation reaction is a good ligand and a powerful inhibitor. Here we report on the crystallographic investigation of the binding to KDO8PS of new derivatives of this original inhibitor. The structures of the enzyme in complex with these compounds, and also with the PEP analogs, 2-phosphoglyceric acid (2-PGA) and Z-methyl-PEP, point to future strategies for the design of novel inhibitors of KDO8PS.  相似文献   

5.
Michaelis-Menten kinetics are observed in studies of highly purified bovine adrenal glucose-6-phosphate dehydrogenase at pH 8.0 in 0.1 M bicine. The Km for NADP+ is 3.8 μM and for glucose-6-phosphate, 61 μM. At pH 6.9, Km for NADP+ increases to 6.5 μM. The enzyme is inhibited by NADPH both at pH 6.8 and at 8.0 with a Kip of 2.36 μM at pH 8.0. Inhibition is competitive with respect to both substrates implying that addition of substrates is random ordered. The data are also interpreted in terms of “reducing charge”, the mole fraction of coenzyme in the reduced form. This appears to be the major mechanism for regulation of the pentose shunt. D-glucose, oxidized by the enzyme at a very slow rate, is also a competitive inhibitor for the natural substrate with a Ki of 0.29 M. Phosphate is a competitive inhibitor for glucose-6-phosphate oxidation but both phosphate and sulfate accelerate glucose oxidation suggesting a common binding site for the two anions and the phosphate of the natural substrate. While binding of ACTH to our enzyme preparations has been observed, we have not been able, in spite of repeated attempts, to demonstrate augmentation of the activity of the enzyme by the addition of ACTH.  相似文献   

6.
Carbon-13 NMR spectroscopy has been used to further document the interaction, at low and high temperatures, of N-acetylglucosamine and its short polymrs with hen egg-white lysozyme. The results have been compared with the corresponding X-ray crystallographic data. Two domains, the active site and the hydrophobic box, have been found by NMR to undergo conformational rearrangement while X-ray crystallography only detected changes located in the active site. The extent of the modifications induced by inhibitor binding was proportional to the inhibitor size. The two techniques concurred to show that even in the presence of monosaccharide (N-acetylglucosamine), more than one subsite of the enzyme was occupied at high temperature, the binding at the C-site being the best defined. The thermal transition of lysozyme still occurred in solution when inhibitors were bound. However, in the solid state, crystallographic data showed that the transition was hindered.  相似文献   

7.
Compactin and related compounds are highly effective inhibitors of HMG-CoA (Hydroxymethylglutaryl-CoA) reductase. These compounds consist of two major structural components: (1) a component resembling hydroxymethyl glutarate and (2) a hydrophobic region. It is concluded that the hydroxymethyl glutarate moiety of these inhibitors interacts with the hydroxymethyl glutarate-binding domain of the active site. It is postulated that the hydrophobic moiety of these inhibitors interacts with a hydrophobic area of the enzyme that is not part of the active site. Strong binding is the consequence of this two-point interation. Peptidyl tri-fluoroketones are effective inhibitors of chymotrypsin and elastase and are probably transition-state analogs. These inhibitors form an adduct with the activesite serine as determined by X-ray crystallography and nuclear magnetic resonance spectroscopy. Maximum inhibition is obtained if inhibitors interact with the S and S′ binding domains. The structure of ovomucoids, protein inhibitors of serine proteases, serves as a good model for the determination of the amino acid sequence to be used in that portion of the inhibitor which interacts with the S′ domain. The best amino-acid sequence to be used in that area of the inhibitor which interacts with the S-binding domain corresponds to the amino-acid sequence found in substrates with the highest V/K.  相似文献   

