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1.
Appl Microbiol Biotechnol ; 103(3): 1131-1141, 2019 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-30511262

RESUMEN

Polyhydroxyalkanoates (PHAs) are biopolymers synthesized by a wide range of bacteria, which serve as a promising candidate in replacing some conventional petrochemical-based plastics. PHA synthase (PhaC) is the key enzyme in the polymerization of PHA, and the crystal structures were successfully determined using the catalytic domain of PhaC from Cupriavidus necator (PhaCCn-CAT) and Chromobacterium sp. USM2 (PhaCCs-CAT). Here, we review the beneficial mutations discovered in PhaCs from a structural perspective. The structural comparison of the residues involved in beneficial mutation reveals that the residues are near to the catalytic triad, but not inside the catalytic pocket. For instance, Ala510 of PhaCCn is near catalytic His508 and may be involved in the open-close regulation, which presumably play an important role in substrate specificity and activity. In the class II PhaC1 from Pseudomonas sp. 61-3 (PhaC1Ps), Ser325 stabilizes the catalytic cysteine through hydrogen bonding. Another residue, Gln508 of PhaC1Ps is located in a conserved hydrophobic pocket which is next to the catalytic Asp and His. A class I, II-conserved Phe420 of PhaCCn is one of the residues involved in dimerization and its mutation to serine greatly reduced the lag phase. The current structural analysis shows that the Phe362 and Phe518 of PhaC from Aeromonas caviae (PhaCAc) are assisting the dimer formation and maintaining the integrity of the core beta-sheet, respectively. The structure-function relationship of PhaCs discussed in this review will serve as valuable reference for future protein engineering works to enhance the performance of PhaCs and to produce novel biopolymers.


Asunto(s)
Aciltransferasas/metabolismo , Aeromonas caviae/enzimología , Chromobacterium/enzimología , Cupriavidus necator/enzimología , Polihidroxialcanoatos/metabolismo , Pseudomonas/enzimología , Aciltransferasas/genética , Aeromonas caviae/genética , Aeromonas caviae/metabolismo , Secuencia de Aminoácidos , Dominio Catalítico/genética , Chromobacterium/genética , Chromobacterium/metabolismo , Cristalografía por Rayos X , Cupriavidus necator/genética , Cupriavidus necator/metabolismo , Ingeniería de Proteínas , Estructura Terciaria de Proteína , Pseudomonas/genética , Pseudomonas/metabolismo , Relación Estructura-Actividad , Especificidad por Sustrato
2.
PLoS Negl Trop Dis ; 12(4): e0006443, 2018 04.
Artículo en Inglés | MEDLINE | ID: mdl-29694346

RESUMEN

Dengue virus (DENV) is the most prevalent and burdensome arbovirus transmitted by Aedes mosquitoes, against which there is only a limited licensed vaccine and no approved drug treatment. A Chromobacterium species, C. sp. Panama, isolated from the midgut of A. aegypti is able to inhibit DENV replication within the mosquito and in vitro. Here we show that C. sp. Panama mediates its anti-DENV activity through secreted factors that are proteinous in nature. The inhibitory effect occurs prior to virus attachment to cells, and is attributed to a factor that destabilizes the virion by promoting the degradation of the viral envelope protein. Bioassay-guided fractionation, coupled with mass spectrometry, allowed for the identification of a C. sp. Panama-secreted neutral protease and an aminopeptidase that are co-expressed and appear to act synergistically to degrade the viral envelope (E) protein and thus prevent viral attachment and subsequent infection of cells. This is the first study characterizing the anti-DENV activity of a common soil and mosquito-associated bacterium, thereby contributing towards understanding how such bacteria may limit disease transmission, and providing new tools for dengue prevention and therapeutics.


Asunto(s)
Aminopeptidasas/farmacología , Antivirales/farmacología , Chromobacterium/enzimología , Virus del Dengue/efectos de los fármacos , Dengue/tratamiento farmacológico , Proteínas del Envoltorio Viral/metabolismo , Proteínas Bacterianas/farmacología , Dengue/virología , Virus del Dengue/fisiología , Sistema Digestivo/virología , Proteolisis , Virión/efectos de los fármacos , Acoplamiento Viral/efectos de los fármacos
3.
Methods Mol Biol ; 1504: 19-23, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-27770411

RESUMEN

This chapter describes methods for enzyme stabilization using micellar solutions. Micellar solutions have been shown to increase the thermal stability, as well as the pH and solvent tolerance of enzymes. This field is traditionally referred to as micellar enzymology. This chapter details the use of ionic and nonionic micelles for the stabilization of polyphenol oxidase, lipase, and catalase, although this method could be used with any enzymatic system or enzyme cascade system.


