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1.
One of the major challenges in the postgenomic era is the functional assignment of proteins using sequence- and structure-based predictive methods coupled with experimental validation. We have used these approaches to investigate the structure and function of the Escherichia coli K-12 protein YfaU, annotated as a putative 4-hydroxy-2-ketoheptane-1,7-dioate aldolase (HpcH) in the sequence databases. HpcH is the final enzyme in the degradation pathway of the aromatic compound homoprotocatechuate. We have determined the crystal structure of apo-YfaU and the Mg (2+)-pyruvate product complex. Despite greater sequence and structural similarity to HpcH, genomic context suggests YfaU is instead a 2-keto-3-deoxy sugar aldolase like the homologous 2-dehydro-3-deoxygalactarate aldolase (DDGA). Enzyme kinetic measurements show activity with the probable physiological substrate 2-keto-3-deoxy- l-rhamnonate, supporting the functional assignment, as well as the structurally similar 2-keto-3-deoxy- l-mannonate and 2-keto-3-deoxy- l-lyxonate (see accompanying paper: Rakus, J. F., Fedorov, A. A., Fedorov, E. V., Glasner, M. E., Hubbard, B. K., Delli, J. D., Babbitt, P. C., Almo, S. C., and Gerlt, J. A. (2008) Biochemistry 47, 9944-9954). YfaU has similar activity toward the HpcH substrate 4-hydroxy-2-ketoheptane-1,7-dioate and synthetic substrates 4-hydroxy-2-ketopentanoic acid and 4-hydroxy-2-ketohexanoic acid. This indicates a relaxed substrate specificity that complicates the functional assignment of members of this enzyme superfamily. Crystal structures suggest these enzymes use an Asp-His intersubunit dyad to activate a metal-bound water or hydroxide for proton transfer during catalysis. 相似文献
2.
Smirnov SV Samsonova NN Novikova AE Matrosov NG Rushkevich NY Kodera T Ogawa J Yamanaka H Shimizu S 《FEMS microbiology letters》2007,273(1):70-77
A two-step enzymatic synthesis process of 4-hydroxyisoleucine is suggested. In the first step, the aldol condensation of acetaldehyde and alpha-ketobutyrate catalyzed by specific aldolase results in the formation of 4-hydroxy-3-methyl-2-keto-pentanoate (HMKP). In the second step, amination of HMKP by the branched-chain amino acid aminotransferase leads to synthesis of 4-hydroxyisoleucine. An enzyme possessing HMKP aldolase activity (asHPAL) was purified 2500-fold from a crude extract of Arthrobacter simplex strain AKU 626. Sequencing of the asHPAL structural gene showed that the purified enzyme belongs to the HpcH/HpaI aldolase family. The 4-hydroxyisoleucine was synthesized in vitro from acetaldehyde, alpha-ketobutyrate and l-glutamate using a coupled aldolase/branched-chain amino acid aminotransferase bienzymatic reaction. 相似文献
3.
Seven new diarylheptanoids, i.e., (3S,5S)-3,5-diacetoxy-1,7-bis(4-hydroxy-3-methoxyphenyl)heptane, (3R,5S)-3-acetoxy-5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)heptane, (3R,5S)-3,5-dihydroxy-1-(4-hydroxy-3,5-dimethoxyphenyl)-7-(4-hydroxy-3-methoxyphenyl)heptane, (5S)-5-acetoxy-1,7-bis(4-hydroxy-3-methoxyphenyl)heptan-3-one, 5-hydroxy-1-(3,4-dihydroxy-5-methoxyphenyl)-7-(4-hydroxy-3-methoxyphenyl)heptan-3-one, 5-hydroxy-1-(4-hydroxy-3-methoxyphenyl)-7-(3,4-dihydroxy-5-methoxy-phenyl)heptan-3-one and 1,5-epoxy-3-hydroxy-1-(4-hydroxy-3,5-dimethoxyphenyl)-7-(4-hydroxy-3-methoxyphenyl)heptane were isolated from the rhizomes of Chinese ginger (Zingiber officinale Roscoe), along with 25 known compounds, i.e., 8 diarylheptanoids, 14 gingerol analogs, a diterpene and 2 steroids. Their structures were elucidated by spectroscopic and chemical methods. 相似文献
4.