8.
STRUCTURE AND FUNCTION OF URIDINE DIPHOSPHATE GLUCURONOSYLTRANSFERASES   总被引:7,自引:0,他引:7  
1. The uridine diphosphate (UDP)-glucuronosyltransferases (UGT) are a family of enzymes that catalyse the covalent addition of glucuronic acid to a wide range of lipophilic chemicals. They play a major role in the detoxification of many exogenous and endogenous compounds by generating products that are more polar and, thus, more readily excreted in bile or urine. 2. Inherited deficiencies in UGT forms are deleterious, as exemplified by the debilitating effects of hyperbilirubinaemia and neurotoxicity in subjects with mutations in the enzyme that converts bilirubin to its more pola. glucuronide. 3. The UGT protein can be conceptually divided into two domains with the amino-terminal half of the protein demonstrating greater sequence divergence between isoforms. This region apparently determines aglycone specificity. The aglycone binding site is presumed to be a ‘loose’ fit, as many structurally diverse substrates can be bound by the same UGT isoform. The carboxyl-terminal half, which is more conserved in sequence between different isoforms, is believed to contain a binding site for the cosubstrate UDP glucuronic acid (UDPGA). 4. Uridine diphosphat. glucuronosyltransfera.se is localized to the endoplasmic reticulum (ER) and spans the membrane with a type I topology. The putative transmembrane domain is located near the carboxyl terminus of the protein such that only a small portion of the protein resides in the cytosol. This cytosolic tail is believed to contain an ER-targeting signal. The major portion of the protein is located in the ER lumen, including the proposed substrate-binding domains and the catalytic site. 5. The microsomal membrane impedes the access of UDPGA to the active site, resulting in latency of UGT activity in intact ER-derived microsomes. Active transport of UDPGA is believed to occur in hepatocytes, but the transport system has not been fully characterized. Uridine diphosphate glucuronosyltransfer-ase activity is also highly lipid dependent and the enzyme may contain regions of membrane association in addition to the transmembrane domain.  相似文献   

9.
Guanylyl cyclases catalyze the formation of cGMP from GTP. This family of enzymes includes soluble (sGC) and particulate guanylyl cyclases (pGC). The sGC are heterodimers containing one active catalytic site and one inactive pseudo-site. They are activated by nitric oxide. The pGC are homodimers whose activity is notably regulated by peptide binding to the extracellular domain and by ATP binding to the intracellular kinase homology domain (KHD). The catalytic mechanism of the pGC is still not well understood. Homology modeling of the structure of the homodimeric guanylyl cyclase domain, based on the crystal structure of adenylyl cyclase, suggests the existence of two functional sites for the substrate GTP. We used a purified and fully active recombinant catalytic domain from mammalian pGC, to document its enzyme kinetics properties in the absence of the KHD. The enzyme presents positive cooperativity with the substrate Mg-GTP. However, a heterodimeric catalytic domain mutant (GC-HET) containing only one active catalytic site is non-cooperative and is more similar to sGC. Structure-activity studies of purine nucleoside analogs indicate that 2'd3'GMP is the most potent inhibitor of pGC tested. It displays mixed non-competitive inhibition properties that are potentiated by the second catalytic product inorganic pyrophosphate (PPi). It appears to be equivalent to purinergic site (P-site) inhibitors characterized on particulate adenylyl cyclase. Inhibition of pGC by 2'd3'GMP in the presence of PPi is accompanied by a loss of cooperative enzyme kinetics. These results are best explained by an allosteric dimer model with positive cooperativity for both the substrate and inhibitors.  相似文献   

10.
Monophosphate nucleotidases are enzymes that dephosphorylate nucleotides to their corresponding nucleosides. They play potentially important roles in controlling the activation of nucleotide-based drugs targeted against viral infections or cancer cells. The human mitochondrial deoxyribonucleotidase (dNT-2) dephosphorylates thymidine and deoxyuridine monophosphates. We describe the high resolution structures of the dNT-2 enzyme in complex with two potent nucleoside phosphonate inhibitors, (S)-1-[2'-deoxy-3',5'-O-(1-phosphono) benzylidene-beta-d-threo-pentofuranosyl]thymine (DPB-T) at 1.6-A resolution and (+/-)-1-trans-(2-phosphonomethoxycyclopentyl)uracil (PMcP-U) at 1.4-A resolution. The mixed competitive inhibitor DPB-T and the competitive inhibitor PMcP-U both bind in the active site of dNT-2 but in distinctly different binding modes, explaining their different kinetics of inhibition. The pyrimidine part of the inhibitors binds with very similar hydrogen bond interactions to the protein but with their phosphonate moieties in different binding sites compared with each other and to the previously determined position of phosphate bound to dNT-2. Together, these phosphate/phosphonate binding sites describe what might constitute a functionally relevant phosphate entrance tunnel to the active site. The structures of the inhibitors in complex with dNT-2, being the first such complexes of any nucleotidase, might provide important information for the design of more specific inhibitors to control the activation of nucleotide-based drugs.  相似文献   

