Reconsideration of the catalytic center and mechanism of mammalian paraoxonase/arylesterase.

For three decades, mammalian paraoxonase (A-esterase, aromatic esterase, arylesterase; PON, EC 3.1.8.1) has been thought to be a cysteine esterase demonstrating structural and mechanistic homologies with the serine esterases (cholinesterases and carboxyesterases). Human, mouse, and rabbit PONs each contain only three cysteine residues, and their positions within PON have been conserved. In purified human PON, residues Cys-41 and Cys-352 form an intramolecular disulfide bond and neither could function as an active-center cysteine. Highly purified, enzymatically active PON contains a single titratable sulfhydryl group. Thus, Cys-283 is the only probable candidate for an active-center cysteine. Through site-directed mutagenesis of the human cDNA, Cys-283 was replaced with either serine (C283S) or alanine (C283A). The expressed C283 (wild-type) enzyme was inactivated by para-hydroxymercuribenzoate, but the C283S and C283A mutant enzymes were not inactivated. C283A and C283S mutant enzymes retained both paraoxonase and arylesterase activities, and the Km values for paraoxon and phenyl acetate were similar to those of the wild type. Clearly, residue Cys-283 is free in active PON, but a free sulfhydryl group is not required for either paraoxonase or arylesterase activities. Consequently, it is necessary to examine other models for the active-site structure and catalytic mechanism of PON.

Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase.

Escherichia coli RuvC protein is a specific endonuclease that resolves Holliday junctions during homologous recombination. Since the endonucleolytic activity of RuvC requires a divalent cation and since 3 or 4 acidic residues constitute the catalytic centers of several nucleases that require a divalent cation for the catalytic activity, we examined whether any of the acidic residues of RuvC were required for the nucleolytic activity. By site-directed mutagenesis, we constructed a series of ruvC mutant genes with similar amino acid replacements in 1 of the 13 acidic residues. Among them, the mutant genes with an alteration at Asp-7, Glu-66, Asp-138, or Asp-141 could not complement UV sensitivity of a ruvC deletion strain, and the multicopy mutant genes showed a dominant negative phenotype when introduced into a wild-type strain. The products of these mutant genes were purified and their biochemical properties were studied. All of them retained the ability to form a dimer and to bind specifically to a synthetic Holliday junction. However, they showed no, or extremely reduced, endonuclease activity specific for the junction. These 4 acidic residues, which are dispersed in the primary sequence, are located in close proximity at the bottom of the putative DNA binding cleft in the three-dimensional structure. From these results, we propose that these 4 acidic residues constitute the catalytic center for the Holliday junction resolvase and that some of them play a role in coordinating a divalent metal ion in the active center.

Gene for the catalytic subunit of the human DNA-activated protein kinase maps to the site of the XRCC7 gene on chromosome 8.

The DNA-activated serine/threonine protein kinase (DNA-PK) is composed of a large (approximately 460 kDa) catalytic polypeptide (DNA-PKcs) and Ku, a heterodimeric DNA-binding component (p70/p80) that targets DNA-PKcs to DNA. A 41-kbp segment of the DNA-PKcs gene was isolated, and a 7902-bp segment was sequenced. The sequence contains a polymorphic Pvu II restriction enzyme site, and comparing the sequence with that of the cDNA revealed the positions of nine exons. The DNA-PKcs gene was mapped to band q11 of chromosome 8 by in situ hybridization. This location is coincident with that of XRCC7, the gene that complements the DNA double-strand break repair and V(D)J recombination defects (where V is variable, D is diversity, and J is joining) of hamster V3 and murine severe combined immunodeficient (scid) cells.

Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases.

The regions surrounding the catalytic amino acids previously identified in a few "retaining" O-glycosyl hydrolases (EC 3.2.1) have been analyzed by hydrophobic cluster analysis and have been used to define sequence motifs. These motifs have been found in more than 150 glycosyl hydrolase sequences representing at least eight established protein families that act on a large variety of substrates. This allows the localization and the precise role of the catalytic residues (nucleophile and acid catalyst) to be predicted for each of these enzymes, including several lysosomal glycosidases. An identical arrangement of the catalytic nucleophile was also found for S-glycosyl hydrolases (myrosinases; EC 3.2.3.1) for which the acid catalyst is lacking. A (beta/alpha)8 barrel structure has been reported for two of the eight families of proteins that have been grouped. It is suggested that the six other families also share this fold at their catalytic domain. These enzymes illustrate how evolutionary events led to a wide diversification of substrate specificity with a similar disposition of identical catalytic residues onto the same ancestral (beta/alpha)8 barrel structure.

A catalytic mechanism for the dual-specific phosphatases.

Dual-specific protein-tyrosine phosphatases have the common active-site sequence motif HCXXGXXRS(T). The role of the conserved hydroxyl was investigated by changing serine-131 to an alanine (S131A) in the dual-specific protein-tyrosine phosphatase VHR. The pH profile of the kcat/Km value for the S131A mutant is indistinguishable from that of the native enzyme. In contrast, the kcat value for S131A mutant is 100-fold lower than that for the native enzyme, and the shape of the pH profile was perturbed from bell-shaped in the native enzyme to a pH-independent curve over the pH range 4.5-9.0. This evidence, along with results from a previous study, suggests that the S131A mutation alters the rate-limiting step in the catalytic mechanism. Formation of a phosphoenzyme intermediate appears to be rate-limiting with the native enzyme, whereas in the S131A mutant breakdown of the intermediate is rate-limiting. This was confirmed by the appearance of a burst of p-nitrophenol formation when p-nitrophenyl phosphate rapidly reacted with the S131A enzyme in a stopped-flow spectrophotometer. Loss of this hydroxyl group at the active site dramatically diminished the ability of the enzyme to hydrolyze the thiol-phosphate intermediate without exerting any significant change in the steps leading to and including the formation of the intermediate. Consistent with rate-limiting intermediate formation in the native enzyme, the rate of burst in the S131A mutant was 1.5 s-1, which agrees well with the kcat value of 5 s-1 observed for native enzyme. The amplitude of the burst was stoichiometric with final enzyme concentration, and the slow linear rate (0.06 s-1) of p-nitrophenol formation after the burst was in agreement with the steady-state determined value of kcat (0.055 s-1).

Catalytic domain of human immunodeficiency virus type 1 integrase: identification of a soluble mutant by systematic replacement of hydrophobic residues.

The integrase protein of human immunodeficiency virus type 1 is necessary for the stable integration of the viral genome into host DNA. Integrase catalyzes the 3' processing of the linear viral DNA and the subsequent DNA strand transfer reaction that inserts the viral DNA ends into host DNA. Although full-length integrase is required for 3' processing and DNA strand transfer activities in vitro, the central core domain of integrase is sufficient to catalyze an apparent reversal of the DNA strand transfer reaction, termed disintegration. This catalytic core domain, as well as the full-length integrase, has been refractory to structural studies by x-ray crystallography or NMR because of its low solubility and propensity to aggregate. In an attempt to improve protein solubility, we used site-directed mutagenesis to replace hydrophobic residues within the core domain with either alanine or lysine. The single substitution of lysine for phenylalanine at position 185 resulted in a core domain that was highly soluble, monodisperse in solution, and retained catalytic activity. This amino acid change has enabled the catalytic domain of integrase to be crystallized and the structure has been solved to 2.5-A resolution [Dyda, F., Hickman, A. B., Jenkins, T. M., Engelman, A., Craigie, R. & Davies, D. R. (1994) Science 266, 1981-1986]. Systematic replacement of hydrophobic residues may be a useful strategy to improve the solubility of other proteins to facilitate structural and biochemical studies.

Alternative splicing generates a second isoform of the catalytic A subunit of the vacuolar H(+)-ATPase.