Isoprenoid precursor biosynthesis occurs through the mevalonate or the methylerythritol phosphate (MEP) pathway, used i.e., by humans and by many human pathogens, respectively. In the MEP pathway, 2-C-methyl-d-erythritol-2,4-cyclo-diphosphate (MEcPP) is converted to (E)-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate (HMBPP) by the iron-sulfur cluster enzyme HMBPP synthase (GcpE). The presented X-ray structure of the GcpE-MEcPP complex from Thermus thermophilus at 1.55 Å resolution provides valuable information about the catalytic mechanism and for rational inhibitor design. MEcPP binding inside the TIM-barrel funnel induces a 60° rotation of the [4Fe-4S] cluster containing domain onto the TIM-barrel entrance. The apical iron of the [4Fe-4S] cluster ligates with the C3 oxygen atom of MEcPP. 相似文献
5.
In the methylerythritol phosphate pathway for isoprenoid biosynthesis, the GcpE/IspG enzyme catalyzes the conversion of 2-C-methyl-d-erythritol 2,4-cyclodiphosphate into (E)-4-hydroxy-3-methylbut-2-enyl diphosphate. This reaction requires a double one-electron transfer involving a [4Fe-4S] cluster. A thylakoid preparation from spinach chloroplasts was capable in the presence of light to act as sole electron donor for the plant GcpE Arabidopsis thaliana in the absence of any pyridine nucleotide. This is in sharp contrast with the bacterial Escherichia coli GcpE, which requires flavodoxin/flavodoxin reductase and NADPH as reducing system and represents the first proof that the electron flow from photosynthesis can directly act in phototrophic organisms as reducer in the 2-C-methyl-d-erythritol 4-phosphate pathway, most probably via ferredoxin, in the absence of any reducing cofactor. In the dark, the plant GcpE catalysis requires in addition of ferredoxin NADP(+)/ferredoxin oxido-reductase and NADPH as electron shuttle. 相似文献
6.
Six xanthones, 1,3,7-trihydroxy-2-(2-hydroxy-3-methyl-3-butenyl)-xanthone (1), 1,7-dihydroxy-2,3-[2'-(1-hydroxy-1-methylethyl)-dihydrofurano]-xanthone (2), 1,3,7-trihydroxy-5-methoxyxanthone (3), 1,7-dihydroxy-5,6-dimethoxyxanthone (4), 4,5-dihydroxy-2,3-dimethoxyxanthone (5), 1,3-dihydroxy-2,4-dimethoxyxanthone (6) and 21 known xanthones were isolated from the leaves and stems of Hypericum chinense. Their structures were established based on spectroscopic studies. 相似文献
7.
From the polar portion of the methanolic extract of the fruit of anise (Pimpinella anisum L.), which has been used as a spice and medicine since antiquity, four aromatic compound glucosides, an alkyl glucoside and a glucide were isolated together with 24 known compounds. The structures of the new compounds were clarified as (E)-3-hydroxyanethole beta-D-glucopyranoside, (E)-1'-(2-hydroxy-5-methoxyphenyl)propane beta-D-glucopyranoside, 3-hydroxyestragole beta-D-glucopyranoside, methyl syringate 4-O-beta-D-glucopyranoside, hexane-1,5-diol 1-O-beta-D-glucopyranoside and 1-deoxy-L-erythritol 3-O-beta-D-glucopyranoside by spectral investigation. 相似文献
8.
From the water-soluble portion of the methanolic extract of caraway (fruit of Carum carvi L.), an aromatic compound, an aromatic compound glucoside and a glucide were isolated together with 16 known compounds. Their structures were clarified as 2-methoxy-2-(4'-hydroxyphenyl)ethanol, junipediol A 2-O-beta-D-glucopyranoside and L-fucitol, respectively. 相似文献
9.