11.
Crystal structures of seven phosphodiesterase families (PDE1-5, 7, 9) show a conserved core catalytic domain that contains about 300 amino acids and fourteen alpha-helices. The catalytic domains of the PDE families 1-4, 7, and 9 have a uniform conformation. However, the H-loop at the active site of PDE5 shows four different conformations upon binding of inhibitors, probably implying a special mechanism for recognition of substrates and inhibitors by PDE5. The active site of all PDE families contains two divalent metal ions: zinc and probably magnesium. The PDE4-AMP and PDE5-GMP structures reveal the conserved interactions of the phosphate groups of the products AMP and GMP, and thus suggest a universal mechanism of nucleophilic attack for all PDE families. The substrate specificity has not been well understood. This review will comment on the early proposal, "glutamine switch", on basis of the recent biochemical and structural information. The PDE-inhibitor structures have identified a common subpocket for non-selective binding of all inhibitors and potential elements for recognition of family-selective inhibitors. The kinetic analysis on the mutations of PDE7 to PDE4 suggests that the multiple elements must work together to define inhibitor selectivity.  相似文献   

12.
Glyphosate tolerance can be conferred by decreasing the herbicide’s ability to inhibit the enzyme 5-enol pyruvylshikimate-3-phosphate synthase, which is essential for the biosynthesis of aromatic amino acids in all plants, fungi, and bacteria. Glyphosate tolerance is based upon the expression of the double mutant 5-enol pyruvylshikimate-3-phosphate synthase (2mEPSPS) protein. The 2mEPSPS protein, with a lower binding affinity for glyphosate, is highly resistant to the inhibition by glyphosate and thus allows sufficient enzyme activity for the plants to grow in the presence of herbicides that contain glyphosate. Based on both a review of published literature and experimental studies, the potential safety concerns related to the transgenic 2mEPSPS protein were assessed. The safety evaluation supports that the expressed protein is innocuous. The 2mEPSPS enzyme does not possess any of the properties associated with known toxins or allergens, including a lack of amino acid sequence similarity to known toxins and allergens, a rapid degradation in simulated gastric and intestinal fluids, and no adverse effects in mice after intravenous or oral administration (at 10 or 2000 mg/kg body weight, respectively). In conclusion, there is a reasonable certainty of no harm resulting from the inclusion of the 2mEPSPS protein in human food or in animal feed.  相似文献   

13.
Quantitative structure-activity relationships (QSAR) of a series of 6-anilinouracil derivatives were developed for their inhibitory activity against the wild-type DNA polymerase III (pol III) and a mutant enzyme, pol III/azp-12, derived from Bacillus subtilis. Interaction between inhibitors and both enzymes appears to result solely from hydrophobic binding. Comparison of the substituent contributions indicates increased hydrophobic character and a minor change of shape of the inhibitor binding site of the mutant enzyme. Because the two enzymes have identical Km values for substrates, the inhibitor binding site is thought to be distinct from the enzyme active site.  相似文献   