Asunto(s)
Agaricales/enzimología , Catalasa/química , Catecol Oxidasa/química , Chromobacterium/enzimología , Lipasa/química , Micelas , Agaricales/química , Animales , Bovinos , Chromobacterium/química , Estabilidad de Enzimas , Concentración de Iones de Hidrógeno , Cinética , Lípidos/química , Hígado/enzimología , Solventes/química , Tensoactivos/química , Temperatura
4.
Langmuir ; 30(9): 2448-59, 2014 Mar 11.
Artículo en Inglés | MEDLINE | ID: mdl-24528191

RESUMEN

This article delineates the formation and characterization of different enzyme-carbon dot conjugates in aqueous medium (pH = 7.0). We used soybean peroxidase (SBP), Chromobacterium viscosum (CV) lipase, trypsin, and cytochrome c (cyt c) for the formation of conjugate either with cationic carbon dot (CCD) or anionic carbon dot (ACD) depending on the overall charge of the protein at pH 7.0. These nanobioconjugates were used to probe the location of enzymes in water-in-oil (w/o) microemulsion. The size of the synthesized water-soluble carbon dots were of 2-3 nm with distinctive emission property. The formation of enzyme/protein-carbon dot conjugates in aqueous buffer was confirmed via fluorescence spectroscopy and zeta potential measurement, and the structural alteration of enzyme/protein was monitored by circular dichroism spectroscopy. Biocatalytic activities of protein/enzymes in conjugation with carbon dots were found to be decreased in aqueous phosphate buffer (pH 7.0, 25 mM). Interestingly, the catalytic activity of the nanobioconjugates of SBP, CV lipase, and cyt c did not reduce in cetyltrimethylammonium bromide (CTAB)-based reverse micelle. It indicates different localization of carbon dots and the enzymes inside the reverse micelle. The hydrophilic carbon dots always preferred to be located in the water pool of reverse micelle, and thus, enzyme must be located away from the water pool, which is the interface. However, in case of trypsin-carbon dot conjugate, the enzyme activity notably decreased in reverse micelle in the presence of carbon dot in a similar way that was observed in water. This implies that trypsin and carbon dots both must be located at the same place, which is the water pool of reverse micelle. Carbon dot induced deactivation was not observed for those enzymes which stay away from the water pool and localized at the interfacial domain while deactivation is observed for those enzymes which reside at the water pool. Thus, the location of enzymes in the microdomain of w/o microemulsion can be predicted by comparing the activity profile of enzyme-carbon dot conjugate in water and w/o microemulsion.


Asunto(s)
Carbono/química , Citocromos c/química , Lipasa/química , Aceites/química , Peroxidasa/química , Tripsina/química , Carbono/metabolismo , Chromobacterium/enzimología , Citocromos c/metabolismo , Emulsiones/química , Lipasa/metabolismo , Micelas , Aceites/metabolismo , Tamaño de la Partícula , Peroxidasa/metabolismo , Glycine max/enzimología , Propiedades de Superficie , Tripsina/metabolismo , Agua/química , Agua/metabolismo
5.
Sci Rep ; 4: 4145, 2014 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-24553401

RESUMEN

The disulfide bond is unusual in natural products and critical for thermal stability, cell permeability and bioactivity. DepH from Chromobacterium violaceum No. 968 is an FAD-dependent enzyme responsible for catalyzing the disulfide bond formation of FK228, an anticancer prodrug approved for the treatment of cutaneous T-cell lymphoma. Here we report the crystal structures of DepH and DepH complexed with a substrate analogue S,S'-dimethyl FK228 at 1.82 Å and 2.00 Å, respectively. Structural and biochemical analyses revealed that DepH, in contrast to the well characterized low molecular weight thioredoxin reductases (LMW TrxRs), is an NADP(+)-independent dithiol oxidase. DepH not only lacks a conserved GGGDXAXE motif necessary for NADP(+) binding in the canonical LMW TrxRs, but also contains a 11-residue sequence which physically impedes the binding of NADP(+). These observations explain the difference between NADP(+)-independent small molecule dithiol oxidases and NADP(+)-dependent thioredoxin reductases and provide insights for understanding the catalytic mechanism of dithiol oxidases involved in natural product biosynthesis.


Asunto(s)
Chromobacterium/enzimología , Depsipéptidos/biosíntesis , Oxidorreductasas actuantes sobre Donantes de Grupos Sulfuro/química , Secuencias de Aminoácidos , Sitios de Unión , Biocatálisis , Chromobacterium/metabolismo , Cristalografía por Rayos X , Depsipéptidos/química , NADP/química , NADP/metabolismo , Oxidorreductasas actuantes sobre Donantes de Grupos Sulfuro/genética , Oxidorreductasas actuantes sobre Donantes de Grupos Sulfuro/metabolismo , Estructura Terciaria de Proteína , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Reductasa de Tiorredoxina-Disulfuro/química , Reductasa de Tiorredoxina-Disulfuro/metabolismo
6.
Angew Chem Int Ed Engl ; 53(8): 2221-4, 2014 Feb 17.
Artículo en Inglés | MEDLINE | ID: mdl-24446392

RESUMEN

Nature provides a rich source of compounds with diverse chemical structures and biological activities, among them, sulfur-containing metabolites from bacteria and fungi. Some of these compounds bear a disulfide moiety that is indispensable for their bioactivity. Specialized oxidoreductases such as GliT, HlmI, and DepH catalyze the formation of this disulfide bridge in the virulence factor gliotoxin, the antibiotic holomycin, and the anticancer drug romidepsin, respectively. We have examined all three enzymes by X-ray crystallography and activity assays. Despite their differently sized substrate binding clefts and hence, their diverse substrate preferences, a unifying reaction mechanism is proposed based on the obtained crystal structures and further supported by mutagenesis experiments.


Asunto(s)
Productos Biológicos/metabolismo , Oxidorreductasas/metabolismo , Aspergillus fumigatus/enzimología , Aspergillus fumigatus/metabolismo , Proteínas Bacterianas/metabolismo , Sitios de Unión , Biocatálisis , Productos Biológicos/química , Chromobacterium/enzimología , Chromobacterium/metabolismo , Cristalografía por Rayos X , Depsipéptidos/química , Depsipéptidos/metabolismo , Disulfuros/química , Disulfuros/metabolismo , Proteínas Fúngicas/metabolismo , Gliotoxina/química , Gliotoxina/metabolismo , Lactamas/química , Lactamas/metabolismo , Oxidación-Reducción , Estructura Terciaria de Proteína , Streptomyces/enzimología , Streptomyces/metabolismo , Especificidad por Sustrato
7.
Biochemistry ; 53(3): 591-600, 2014 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-24401123

RESUMEN

In bacteria, 3',5'-adenosine bisphosphate (pAp) is generated from 3'-phosphoadenosine 5'-phosphosulfate in the sulfate assimilation pathway, and from coenzyme A by the transfer of the phosphopantetheine group to the acyl-carrier protein. pAp is subsequently hydrolyzed to 5'-AMP and orthophosphate, and this reaction has been shown to be important for superoxide stress tolerance. Herein, we report the discovery of the first instance of an enzyme from the amidohydrolase superfamily that is capable of hydrolyzing pAp. Crystal structures of Cv1693 from Chromobacterium violaceum have been determined to a resolution of 1.9 Å with AMP and orthophosphate bound in the active site. The enzyme has a trinuclear metal center in the active site with three Mn(2+) ions. This enzyme (Cv1693) belongs to the Cluster of Orthologous Groups cog0613 from the polymerase and histidinol phosphatase family of enzymes. The values of kcat and kcat/Km for the hydrolysis of pAp are 22 s(-1) and 1.4 × 10(6) M(-1) s(-1), respectively. The enzyme is promiscuous and is able to hydrolyze other 3',5'-bisphosphonucleotides (pGp, pCp, pUp, and pIp) and 2'-deoxynucleotides with comparable catalytic efficiency. The enzyme is capable of hydrolyzing short oligonucleotides (pdA)5, albeit at rates much lower than that of pAp. Enzymes from two other enzyme families have previously been found to hydrolyze pAp at physiologically significant rates. These enzymes include CysQ from Escherichia coli (cog1218) and YtqI/NrnA from Bacillus subtilis (cog0618). Identification of the functional homologues to the experimentally verified pAp phosphatases from cog0613, cog1218, and cog0618 suggests that there is relatively little overlap of enzymes with this function in sequenced bacterial genomes.


Asunto(s)
Adenosina Difosfato/metabolismo , Amidohidrolasas/metabolismo , Proteínas Bacterianas/metabolismo , Monoéster Fosfórico Hidrolasas/metabolismo , Adenosina Difosfato/biosíntesis , Secuencia de Aminoácidos , Proteínas Bacterianas/aislamiento & purificación , Chromobacterium/enzimología , Cristalización , Cristalografía por Rayos X , Modelos Moleculares , Datos de Secuencia Molecular , Fosfoadenosina Fosfosulfato/metabolismo , Monoéster Fosfórico Hidrolasas/aislamiento & purificación , Alineación de Secuencia , Especificidad por Sustrato
8.
Braz. j. microbiol ; Braz. j. microbiol;42(1): 84-88, Jan.-Mar. 2011. tab
Artículo en Inglés | LILACS | ID: lil-571378

RESUMEN

Phytases are a group of enzymes that catalyze phytic acid hydrolysis with release of phosphorus (P). The ability of Chromobacterium sp. to produce phytase was detected in 115 out of 118 candidate bacteria isolated from different Brazilian biomas. This is the first report revealing the genus Chromobacterium as phytase producer.


Asunto(s)
Secuencia de Bases , Biomasa , Chromobacterium/enzimología , Chromobacterium/aislamiento & purificación , Microbiología Ambiental , Reactivadores Enzimáticos , Eutrofización , Monoéster Fosfórico Hidrolasas , Péptido Hidrolasas/análisis , Catálisis , Activación Enzimática , Variación Genética , Hidrólisis , Métodos , Métodos , Ecosistema Tropical
9.
Chem Biol ; 16(6): 585-93, 2009 Jun 26.
Artículo en Inglés | MEDLINE | ID: mdl-19549597

RESUMEN

Disulfide bonds are rare in bacterial natural products, and the mechanism of disulfide bond formation in those products is unknown. Here we characterize a gene and its product critical for a disulfide bond formation in FK228 anticancer depsipeptide in Chromobacterium violaceum. Deletion of depH drastically reduced FK228 production, whereas complementation of the depH-deletion mutant with a copy of depH on a medium copy-number plasmid not only fully restored the FK228 production but also significantly increased the FK228 yield. Purified 6xHis-tagged DepH fusion protein in native form is a homodimer of 71.0 kDa, with each monomer containing one molecule of FAD. DepH efficiently converts an immediate FK228 precursor to FK228 in the presence of NADP(+). We conclude that DepH is an FAD-dependent pyridine nucleotide-disulfide oxidoreductase, specifically and efficiently catalyzing a disulfide bond formation in FK228.


Asunto(s)
Antibióticos Antineoplásicos/metabolismo , Depsipéptidos/metabolismo , Disulfuros/metabolismo , Flavina-Adenina Dinucleótido/metabolismo , NADH NADPH Oxidorreductasas/metabolismo , Antibióticos Antineoplásicos/química , Chromobacterium/enzimología , Chromobacterium/genética , Depsipéptidos/biosíntesis , Depsipéptidos/química , Cinética , Datos de Secuencia Molecular , Familia de Multigenes , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , NADH NADPH Oxidorreductasas/clasificación , NADH NADPH Oxidorreductasas/genética , Filogenia
10.
J Biol Chem ; 283(10): 6459-66, 2008 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-18171677

RESUMEN

Violacein and the indolocarbazoles are naturally occurring bisindole products with various biological activities, including antitumor activity. Although these compounds have markedly different molecular skeletons, their biosynthetic pathways share the same intermediate "compound X," which is produced from L-tryptophan via indole-3-pyruvic acid imine. Compound X is a short-lived intermediate that is spontaneously converted to chromopyrrolic acid for indolocarbazole biosynthesis, whereas VioE transforms compound X into protodeoxyviolaceinic acid, which is further modified by other enzymes to produce violacein. Thus, VioE plays a key role in the construction of the molecular skeleton of violacein. Here, we present the crystal structure of VioE, which consists of two subunits, each of which forms a structure resembling a baseball glove. Each subunit has a positively charged pocket at the center of the concave surface of the structure. Mutagenesis analysis of the surface pocket and other surface residues showed that the surface pocket serves as an active site. We have also solved the crystal structure of a complex of VioE and phenylpyruvic acid as an analogue of a VioE-substrate complex. A docking simulation with VioE and the IPA imine dimer, which is proposed to be compound X, agreed with the results from the mutational analysis and the VioE-phenylpyruvic acid complex structure. Based on these results, we propose that VioE traps the highly reactive substrate within the surface pocket to suppress CPA formation and promote protodeoxyviolaceinic acid formation caused by proximity and orientation effects.


Asunto(s)
Proteínas Bacterianas/química , Chromobacterium/enzimología , Indoles/química , Oxidorreductasas/química , Ácidos Fenilpirúvicos/química , Sustitución de Aminoácidos , Antineoplásicos/química , Antineoplásicos/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión/fisiología , Chromobacterium/genética , Cristalografía por Rayos X , Dimerización , Indoles/metabolismo , Mutagénesis Sitio-Dirigida , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Ácidos Fenilpirúvicos/metabolismo , Estructura Cuaternaria de Proteína/fisiología , Propiedades de Superficie , Triptófano/química , Triptófano/metabolismo
11.
J Mol Biol ; 364(3): 388-99, 2006 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-17010375

RESUMEN

N-Acetylglucosamine (GlcNAc), a major component of complex carbohydrates, is synthesized de novo or salvaged from lysosomally degraded glycoconjugates and from nutritional sources. The salvage pathway requires that GlcNAc kinase converts GlcNAc to GlcNAc-6-phosphate, a component utilized in UDP-GlcNAc biosynthesis or energy metabolism. GlcNAc kinase belongs to the sugar kinase/Hsp70/actin superfamily that catalyze phosphoryl transfer from ATP to their respective substrates, and in most cases catalysis is associated with a large conformational change in which the N-terminal small and C-terminal large domains enclose the substrates. Here we report two crystal structures of homodimeric human GlcNAc kinase, one in complex with GlcNAc and the other in complex with ADP and glucose. The active site of GlcNAc kinase is located in a deep cleft between the two domains of the V-shaped monomer. The enzyme adopts a "closed" configuration in the GlcNAc-bound complex and GlcNAc interacts with residues of both domains. In addition, the N-acetyl methyl group contacts residues of the other monomer in the homodimer, a unique feature compared to other members of the sugar kinase/Hsp70/actin superfamily. This contrasts an "open" configuration in the ADP/glucose-bound structure, where glucose cannot form these interactions, explaining its low binding affinity for GlcNAc kinase. Our results support functional implications derived from apo crystal structures of GlcNAc kinases from Chromobacter violaceum and Porphyromonas gingivalis and show that Tyr205, which is phosphorylated in thrombin-activated platelets, lines the GlcNAc binding pocket. This suggests that phosphorylation of Tyr205 may modulate GlcNAc kinase activity and/or specificity.


Asunto(s)
Adenosina Difosfato/química , Fucosa/análogos & derivados , Glucosa/química , Modelos Moleculares , Fosfotransferasas (Aceptor de Grupo Alcohol)/química , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Sitios de Unión , Chromobacterium/enzimología , Dimerización , Activación Enzimática , Fucosa/química , Humanos , Datos de Secuencia Molecular , Fosforilación , Porphyromonas gingivalis/enzimología , Unión Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Especificidad por Sustrato
12.
Inorg Chem ; 45(10): 4277-83, 2006 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-16676991

RESUMEN

Phenylalanine hydroxylase from Chromobacterium violaceum (cPAH), which catalyzes phenylalanine oxidation to tyrosine, is homologous to the catalytic domain of eukaryotic PAHs. Previous crystallographic and spectroscopic studies on mammalian PAH conflict on whether O2 binds to the open-coordination site or displaces the remaining water ligand to yield either a six- or a five-coordinate iron, respectively. The abilities of nitric oxide to behave as an oxygen mimic and a spectroscopic probe of ferrous iron are used to investigate the geometric and electronic effects of cofactor and substrate binding to cPAH by electron paramagnetic resonance (EPR) and UV-vis spectroscopies. A rhombic distortion observed for the ternary complex is due to two factors: a decrease in the Fe-NO angle and an alteration in the equatorial ligand geometry. Both factors are consistent with NO displacing the sole remaining water ligand to yield a five-coordinate iron center. Hyperfine broadening of the EPR resonances of the nitrosyl complexes by 17O-enriched water is observed in the absence of substrates or presence of cofactor only (binary complex), demonstrating that water is bound to the Fe(II). However, in the presence of substrate and cofactor (ternary complex), the EPR resonances of the nitrosyl complex are not broadened by 17O-enriched water, indicating the displacement of water by NO to afford a five-coordinate iron. Furthermore, the increased intensity in the 500-600 nm range of the UV-vis spectrum of the ternary nitrosyl complex indicates an increased overlap between the in-plane NO 2pi and d(x2-y2) and d(xz) orbitals, which corroborates a five-coordinate iron.


Asunto(s)
Proteínas Bacterianas/química , Chromobacterium/enzimología , Hierro/química , Óxido Nítrico/química , Fenilalanina Hidroxilasa/química , Sitios de Unión , Espectroscopía de Resonancia por Spin del Electrón/métodos , Ligandos , Sensibilidad y Especificidad , Espectrofotometría Ultravioleta/métodos , Relación Estructura-Actividad , Especificidad por Sustrato , Termodinámica
13.
J Colloid Interface Sci ; 289(2): 566-73, 2005 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-16112238

RESUMEN

The catalytic activity of Chromobacterium viscosum lipase (CV-lipase) was estimated across varying surfactant tail lengths (C-10-C-18) in water-in-oil (w/o) microemulsions of cationic surfactants containing four different hydroxyethyl-substituted head groups. An attempt to find a correlation, if any, between the activity of interfacially solubilized lipase and the varying surfactant tails was made for the first time in micellar enzymology. The second-order rate constant, k2, in lipase-catalyzed hydrolysis of p-nitrophenyl-n-hexanoate at pH 6.0 and 25 degrees C shows an improvement in enzyme activity (approximately 30-140%) across different head groups of amphiphiles with increasing tail lengths in varying solution compositions. Improvement of enzyme activity is prominent in ascending from C-10 to C-14/C-16, depending on the nature of polar head group. The hydrolytic activity of lipase in different surfactant (50 mM)/water/isooctane/n-hexanol with varying z= [alcohol]/[surfactant] (6.4 or 4.8) was amplified by 25-250% with increment in surfactant tail length in comparison with widely used cationic w/o microemulsions having solution compositions (z=16). As a notable outcome of this research, we found w/o microemulsions of 25 mM tetradecyltrimethylammonium bromide/water/isooctane/n-hexanol (z=8) producing the highest ever activity of lipase in any w/o microemulsions.


Asunto(s)
Lipasa/química , Aceites/química , Tensoactivos/química , Catálisis , Cationes/química , Chromobacterium/enzimología , Emulsiones , Activación Enzimática , Hidrólisis , Micelas , Estructura Molecular , Propiedades de Superficie , Tensoactivos/síntesis química , Agua/química
14.
J Mol Biol ; 320(3): 645-61, 2002 Jul 12.
Artículo en Inglés | MEDLINE | ID: mdl-12096915

RESUMEN

Structure determination of bacterial homologues of human disease-related proteins provides an efficient path to understanding the three-dimensional fold of proteins that are associated with human diseases. However, the precise locations of active-site residues are often quite different between bacterial and human versions of an enzyme, creating significant differences in the biological understanding of enzyme homologs. To study this hypothesis, phenylalanine hydroxylase from a bacterial source has been structurally characterized at high resolution and comparison is made to the human analog. The enzyme phenylalanine hydroxylase (PheOH) catalyzes the hydroxylation of l-phenylalanine into l-tyrosine utilizing the cofactors (6R)-l-erythro-5,6,7,8 tetrahydrobiopterin (BH(4)) and molecular oxygen. Previously determined X-ray structures of human and rat PheOH, with a sequence identity of more than 93%, show that these two structures are practically identical. It is thus of interest to compare the structure of the divergent Chromobacterium violaceum phenylalanine hydroxylase (CvPheOH) ( approximately 24% sequence identity overall) to the related human and rat PheOH structures. We have determined crystal structures of CvPheOH to high resolution in the apo-form (no Fe-added), Fe(III)-bound form, and 7,8-dihydro-l-biopterin (7,8-BH(2)) plus Fe(III)-bound form. The bacterial enzyme displays higher activity and thermal melting temperature, and structurally, differences are observed in the N and C termini, and in a loop close to the active-site iron atom.


Asunto(s)
Biopterinas/análogos & derivados , Chromobacterium/enzimología , Fenilalanina Hidroxilasa/química , Secuencia de Aminoácidos , Animales , Biopterinas/metabolismo , Dominio Catalítico/genética , Chromobacterium/genética , Secuencia Conservada , Cristalografía por Rayos X , Estabilidad de Enzimas , Humanos , Hierro/metabolismo , Cinética , Metales/metabolismo , Modelos Moleculares , Datos de Secuencia Molecular , Mutación , Fenilalanina Hidroxilasa/genética , Fenilalanina Hidroxilasa/metabolismo , Fenilcetonurias/enzimología , Fenilcetonurias/genética , Conformación Proteica , Pliegue de Proteína , Ratas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Homología de Secuencia de Aminoácido , Especificidad de la Especie
15.
J Org Chem ; 67(13): 4513-9, 2002 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-12076150

RESUMEN

A short and convenient synthesis of 3'- and 5'-O-levulinyl-2'-deoxynucleosides has been developed from the corresponding 3',5'-di-O-levulinyl derivatives by regioselective enzymatic hydrolysis, avoiding several tedious chemical protection/deprotection steps. Thus, Candida antartica lipase B (CAL-B) was found to selectively hydrolyze the 5'-levulinate esters, furnishing 3'-O-levulinyl-2'-deoxynucleosides 3 in >80% isolated yields. On the other hand, immobilized Pseudomonas cepacia lipase (PSL-C) and Candida antarctica lipase A (CAL-A) exhibit the opposite selectivity toward the hydrolysis at the 3'-position, affording 5'-O-levulinyl derivatives 4 in >70% yields. A similar hydrolysis procedure was successfully extended to the synthesis of 3'- and 5'-O-levulinyl-protected 2'-O-alkylribonucleosides 7 and 8. This work demonstrates for the first time application of commercial CAL-B and PSL-C toward regioselective hydrolysis of levulinyl esters with excellent selectivity and yields. It is noteworthy that protected cytidine and adenosine base derivatives were not adequate substrates for the enzymatic hydrolysis with CAL-B, whereas PSL-C was able to accommodate protected bases during selective hydrolysis. In addition, we report an improved synthesis of dilevulinyl esters using a polymer-bound carbodiimide as a replacement for dicyclohexylcarbodiimide (DCC), thus considerably simplifying the workup for esterification reactions.


Asunto(s)
Lipasa/metabolismo , Oligonucleótidos/síntesis química , Burkholderia cepacia/enzimología , Candida/enzimología , Catálisis , Química Orgánica/métodos , Cromatografía Líquida de Alta Presión , Chromobacterium/enzimología , Esterificación , Proteínas Fúngicas , Hidrólisis , Espectroscopía de Resonancia Magnética , Estructura Molecular , Estereoisomerismo
16.
J Chromatogr A ; 849(2): 413-9, 1999 Jul 23.
Artículo en Inglés | MEDLINE | ID: mdl-10457439

RESUMEN

The fractionation of Chromobacterium viscosum lipase was performed using a polypropylene glycol-Sepharose gel. The influence of mobile phase composition on the adsorption of lipase on the gel was studied and it was found that the retention of lipase depends on the salt used and increased with increasing the ionic strength. The retention was not strongly affected by changing the pH value of the mobile phase. By using 20% (w/v) ammonium sulphate in phosphate buffer a total retention of lipase on the column was obtained and by simply decreasing the ionic strength of the buffer, desorption of lipase could be achieved. The chromatographic purification of Chromobacterium viscosum lipase by hydrophobic interaction chromatography on Sepharose CL-6B modified by covalent immobilisation of 1,4-butanediol diglycidyl ether, polyethylene glycol and polypropylene glycol was also compared.


Asunto(s)
Cromatografía en Agarosa/métodos , Chromobacterium/enzimología , Lipasa/aislamiento & purificación , Polímeros/química , Glicoles de Propileno/química , Butileno Glicoles/química , Polietilenglicoles/química
17.
J Biol Chem ; 273(40): 25594-601, 1998 Oct 02.
Artículo en Inglés | MEDLINE | ID: mdl-9748224

RESUMEN

A gene encoding phenylalanine hydroxylase has been cloned from Chromobacterium violaceum and expressed in Escherichia coli. The purified phenylalanine hydroxylase contains copper, which does not support enzymatic activity. Upon removal of copper by dithiothreitol (DTT), the enzyme contains substoichiometric amounts of calcium and zinc but little or no redox-active metal ions. The copper-depleted hydroxylase catalyzes the phenylalanine-dependent oxidation of 6, 7-dimethyltetrahydropterin (DMPH4) by O2 in a reaction in which phenylalanine is not hydroxylated and does not appear to undergo a chemical change, and hydrogen peroxide is produced. Analogs of phenylalanine also activate the oxidation of DMPH4. Both the copper-phenylalanine hydroxylase and the copper-depleted hydroxylase catalyze the hydroxylation of phenylalanine in the presence of DTT and FeSO4 in a reaction in which hydrogen peroxide is not produced. The apparent values of Km for Fe2+ and DTT are 0.28 microM and 1.1 mM, respectively, at 1.0 mM phenylalanine, 120 microM DMPH4 and pH 7. 4 and 23 degreesC. The apparent value of kcat is 14.3 s-1 under these conditions. Glutathione, mercaptoethanol, and dihydrolipoate support the hydroxylation of phenylalanine essentially as well as DTT. Incubation of copper-depleted hydroxylase with FeSO4, phenylalanine, and DTT followed by gel permeation chromatography leads to an iron-hydroxylase containing approximately 1 molecule of iron per molecule of enzyme. The iron-hydroxylase displays an optical absorption band extending from 300 to 600 nm, and it catalyzes the hydroxylation of phenylalanine at the same maximum rate as the iron-activated hydroxylase but does not require added Fe2+. We conclude that iron participates in the hydroxylation of phenylalanine. Iron is not required for the oxidation of DMPH4, although it may exert a modest acceleration effect. A hypothetical mechanism is presented wherein the reaction of iron with the putative 4a-hydroperoxy-DMPH4 leads to 4a-hydroxy-DMPH4 and a high valent iron-oxy species. The iron-oxy species is postulated to react with phenylalanine in the hydroxylation process.


Asunto(s)
Chromobacterium/enzimología , Fenilalanina Hidroxilasa/química , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Clonación Molecular , Cobre/metabolismo , Escherichia coli/genética , Peróxido de Hidrógeno/metabolismo , Hidroxilación , Hierro/metabolismo , Cinética , Metaloproteínas/química , Metales/análisis , Datos de Secuencia Molecular , Estructura Molecular , Oxígeno/metabolismo , Fenilalanina/metabolismo , Pteridinas/metabolismo , Proteínas Recombinantes/química , Alineación de Secuencia , Análisis de Secuencia , Espectrofotometría , Compuestos de Sulfhidrilo/farmacología
18.
J Chromatogr A ; 796(1): 177-80, 1998 Feb 13.
Artículo en Inglés | MEDLINE | ID: mdl-9513291

RESUMEN

The purification of Chromobacterium viscosum lipase was performed using a polypropylene glycol-Sepharose gel. The influence of the mobile phase composition on the chromatographic behaviour of Chromobacterium viscosum lipase was studied and it was found that the retention of lipase depends on the salt used and increased with ionic strength. Using 20% (w/v) ammonium sulphate in the eluent, a total retention of lipase on the column was obtained.


Asunto(s)
Proteínas Bacterianas/aislamiento & purificación , Cromatografía Liquida/métodos , Chromobacterium/enzimología , Lipasa/aislamiento & purificación , Polietilenglicoles/química , Sefarosa/química , Lipasa/metabolismo
19.
J Mol Biol ; 259(4): 704-17, 1996 Jun 21.
Artículo en Inglés | MEDLINE | ID: mdl-8683577

RESUMEN

The crystal structure of a lipase from the bacterium Chromobacterium viscosum ATCC 6918 (CVL) has been determined by isomorphous replacement and refined at 1.6 angstroms resolution to an R-factor of 17.8%. The lipase has the overall topology of an alpha/beta type protein, which was also found for previously determined lipase structures. The catalytic triad of the active center consists of the residues Ser87, Asp263 and His285. These residues are not exposed to the solvent, but a narrow channel connects them with the molecular surface. This conformation is very similar to the previously reported closed conformation of Pseudomonas glumae lipase (PGL), but superposition of the two lipase structures reveals several conformational differences. r.m.s. deviations greater than 2 angstroms are found for the C alpha-atoms of the polypeptide chains from His15 to Asp28, from Leu49 to Ser54 and from Lys128 to Gln158. Compared to the PGL structure in the CVL structure, three alpha-helical fragments are shorter, one beta-strand is longer and an additional antiparallel beta-sheet is found. In contrast to PGL, CVL displays an oxyanion hole, which is stabilized by the amide nitrogen atoms of Leu17 and Gln88, and a cis-peptide bond between Gln291 and Leu292. CVL contains a Ca2+, like the PGL, which is coordinated by four oxygen atoms from the protein and two water molecules.


Asunto(s)
Chromobacterium/enzimología , Lipasa/química , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Sitios de Unión , Calcio/metabolismo , Gráficos por Computador , Cristalización , