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At least 253 records · Page 14Linked to original sources
PubMed2006

Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.

RluA is a dual-specificity enzyme responsible for pseudouridylating 23S rRNA and several tRNAs. The 2.05 A resolution structure of RluA bound to a substrate RNA comprising the anticodon stem loop of tRNA(Phe) reveals that enzyme binding induces a dramatic reorganization of the RNA. Instead of adopting its canonical U turn conformation, the anticodon loop folds into a new structure with a reverse-Hoogsteen base pair and three flipped-out nucleotides. Sequence conservation, the cocrystal structure, and the results of structure-guided mutagenesis suggest that RluA recognizes its substrates indirectly by probing RNA loops for their ability to adopt the reorganized fold. The planar, cationic side chain of an arginine intercalates between the reverse-Hoogsteen base pair and the bottom pair of the anticodon stem, flipping the nucleotide to be modified into the active site of RluA. Sequence and structural comparisons suggest that pseudouridine synthases of the RluA, RsuA, and TruA families employ an equivalent arginine for base flipping.

Amino Acid Sequence↗
PubMed2006

Biosynthetic diversity in plant triterpene cyclization.

Plants produce a wealth of terpenoids, many of which have been the tools of healers and chiefs for millennia. Recent research has led to the identification and characterization of many genes that are responsible for the biosynthesis of triterpenoids. Cyclases that generate sterol precursors can be recognized with some confidence on the basis of sequence; several catalytically important residues are now known, and the product profiles of sterol-generating cyclases typically reflect their phylogenetic position. By contrast, the phylogenetic relationships of cyclases that generate nonsteroidal triterpene alcohols do not consistently reflect their catalytic properties and might indicate recent and rapid catalytic evolution.

Cyclization↗
PubMed2005

Cloning and characterization of a cDNA encoding beta-amyrin synthase from petroleum plant Euphorbia tirucalli L.

Euphorbia tirucalli L., known as the petroleum plant, produces a large amount of triterpenes, such as beta-amyrin. Degenerate RT-PCR based on the sequences conserved among known beta-amyrin synthases led to cloning of a putative triterpene synthase cDNA, EtAS, from leaves of E. tirucalli. The deduced amino acid sequence of the EtAS cDNA showed the highest identity of 82% to the Panax ginseng beta-amyrin synthase. Heterologous expression of the EtAS ORF in the methylotrophic yeast, Pichia pastoris, resulted in production of beta-amyrin, revealing that the EtAS cDNA codes for a beta-amyrin synthase. This is the first report of a gene involved in the triterpene synthetic pathway from Euphorbiaceae plants.

Amino Acid Sequence↗
PubMed2004

S-adenosylmethionine: nothing goes to waste.

S-adenosylmethionine (SAM or AdoMet) is a biological sulfonium compound known as the major biological methyl donor in reactions catalyzed by methyltransferases. SAM is also used as a source of methylene groups (in the synthesis of cyclopropyl fatty acids), amino groups (in the synthesis of 7,8-diaminoperlagonic acid, a precursor of biotin), ribosyl groups (in the synthesis of epoxyqueuosine, a modified nucleoside in tRNAs) and aminopropyl groups (in the synthesis of ethylene and polyamines). Even though the mechanism of most of these reactions has not been extensively characterized, it is likely that the chemistry at work is mainly driven by the electrophilic character of the carbon centers that are adjacent to the positively charged sulfur atom of SAM. In addition, SAM, upon one-electron reduction, is a source of 5'-deoxyadenosyl radicals, which initiate many metabolic reactions and biosynthetic pathways by hydrogen-atom abstraction. SAM presents a unique situation in which all constituent parts have a chemical use.

4-Butyrolactone↗
PubMed2005

Lord of the rings--the mechanism for oxidosqualene:lanosterol cyclase becomes crystal clear.

The enzyme oxidosqualene:lanosterol cyclase (OSC) represents a novel target for the treatment of hypercholesterolemia. OSC catalyzes the cyclization of the linear 2,3-monoepoxysqualene to lanosterol, the initial four-ringed sterol intermediate in the cholesterol biosynthetic pathway. OSC also catalyzes the formation of 24(S),25-epoxycholesterol, a ligand activator of the liver X receptor. Inhibition of OSC reduces cholesterol biosynthesis and selectively enhances 24(S),25-epoxycholesterol synthesis. Through this dual mechanism, OSC inhibition decreases plasma levels of low-density lipoprotein (LDL)-cholesterol and prevents cholesterol deposition within macrophages. The recent crystallization of OSC identifies the mechanism of action for this complex enzyme, setting the stage for the design of OSC inhibitors with improved pharmacological properties for cholesterol lowering and treatment of atherosclerosis.

Animals↗
PubMed2005

Improvement of nikkomycin production by enhanced copy of sanU and sanV in Streptomyces ansochromogenes and characterization of a novel glutamate mutase encoded by sanU and sanV.

Previous studies revealed that two genes-sanU and sanV were associated with nikkomycin biosynthesis in Streptomyces ansochromogenes. A plasmid used to increase an extra copy of sanU and sanV was constructed and introduced into wild-type strain. HPLC results showed that nikkomycin production of recombinant strain was about 1.8 fold than that of wild-type strain. RT-PCR analysis indicated that the transcriptional level of sanU and sanV in this recombinant strain was about two folds than that of wild-type strain. The sanU and sanV were expressed in E. coli BL21 (DE3). SanU and SanV were purified individually. SanU and SanV assembled with coenzyme B12 to form a complete enzyme in vitro, which showed glutamate mutase activity. The glutamate mutase converted L-glutamate toL-threo-beta-Methylaspartic acid, and then l-threo-beta-Methylaspartic acid was probably deaminated to form 2-oxo-3-methylsuccinic acid to join biosynthetic pathway of the peptidyl moiety HPHT in S. ansochromogenes. SanU is the coenzyme B12-binding component and more than two folds of SanU are required for maximal enzyme activity. The optimal pH and temperature for the formed enzyme are 7.5-8.5 and 35-42 degrees C, respectively. Sulfhydryl compounds are important for activity of the reassembled enzyme.

Aminoglycosides↗
PubMed2003

Adenosyl coenzyme and pH dependence of the [4Fe-4S]2+/1+ transition in lysine 2,3-aminomutase.

5'-[N-[(3S)-3-Amino-carboxypropyl]-N-methylamino]-5(')-deoxyadenosine (azaSAM), an analog of S-adenosyl-L-methionine (SAM), was used to study the cofactor-dependent reduction of the [4Fe-4S](2+) center in lysine 2,3-aminomutase to the +1 oxidation state. azaSAM has a tertiary nitrogen in place of the sulfonium center of SAM. The analog binds to lysine 2,3-aminomutase with K(d)s of 1.4+/-0.3 microM at pH 8.0 and 2.2+/-0.6 microM at pH 6.5. Reduction of the [4Fe-4S](2+) center in the presence of this analog gives a 10K [4Fe-4S](1+) electron paramagnetic resonance (EPR) signal similar to that seen with SAM or S-adenosyl-L-homocysteine (SAH). The pH dependence of cofactor-induced reduction was examined to determine whether ionization of the tertiary nitrogen (pK(a)=7.08) might affect reduction of the [4Fe-4S](2+) center. The results show similar behavior in azaSAM and SAH, demonstrating that ionization of the aza group in azaSAM does not account for pH dependence in cofactor-dependent reduction of the [4Fe-4S](2+) center. The signal shape of the low-temperature EPR signal for the [4Fe-4S](1+) center in the SAM-induced reduction displayed a pH dependence that was not observed in the azaSAM- or SAH-induced spectra. Unique features of the signal are at a maximum at the pH activity optimum of pH 8 and are diminished as the pH is lowered or raised. These features are also absent in the spectra at all pHs examined when reduction is induced by azaSAM or SAH.

Coenzymes↗
PubMed2003

Kinetic and biochemical analysis of the mechanism of action of lysine 5,6-aminomutase.

Lysine 5,6-aminomutase (5,6-LAM) catalyzes the reversible and nearly isoenergetic transformations of D-lysine into 2,5-diaminohexanoate (2,5-DAH) and of L-beta-lysine into 3,5-diaminohexanoate (3,5-DAH). The activity of 5,6-LAM depends on pyridoxal-5(')-phosphate (PLP) and adenosylcobalamin. The currently postulated multistep mechanism involves at least 12 steps, two of which involve hydrogen transfer. The deuterium kinetic isotope effects on k(cat) and k(cat)/K(m) have been found to be 10.4+/-0.3 and 8.3+/-1.9, respectively, in the reaction of DL-lysine-3,3,4,4,5,5,6,6-d(8). The corresponding isotope effects for reaction of DL-lysine-4,4,5,5-d(4) are 8.5+/-0.7 and 7.1+/-1.2, respectively. Neither cob(II)alamin nor a free radical can be detected in the steady state by UV-Vis spectrophotometry or electron paramagnetic resonance (EPR) spectroscopy. Therefore, hydrogen abstraction from carbon-5 of the substrate side chain is rate limiting in the mechanism. DL-4-Oxalysine is an alternative substrate for 5,6-LAM. DL-4-Oxalysine reacts irreversibly because the product breaks down into ammonia, acetaldehyde, and DL-serine. The value of K(m) for the reaction of DL-4-oxalysine is lower than that for DL-lysine and that of k(cat) for DL-4-oxalysine is slightly lower than that for DL-lysine. As measured by values of k(cat)/K(m), 5,6-LAM uses DL-4-oxalysine essentially as efficiently as the best substrates, D-lysine and L-beta-lysine, and more efficiently than DL-lysine. DL-4-Oxalysine induces the same suicide inactivation by electron transfer as do the biological substrates. The putative substrate-related radical intermediate is not sufficiently stabilized by the nonbonding 4-oxa electrons to be detectable by EPR spectroscopy.

Bacterial Proteins↗
PubMed1998

Squalene-hopene cyclase from Methylococcus capsulatus (Bath): a bacterium producing hopanoids and steroids.

We report the cloning and characterisation of the Methylococcus capsulatus shc gene, which encodes the squalene-hopene cyclase (SHC). This enzyme catalyses the complex cyclization of squalene to the pentacyclic triterpene skeleton of hopanoids and represents the key reaction in this biosynthesis. Using a combination of PCR amplification and DNA hybridization, two overlapping 2.6 kb PstI and 3.3 kb SalI DNA fragments were cloned bearing a 1962 bp open reading frame encoding a 74 kDa protein with 654 amino acids and a predicted isoelectric point at about pH 6.3. The deduced amino acid sequence of the M. capsulatus shc gene showed significant similarity to known prokaryotic SHCs and to a lesser degree to the related eukaryotic oxidosqualene cyclases (OSCs). Like other triterpene cyclases, the M. capsulatus SHC contains seven so-called QW-motifs as well as an aspartate-rich domain. The recombinant M. capsulatus SHC was expressed in Escherichia coli and in vitro activity of the recombinant cyclase was demonstrated using crude cell-free lysate or solubilized membrane preparation. The cyclization products hop-22-ene and hopan-22-ol (diplopterol) were identified by GC and GC-MS.

Amino Acid Sequence↗
PubMed1998

Cloning of conserved genes from Zymomonas mobilis and Bradyrhizobium japonicum that function in the biosynthesis of hopanoid lipids.

The squalene-hopene cyclase (SHC) is the only enzyme involved in the biosynthesis of hopanoid lipids that has been characterized on the genetic level. To investigate if additional genes involved in hopanoid biosynthesis are clustered with the shc gene, we cloned and analyzed the nucleotide sequences located immediately upstream of the shc genes from Zymomonas mobilis and Bradyrhizobium japonicum. In Z. mobilis, five open reading frames (ORFs, designated as hpnA-E) were detected in a close arrangement with the shc gene. In B. japonicum, three similarly arranged ORFs (corresponding to hpnC-E from Z. mobilis) were found. The deduced amino acid sequences of hpnC-E showed significant similarity (58-62%) in both bacteria. Similarities to enzymes of other terpenoid biosynthesis pathways (carotenoid and steroid biosynthesis) suggest that these ORFs encode proteins involved in the biosynthesis of hopanoids and their intermediates. Expression of hpnC to hpnE from Z. mobilis as well as expression of hpnC from B. japonicum in Escherichia coli led to the formation of the hopanoid precursor squalene. This indicates that hpnC encodes a squalene synthase. The two additional ORFs (hpnA and hpnB) in Z. mobilis showed similarities to enzymes involved in the transfer and modification of sugars, indicating that they may code for enzymes involved in the biosynthesis of the complex, sugar-containing side chains of hopanoids.

Amino Acid Sequence↗
PubMed2002

C-terminus modification of Streptomyces clavuligerus deacetoxycephalosporin C synthase improves catalysis with an expanded substrate specificity.

The biosynthesis of cephalosporins is catalyzed by deacetoxycephalosporin C synthase (DAOCS). Based on computational, biochemical, and structural analyses, it has been proposed that modification of the C-terminus of DAOCS might be a constructive strategy for engineering improvement in enzyme activity. Therefore, five hydrophilic residues namely N301, Y302, N304, R306, and R307 located in proximity to the C-terminus of Streptomyces clavuligerus DAOCS (scDAOCS) were selected and each substituted with a hydrophobic leucine residue. Substitutions at positions 304, 306, and 307 created mutant scDAOCSs with improved efficiencies in penicillin analog conversion up to 397%. And since it has been previously advocated that the C-terminus is crucial for guiding substrate entry, a truncated mutant DAOCS was constructed to assess its involvement. The truncation of the C-terminus at position 310 in the wild-type scDAOCS resulted in reduction of indiscriminate conversion of penicillin analog but this defect was compensated by the replacement of asparagine with leucine at position 304.