14.
The urokinase-type plasminogen activator (uPA) protein is a multifunctional protein involved in a myriad of biological activities including extracellular matrix degradation and cell invasion. Active uPA is a 411 amino acid protein consisting of 3 domains, each of which confers a particular biological function to the overall protein. The amino terminal domain or growth factor domain (GFD), comprised of amino acid residues 1 – 48, is involved in uPA interaction with its cell surface receptor, urokinase-type plasminogen activator receptor (UPAR). The interaction of uPA with UPAR promotes, in part, cell adhesion, migration and invasion. A second domain is the kringle domain, comprising amino acid residues 49 – 135. Initially thought to bind heparin, the kringle domain has more recently been shown to possess antiangiogenic activity. A third domain comprising amino acid residues 159 – 411, the serine protease domain, is involved in the proteolytic activation of plasminogen to plasmin. The production of plasmin by uPA begins a cascade of events manifested by extracellular matrix degradation. The recent patent literature describes small molecule compounds, which inhibit the interaction of uPA with UPAR, inhibit the proteolytic activity of the uPA serine protease domain and inhibit the interaction of uPA with its natural inhibitor, plasminogen activator inhibitor-1 (PAI-1). Small peptides encompassing residues 19 – 31 of the GFD have been developed which exhibit potent inhibition of the uPA–UPAR interaction and show efficacy in tumour-bearing animal models. Small molecules have been disclosed by Corvas, which are reported to be inhibitors of PAI-1. Finally, two approaches toward the development of inhibitors of the uPA serine protease domain have been described in the recent patent literature. The first approach describes non-covalent peptidederived inhibitors discovered by phage display techniques, which bind in the substrate-binding groove of the uPA active site. An alternative approach describes non-covalent small molecule inhibitors, which bind in the enzyme active site in a slightly different binding mode than the peptide-derived inhibitors. These small molecule non-peptide analogues inhibit the uPA proteolytic activity quite effectively and are reported to possess excellent enzyme selectivity and highly improved oral activity. The clinical utility of small molecule uPA enzyme inhibitor analogues awaits the results of a preliminary clinical evaluation of compounds described by Wilex.  相似文献   

15.
Aldose reductase (AR) has been implicated in the etiology of the secondary complications of diabetes. This enzyme catalyzes the reduction of glucose to sorbitol using nicotinamide adenine dinucleotide phosphate as an essential cofactor. AR has been localized at the sites of tissue damage, and inhibitors of this enzyme prevent the development of neuropathy, nephropathy, retinopathy, and cataract formation in animal models of diabetes. The crystal structure of AR complexed with zopolrestat, a potent inhibitor of AR, has been described.(1) We have generated a model of the AR-inhibitor complex based on the reported Calpha coordinates of the protein and results of a structure-activity relationship study using four structurally distinct classes of inhibitors, recombinant human AR, and four single-site-directed mutants of this enzyme. The effects of the site-directed mutations on residues within the active site of the enzyme were evaluated by average interaction energy calculations and by calculations of carbon atom surface area changes. These values correlated well with the IC(50) values for zopolrestat with the wild-type and mutant enzymes, validating the model. On the basis of the zopolrestat-binding model, we have proposed binding models for 10 other AR inhibitors. Our models have enabled us to gain a qualitative understanding of the binding domains of the enzyme and how different inhibitors impact the size and shape of the binding site.  相似文献   

16.
Integrins contain either one or two von Willebrand factor A-like domains, which are primary ligand and cation binding regions in the molecules. Here we examine the first structure of an A domain of a beta subunit, in alphanubeta3 and compare it to known A domain structures of alpha subunits. Ligand binding to immobilized alphanubeta3 domain is stimulated by Ca2+ rather than inhibited by it. Biochemical, cell biological and structural evidence suggests that the A domain is a major site of ligand interaction in alphanubeta3. The Arg-Gly-Asp based inhibitor cilengitide (EMD 121974) inhibites ligand interaction with transmembrane-truncated alphanubeta3 in the presence of either Ca2+ or Mn2+ ions, and does so with similar kinetics. The alphanubeta3 structure reveals that both the alphaA and betaA domains share common structural cores. But, in contrast to alphaA, the betaA domain has three cation binding sites, that are involved either directly or indirectly in ligand binding. Structural alignment of alphaA and betaA domains reveals additional loops unique only to the betaA domain and much evidence support that that these loops are important for ligand binding specificity and for the interaction between alpha and beta subunits. Since the position of these loops are evolutionary conserved but their primary sequence varies between the various betaA domains, they represents potential targets for dissecting functional diversity among integrins.  相似文献   