Fructose-bisphosphate aldolase (EC 4.1.2.13) is a key enzyme in glycolysis. We have characterized full-length coding sequences for aldolase genes from the cyst nematodes Heterodera glycines and Globodera rostochiensis, the first for any plant-parasitic nematode. Nucleotide homology is high (83% identity), and the respective sequences encode 40 kDa proteins with 89% amino acid identity. Genomic sequences contain six introns located at identical positions in both genes. Intron 4 in the H. glycines gene is >500 bp. Partial genomic sequences determined for seven other cyst nematode species reveal that the large fourth intron is characteristic of Heterodera but not Globodera aldolase genes. Total aldolase-like specific activity in homogenates from H. glycines was 2-fold lower than in either Caenorhabditis elegans or Panagrellus redivivus (P = 0.001). Activity in H. glycines samples was higher in juvenile stages than in adults (P = 0.003). Heterodera glycines aldolase has Km = 41 µM and is inhibited by treatment with carboxypeptidase A or sodium borohydride. 相似文献
10.
Ingo Rekittke Elena Olkhova Jochen Wiesner Ulrike Demmer Eberhard Warkentin Hassan Jomaa Ulrich Ermler 《FEBS letters》2013
Terpenoid precursor biosynthesis occurs in human and many pathogenic organisms via the mevalonate and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, respectively. We determined the X-ray structure of the Fe/S containing (E)-4-hydroxy-3-methyl-but-2-enyl-diphosphate reductase (LytB) of the pathogenic protozoa Plasmodium falciparum which catalyzes the terminal step of the MEP pathway. The cloverleaf fold and the active site of P. falciparum LytB corresponds to those of the Aquifex aeolicus and Escherichia coli enzymes. Its distinct electron donor [2Fe–2S] ferredoxin was modeled to its binding site by docking calculations. The presented structural data provide a platform for a rational search of anti-malarian drugs. 相似文献
11.
Feeding tobacco BY-2 cells with [2-13C,4-2H]deoxyxylulose revealed from the 13C labeling that the plastid isoprenoids, synthesized via the MEP pathway, are essentially derived from the labeled precursor. The ca. 15% 2H retention observed in all isoprene units corresponds to the isopentenyl diphosphate (IPP)/dimethylallyl diphosphate (DMAPP) ratio (85:15) directly produced by the hydroxymethylbutenyl diphosphate reductase, the last enzyme of the MEP pathway. 2H retention characterizes the isoprene units derived from the DMAPP branch, whereas 2H loss represents the signature of the IPP branch. Taking into account the enantioselectivity of the reactions catalyzed by the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase, the IPP isomerase and the trans-prenyl transferase, a single biogenetic scheme allows to interpret all labeling patterns observed in bacteria or plants upon incubation with 2H labeled deoxyxylulose. 相似文献
12.
Mathieu Coincon Weijun Wang Jurgen Sygusch Stephen Y. K. Seah 《The Journal of biological chemistry》2012,287(43):36208-36221
Crystal structures of divalent metal-dependent pyruvate aldolase, HpaI, in complex with substrate and cleavage products were determined to 1.8–2.0 Å resolution. The enzyme·substrate complex with 4-hydroxy-2-ketoheptane-1,7-dioate indicates that water molecule W2 bound to the divalent metal ion initiates C3–C4 bond cleavage. The binding mode of the aldehyde donor delineated a solvent-filled capacious binding locus lined with predominantly hydrophobic residues. The absence of direct interactions with the aldehyde aliphatic carbons accounts for the broad specificity and lack of stereospecific control by the enzyme. Enzymatic complex structures formed with keto acceptors, pyruvate, and 2-ketobutyrate revealed bidentate interaction with the divalent metal ion by C1-carboxyl and C2-carbonyl oxygens and water molecule W4 that is within close contact of the C3 carbon. Arg70 assumes a multivalent role through its guanidinium moiety interacting with all active site enzymatic species: C2 oxygen in substrate, pyruvate, and ketobutyrate; substrate C4 hydroxyl; aldehyde C1 oxygen; and W4. The multiple interactions made by Arg70 stabilize the negatively charged C4 oxygen following proton abstraction, the aldehyde alignment in aldol condensation, and the pyruvate enolate upon aldol cleavage as well as support proton exchange at C3. This role is corroborated by loss of aldol cleavage ability and pyruvate C3 proton exchange activity and by a 730-fold increase in the dissociation constant toward the pyruvate enolate analog oxalate in the R70A mutant. Based on the crystal structures, a mechanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis that facilitates reversible aldol cleavage. The same reaction mechanism promotes decarboxylation of oxaloacetate. 相似文献
13.
Clostridium perfringens (a versatile pathogenic bacterium) secretes enterotoxins (the deltatoxin, virulent factor) and causes food borne gastroenteritis and gasgangrene. The organism was isolated and characterized from improperly cooked meat and poultry samples. The isolated organism showed multiple drug resistance indicating that the treatment is challenging. Hence, there is need for improved therapeutic agents. The rational design of improved therapeutics requires the crystal structure for the toxin. However, the structure for the toxin is not yet available in its native form. Thus, we modeled the toxin structure using α- hemolysin of Staphylococcus aureus (PDB: 3M4D chain A) as template. The docking of the toxin with the herbal extract curcumin (1,7-bis(4-hydroxy-3- methoxyphenyl)hepta-1,6-diene-3,5-dione) showed a binding energy of -8.6 Kcal/mol, in comparison to the known antibiotic Linezolid with binding energy of -6.1 Kcal/mol. This data finds application in the design and development of novel compounds against the deltatoxin from Clostridium perfringens. 相似文献
14.
Nguemeving JR Azebaze AG Kuete V Eric Carly NN Beng VP Meyer M Blond A Bodo B Nkengfack AE 《Phytochemistry》2006,67(13):1341-1346
A phytochemical investigation of the constituents of the roots of Vismia laurentii has resulted in the isolation of two xanthone derivatives named laurentixanthone A (1) (6-hydroxy-3,3-dimethyl-11-(3-methylbut-2-enyl)pyrano[2,3-c]xanthen-7(3H)-one) and laurentixanthone B (2) (1-hydroxy-5,6,7,8-tetramethoxyxanthone), along with 11 known compounds: 1,7-dihydroxyxanthone, vismiaquinone, vismiaquinone B, bivismiaquinone, 3-geranyloxy-6-methyl-1,8-dihydroxyanthraquinone, O(1)-demethyl-3',4'-deoxypsorospermin-3',4'-diol, 6-deoxyisojacareubin, 1,8-dihydroxy-6-methoxy-3-methylanthraquinone, kaempferol, friedelin and stigmasterol. The structures of compounds were established by means of spectroscopic methods. Furthermore, the compounds were screened for antimicrobial activities in vitro. 相似文献
15.
Lannang AM Komguem J Ngninzeko FN Tangmouo JG Lontsi D Ajaz A Choudhary MI Ranjit R Devkota KP Sondengam BL 《Phytochemistry》2005,66(19):2351-2355
Two xanthones, bangangxanthone A (1) [1,5,8-trihydroxy-6'-methyl-6'-(4-methylpent-3-enyl)- pyrano[2',3':3,4]xanthone] and B (2) [1,4,8-trihydroxy-2-prenylxanthone], along with two known xanthones, 1,5-dihydroxyxanthone, 2-hydroxy-1,7-dimethoxyxanthone and the pentacyclic triterpenoids, friedelin, oleanolic acid and lupeol were isolated from the chloroform extract of the stem bark of Garcinia polyantha. The structures of these compounds were assigned by spectroscopic analysis. Compounds 1-4 showed antioxidant DPPH radical scavenging activities. 相似文献
16.
A.A. Leslie Gunatilaka A.M.Y. Jasmin De Silva Subramaniam Sotheeswaran 《Phytochemistry》1982,21(7):1751-1753
2-Hydroxyxanthone, 1,7-dihydroxyxanthone, 1-hydroxy-7-methoxyxanthone, 6,7-dimethoxy-1-hydroxyxanthone and a new natural product, 2-hydroxy-3-methoxyxanthone, have been isolated and characterized from the phenolic fraction of the chloroform extract of the timber of Hypericum mysorense. The presence of simple xanthones in this genus supports the classification of Hypericum in the subfamily Hypericoideae in Guttiferae. 相似文献
17.
A total of eleven alkali-released, aromatic compounds were identified by HPLC, MS and NMR analyses in cell wall extracts from Arabidopsis thaliana roots. Nine of them together constituted the three complete series of 4-hydroxy-, 4-hydroxy-3-methoxy, and 4-hydroxy-3,5-dimethoxy-substituted benzaldehydes, benzoic acids and cinnamic acids. The other two were indolic metabolites: indole-3-carboxylic acid and indole-3-carbaldehyde. Qualitatively similar, but quantitatively distinct profiles were obtained using cell-wall extracts from A. thaliana leaves. Several of these compounds, particularly indole-3-carboxylic acid, 4-hydroxybenzoic acid and all four aldehydes, increased considerably in concentration upon infection of roots with Pythium sylvaticum, as did at least some of them upon infection of leaves with Pseudomonas syringae pv tomato. Comparison of these results with analogous data on a variety of different plant species suggests a remarkable structural uniformity among the majority of constitutive as well as infection-induced, aromatic cell wall-bound compounds throughout the entire plant kingdom-in sharp contrast to the highly species-specific, chemically highly divers bouquets of soluble aromatic metabolites. 相似文献
18.
Cinnamate 4-hydroxylase (C4H), a monooxygenase in the plant phenylpropanoid pathway, was assayed for its ability to hydroxylate 29 substrate analogues. Nine of the tested analogues with various aromatic side chains, including 3-coumaric acid, were metabolized by C4H. Seven products from these reactive analogues were characterized using LC/MS, 1H NMR and 13C NMR spectroscopic analysis. For example, caffeic acid was the product of 3-coumaric acid. The products 4-hydroxy-2-chlorocinnamic acid and 4-hydroxy-2-ethoxycinnamic acid are novel compounds that have not been previously reported. The kinetic parameters of C4H towards these analogues were determined. 相似文献
19.
The GcpE enzyme converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (MEcPP) into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) in the penultimate step of the DOXP pathway for isoprene biosynthesis. Purification of the enzyme under exclusion of air leads to a preparation that contains solely [4Fe-4S] clusters. Kinetic studies showed that in the presence of the artificial reductant dithionite and MEcPP a new transient iron-sulfur-based signal is detected in electron paramagnetic resonance (EPR) spectroscopy. Similarity of this EPR signal to that detected in ferredoxin:thioredoxin reductase indicates that during the reaction an intermediate is directly bound to the active-site cluster. 相似文献
20.
Lee SJ Ko JH Kang HY Lee Y 《Biochemical and biophysical research communications》2006,346(3):1009-1015
MhpE (4-hydroxy-2-ketovalerate aldolase) and MhpF [acetaldehyde dehydrogenase (acylating)] are responsible for the last two reactions in the 3-(3-hydroxyphenyl)propionate (3-HPP) catabolic pathway in Escherichia coli, which is homologous to the meta-cleavage pathway in Pseudomonas species. Here, we report that the MhpE aldolase is associated with the MhpF dehydrogenase and that MhpF is indispensable for the folding of MhpE. Moreover, our results suggest that the mhpF and mhpE genes are translationally coupled through a reinitiation mechanism. This reinitiation mechanism may function in ensuring that the expression of mhpE occurs only when MhpF is available for the formation of a complex. 相似文献