Amino Acid Substitution↗
PubMed1992

The enantioselective participation of (S)- and (R)-diaminovaleric acids in the formation of delta-aminolevulinic acid in cyanobacteria.

Although it is recognized that 4,5-diaminovaleric acid, formed from glutamate 1-semialdehyde, functions as the intermediate in the last step of delta-aminolevulinic acid formation from glutamate, the enantioselectivity of the participating glutamate 1-semialdehyde aminotransferase for 4,5-diaminovaleric acid has remained unknown. In the present work the involvement of (S)- and (R)-4,5-diaminovaleric acids, newly available by organic synthesis, was investigated, using glutamate 1-semialdehyde aminotransferase from Synechococcus. The preferred enantiomer was (S)-4,5-diaminovalerate. In experiments on the transformation of (S)-4,5-diaminovalerate to delta-aminolevulinate it was found that glutamate 1-semialdehyde aminotransferase was unusual among aminotransferases in that the common amino acceptors pyruvate, oxaloacetate, alpha-ketoglutarate were inactive, while 4,5-dioxovaleric acid could be utilized as a sluggish amino acceptor in place of glutamate 1-semialdehyde. In conclusion, glutamate 1-semialdehyde aminotransferase is highly but not absolutely enantioselective for (S)-4,5-diaminovaleric acid, and 4,5-dioxovaleric acid can function as amino acceptor not because of a physiological role in the C5 pathway of delta-aminolevulinic acid formation, but because of its structural resemblance to glutamate 1-semialdehyde.

Amino Acids, Diamino↗
PubMed1992

Affinity labeling of vertebrate oxidosqualene cyclases with a tritiated suicide substrate.

Pig and rat liver oxidosqualene cyclase (OSC) enzymes were purified to homogeneity and showed single bands on SDS-polyacrylamide gel electrophoresis with molecular masses of 75 kDa (pig) and 78 kDa (rat). Pig liver OSC was purified for the first time (441-fold with a yield of 39%). Chemical affinity labeling of pure or crude preparations of the liver cyclases using the mechanism-based irreversible inhibitor of OSC, [3H]29-methylidene-2,3-oxidosqualene ([3H]29-MOS), showed a single radioactive band at 75 kDa (pig) and 78 kDa (rat). Affinity labeling experiments were also performed with dog and human microsomal preparations and with yeast and plant cyclases. All of the vertebrate OSC enzymes were specifically labeled with [3H]29-MOS and gave a single band with molecular masses ranging from 70 to 80 kDa (rat, 78 kDa; dog, 73 kDa; pig, 75 kDa; and human, 73 kDa). In contrast, yeast lanosterol cyclase and plant cycloartenol cyclase were not labeled, demonstrating subtle differences in the active sites of animal, plant, and fungal enzymes.

Affinity Labels↗
PubMed1986

N-[(1,5,9)-trimethyl-decyl]-4 alpha,10-dimethyl-8-aza-trans-decal-3 beta-ol a novel potent inhibitor of 2,3-oxidosqualene cycloartenol and lanosterol cyclases.

N-[(1,5,9)-trimethyl-decyl)]-4 alpha,10-dimethyl-8-aza-trans-decal-3 beta-ol 9 was designed to mimic the C9 or C8 high energy carbocationic intermediates postulated during the enzymic cyclization of 2,3-oxidosqualene to different triterpenes. The structurally new molecule 9 inhibits strongly cycloartenol and lanosterol cyclases in maize seedlings and rat liver microsomes respectively, whereas it does not inhibit beta-amyrin cyclase in the plant system. For the first time 2,3-oxidosqualene cycloartenol cyclase and beta-amyrin cyclase have been differentiated in the same plant material by use of a specific inhibitor.

Animals↗
PubMed1988

Partial purification of 2,3-oxidosqualene-lanosterol cyclase from hog-liver. Evidence for a functional thiol residue.

2,3-Oxidosqualene-lanosterol cyclase is an intrinsic microsomal protein which can be solubilized by ionic (deoxycholate) and nonionic (emulphogene) detergents with good yields. The hog-liver microsomal cyclase was purified approximately 140-fold by chromatography on DEAE-cellulose and hydroxylapatite. The partially purified enzyme was inactivated by N-ethylmaleimide, following pseudo-first order kinetics, indicating that a cysteine residue is essential for activity.

Animals↗
PubMed1998

Down-regulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase mRNA levels and synthesis in syrian hamster C100 cells by the oxidosqualene cyclase inhibitor [4'-(6-allyl-ethyl-amino-hexyloxy)-2'-fluoro-phenyl]-(4-bromophenyl)-me thanone (Ro 48-8071): comparison to simvastatin.

In vivo inhibition of 2,3-oxidosqualene:lanosterol cyclase (OSC, E.C. 5.4.99.7)--the enzyme which catalyzes the cyclization of monooxidosqualene to lanosterol--does not result in elevated 3-hydroxy-3-methylglutaryl CoA reductase (HMGR) activity. This trait is attributed to increased levels of oxysterols, produced upon partial inhibition of OSC, that suppress HMGR and other sterol-responsive genes. The OSC inhibitor [4'-(6-allyl-ethyl-amino-hexyloxy)-2'-fluoro-phenyl]-(4-bromopheny l)-methanone (Ro 48-8071) was shown earlier to lower low-density lipoprotein (LDL) cholesterol in hamsters with no increase in hepatic HMGR, in contrast to simvastatin. To delineate the regulatory mechanism(s) by which Ro 48-8071 reduces cholesterol synthesis without raising HMGR levels, Syrian hamster C100 cells were incubated with either Ro 48-8071 or simvastatin, and their effects on cholesterol synthesis and LDL uptake, as well as on HMGR mRNA levels and rates of synthesis, were determined. Using RNase protection and radioimmunoprecipitation assays, we found that, in the absence of LDL in the culture medium, both HMGR mRNA levels and synthesis were reduced with concentrations of Ro 48-8071 inhibiting cholesterol synthesis by 50-75%, whereas LDL uptake was either reduced or unchanged. In contrast, simvastatin, at concentrations inhibiting cholesterol synthesis by the same 50-75%, increased both HMGR mRNA levels and synthesis, as well as LDL uptake. In the presence of LDL, HMGR mRNA levels and synthesis along with LDL uptake were little affected after incubation with Ro 48-8071. Still, simvastatin markedly increased both HMGR mRNA levels and synthesis in cells incubated in the presence of LDL, leaving LDL uptake unaffected. These data suggest that inhibition of OSC by Ro 48-8071 results in an indirect down-regulation of HMGR mRNA levels and synthesis.

Animals↗
PubMed2000

Enzymatic synthesis of UDP-(3-deoxy-3-fluoro)-D-galactose and UDP-(2-deoxy-2-fluoro)-D-galactose and substrate activity with UDP-galactopyranose mutase.

The novel UDP-sugar uridine 5'-(3-deoxy-3-fluoro-D-galactopyranosyl diphosphate) (1) and UDP-(2-deoxy-2-fluoro)-D-galactose (2) have been prepared enzymatically and tested as substrate analogues for the enzyme UDP-galactopyranose mutase (UDP-Galp mutase EC 5.4.99.9). Turnover of both 1 and 2 by UDP-Galp mutase was observed by HPLC and 19F NMR. The HPLC elution profile and 19F chemical shift of the products are consistent with the formation of the predicted furanose forms of 1 and 2. The Km values for compounds 1 and 2 were similar to those of the natural substrate UDP-Galp (0.26 mM for 1, 0.2 mM for 2, and 0.6 mM for UDP-Galp), but the values for kcat were substantially different (1.6/min for 1, 0.02/min for 2, and 1364/min for UDP-Galp). A correlation was also observed between the equilibrium yield of product formed during turnover of UDP-sugar by UDP-Galp mutase (UDP-Galp, compound 1 or compound 2), and the amount of furanose present for the free sugar at thermal equilibrium in aqueous solution, using 1H and 19F NMR spectroscopy. The implications of these results to the mechanism of the unusual enzymatic reaction are discussed.

Bacterial Proteins↗
PubMed2001

Bicyclic triterpenes as new main products of squalene-hopene cyclase by mutation at conserved tyrosine residues.

The catalytic cavity of the Alicyclobacillus acidocaldarius squalene-hopene cyclase is predominantly lined by aromatic amino acids. In mutant cyclases, the four tyrosine residues in the catalytic cavity were replaced by different amino acids. The mutants showed significant differences in catalytic behavior compared to the wild-type and to each other. Mutants Y609L, Y609C and Y609S produced the bicyclic main product gamma-polypodatetraene, while Y495L and Y612L showed a wild-type product pattern and produced hopene as the main product. Altered product patterns were also found with Y420 mutations.

Bacillus↗