We have identified a second isoform of the catalytic A subunit of the vacuolar H+ pump in chicken osteoclasts. In this isoform (A2) a 72-bp cassette replaces a 90-bp cassette present in the classical A1 isoform. The A1-specific cassette encodes a region of the protein that contains one of the three ATP-binding consensus sequences (the P-loop) identified in this polypeptide, as well as the pharmacologically relevant Cys254. In contrast, the A2-specific cassette does not contain any of these features. These two isoforms, which appear to be ubiquitously expressed, are encoded by a single gene and are generated by alternative splicing of two mutually exclusive exons. The alternative RNA processing involves the recognition of a single site, the boundary between the A2- and A1-specific exons, as either acceptor (in A1) or donor (in A2) splice site.

Disease specificity of kinase domains: the src-encoded catalytic domain converts erbB into a sarcoma oncogene.

src and erbB are two tyrosine kinase-encoding oncogenes carried by retroviruses, which have distinct disease specificities. The former induces predominantly sarcomas, and the latter, leukemias. Src and ErbB have similar catalytic domains but have very different regulatory domains. A wealth of information exists concerning how different regulatory domains [Src homology 2 (SH2) and SH3 domains and autophosphorylation sites] control substrate and disease specificities. Whether the catalytic domain helps determine these specificities remains to be explored. Here we show that the Src catalytic domain is enzymatically active when substituted into the ErbB backbone and interacts with the ErbB regulatory domain. This ErbB/Src chimera displays autophosphorylation and substrate phosphorylation patterns different from those of both Src and ErbB. Neither SH2 and SH3 nor autophosphorylation sites are required for the Src catalytic domain to exert its fibroblast transforming ability. Most significantly, the catalytic domain can convert erbB from a leukemogenic oncogene into a sarcomagenic oncogene, suggesting that the leukemogenic determinants in part reside within the ErbB catalytic domain.

Loss of the catalytic subunit of the DNA-dependent protein kinase in DNA double-strand-break-repair mutant mammalian cells.

The DNA-dependent protein kinase (DNA-PK) consists of three polypeptide components: Ku-70, Ku-80, and an approximately 350-kDa catalytic subunit (p350). The gene encoding the Ku-80 subunit is identical to the x-ray-sensitive group 5 complementing gene XRCC5. Expression of the Ku-80 cDNA rescues both DNA double-strand break (DSB) repair and V(D)J recombination in group 5 mutant cells. The involvement of Ku-80 in these processes suggests that the underlying defect in these mutant cells may be disruption of the DNA-PK holoenzyme. In this report we show that the p350 kinase subunit is deleted in cells derived from the severe combined immunodeficiency mouse and in the Chinese hamster ovary cell line V-3, both of which are defective in DSB repair and V(D)J recombination. A centromeric fragment of human chromosome 8 that complements the scid defect also restores p350 protein expression and rescues in vitro DNA-PK activity. These data suggest the scid gene may encode the p350 protein or regulate its expression and are consistent with a model whereby DNA-PK is a critical component of the DSB-repair pathway.

Catalytic effect of MCM-41 in the pyrolysis of tobacco and several substances used as additives in the preparation of commercial cigarettes

Comunicación presentada en forma de póster en el "12th Mediterranean Congress of Chemical Engineering", Barcelona (Spain), November 15-18, 2011.

Enantioselective catalytic lithiation using a chiral binaphthyl derivative as electron carrier

The lithiation, of the secondary chloride 2, catalyzed by binaphthyl derivatives, i.e. BINAM 4, BINOL 5, BINAP 6, H8-BINAP 7, Tol-BINAP 8, 2,2’-bis(pyrrolidin-1-yl)-1,1’-binaphthalene 9, and 2,2’-dimethyl-1,1’-binaphthalene 11, in the presence of different ketones has been studied, yielding the corresponding alcohol derivatives 3 and 12-16 in moderate to good yields. Binaphthyl derivative 11 has revealed to be very active as catalyst in the lithiation process at room temperature, and has allowed the preparation of the alcohol derivatives with enantioselectivities up to 50%.

TGA/FTIR study of the MCM-41-catalytic pyrolysis of tobacco and tobacco–glycerol mixtures

In this work, the catalytic effect of MCM-41 on the qualitative composition of the gases evolved in the pyrolysis of glycerol, tobacco and tobacco–glycerol mixtures has been studied by TGA/FTIR. The results obtained reflect that the amount of volatile products obtained from tobacco or from tobacco containing mixtures is noticeably decreased if the catalyst is used as a tobacco additive. The addition of the catalyst also produces noticeable changes in the composition of the gases obtained at each temperature. Such changes are more significant in the case of the pyrolysis of the tobacco–glycerol–mixture than in the pyrolysis of tobacco. The evolution patterns for different types of compounds reveal that the catalyst contributes to a noticeable decrease of the yields of methane, CO, CO2 and carbonylic compounds, which could be interesting from the point of view of the use of MCM-41 as a tobacco additive in order to reduce tobacco smoke toxicity.

Refinery Nonconventional Feedstocks: Influence of the Coprocessing of Vacuum Gas Oil and Low Density Polyethylene in Fluid Catalytic Cracking Unit on Full Range Gasoline Composition

Gasoline coming from refinery fluid catalytic cracking (FCC) unit is a major contributor to the total commercial grade gasoline pool. The contents of the FCC gasoline are primarily paraffins, naphthenes, olefins, aromatics, and undesirables such as sulfur and sulfur containing compounds in low quantities. The proportions of these components in the FCC gasoline invariable determine its quality as well as the performance of the associated downstream units. The increasing demand for cleaner and lighter fuels significantly influences the need not only for novel processing technologies but also for alternative refinery and petrochemical feedstocks. Current and future clean gasoline requirements include increased isoparaffins contents, reduced olefin contents, reduced aromatics, reduced benzene, and reduced sulfur contents. The present study is aimed at investigating the effect of processing an unconventional refinery feedstock, composed of blend of vacuum gas oil (VGO) and low density polyethylene (LDPE) on FCC full range gasoline yields and compositional spectrum including its paraffins, isoparaffins, olefins, napthenes, and aromatics contents distribution within a range of operating variables of temperature (500–700 °C) and catalyst-feed oil ratio (CFR 5–10) using spent equilibrium FCC Y-zeolite based catalyst in a FCC pilot plant operated at the University of Alicante’s Research Institute of Chemical Process Engineering (RICPE). The coprocessing of the oil-polymer blend led to the production of gasoline with very similar yields and compositions as those obtained from the base oil, albeit, in some cases, the contribution of the feed polymer content as well as the processing variables on the gasoline compositional spectrum were appreciated. Carbon content analysis showed a higher fraction of the C9–C12 compounds at all catalyst rates employed and for both feedstocks. The gasoline’s paraffinicity, olefinicity, and degrees of branching of the paraffins and olefins were also affected in various degrees by the scale of operating severity. In the majority of the cases, the gasoline aromatics tended toward the decrease as the reactor temperature was increased. While the paraffins and iso-paraffins gasoline contents were relatively stable at around 5 % wt, the olefin contents on the other hand generally increased with increase in the FCC reactor temperature.

Recent Advances in the Catalytic Enantioselective Reformatsky Reaction

This paper reviews the present state of the catalytic enantioselective Reformatsky reaction. Advancements in asymmetric versions of this reaction have recently led to a considerable extension of its scope and applicability, principally due to the use of highly active chiral ligands and very specific reaction conditions.

Abatement of hydrocarbons by acid ZSM-5 and BETA zeolites under cold-start conditions

Simulated cold-start tests have been carried out to evaluate the performance of H-ZSM-5 and H-BETA zeolites as hydrocarbon traps under simulated gasoline car exhaust gases, paying special attention to the effect of water on their behaviour. It is concluded that the hydrothermal treatment of the zeolites in the acidic form contributes to the better performance of these materials as hydrocarbon traps since the stabilization of the zeolites takes place. Moreover, the decrease of the surface acidity of the zeolites results in an increase of the Si/Al ratio, which contributes to the decrease of the water affinity for adsorption sites. Thus, the competition with hydrocarbon molecules in the exhaust for the adsorption sites is reduced which increases their trap efficiency. The stabilized H-ZSM-5 is the zeolite that showed the best performance with a propene offset temperature of 240 °C, which should be high enough for the three-way catalyst to carry out its role as catalytic converter.