17.
Thrombomodulin (TM) is a type 1 membrane bound glycoprotein that has a C-type lectin domain at its Nterminus, 6 copies of the epidermal growth factor-like (EGF) motif and serine/threonine rich domain carrying a glycosoaminoglycan external to the membrane. TM binds thrombin changing thrombin's substrate specificity from procoagulant and pro-inflammatory to anti-coagulant and anti-inflammatory because of the activation of protein C (PC) and thrombin-activatable fibrinolysis inhibitor (TAFI). Thrombin's anion binding site 1 binds to TM's EGF domains 5 and 6. EGF4 is required for PC activation and EGF3 and 4 for TAFI activation in addition to EGF56. The X-ray structure of thrombin bound to TM has been solved and shows few major alterations in the active site of thrombin. The lectin domain can bind high mobility group box protein 1 (HMGB1) and a sugar, Lewisy. TM's lectin domain behaves as an antagonist to HMGB1 endowing it with intrinsic anti-inflammatory activity. Treatment of dendritic cells with TM converts them from immunogenic to tolerogenic. TM is necessary for maintenance of pregnancy as well as prevention of coagulation throughout life. Soluble TM has been developed as an anticoagulant possessing favorable pharmacokinetics that has been approved for treatment of disseminated intravascular coagulation in Japan.  相似文献   

18.
X-ray studies of phosphoglycerate kinase (EC 2.7.2.3, PGK) have shown that the enzyme's single polypeptide chain is organized into two separate domains that correspond to the N- and C-terminal halves of the chain. Substrate binding studies and the incorporation of the complete amino acid sequence of horse-muscle PGK into its X-ray model suggest that the C-domain is an ADP/ATP binding unit and that the N-terminal domain contains the phosphoglycerate binding site and the active site located in a prominent cluster of positively charged residues. Because the distance between these two sites is 12–15 Å, a hinge-bending of 10°–20° has been proposed to bring the two sites together for catalysis. Independent solution studies of yeast PGK have shown that the radius of gyration decreases significantly on the formation of the ternary complex. This change has been interpreted in terms of a 9°–12° rotation about a hinge in the interdomain region that brings the two domains together. We suggest here a structural basis for the proposed hinge-bending that involves the rotation of the two helices that form the domain interface about their contact normal carrying their respective domains with them.  相似文献   

19.
A study has been made of the binding of the active site-directed inhibitor [14C]phenethylhydrazine to native rat liver monoamine oxidase (MAO), its multiple forms and sub-units. Inhibition of enzyme activity was time-dependent and was accompanied by irreversible binding of the drug to the enzyme protein. When fully inhibited, the ratio of moles inhibitor bound per 150.000 g of enzyme was in all cases approximately 1:1. It is concluded that each molecule of native enzyme and its multiple forms consists of two sub-units, only one of which possesses an active site. Other evidence presented suggests that the preparation contains two types of MAO.  相似文献   

20.
Azidothiorphan and its [14C]-labeled analogue have been developed as photoaffinity ligands for the active site of the neutral endopeptidase 24.11. In in vitro assays azidothiorphan inhibits the endopeptidase activity with a Ki of 0.75 nM. After ultraviolet irradiation the inhibitor binds irreversibly to the enzyme, and many factors suggest that the photolabeling occurs at the active site. The binding is accompanied by a loss of enzymatic activity, and the inclusion of the competitive inhibitor thiorphan protects the endopeptidase from this inactivation. In addition the binding of another competitive inhibitor [3H]N-[(R,S)-3-hydroxyaminocarbonyl-2-benzyl-1-oxopropyl]-glycine to the active site of endopeptidase-24.11 is inhibited after irradiation with azidothiorphan. Experiments with [14C]-azidothiorphan have shown that very little nonspecific binding of inhibitor to enzyme occurs and the the labeled probe remains bound under denaturing conditions. Azidothiorphan has also been found to produce a long-lasting naloxone-reversible analgesia after intracerebroventricular administration. The results show that azidothiorphan should prove useful both for structural studies and for investigations on the synthesis and turnover of the neutral endopeptidase-24.11.  相似文献   

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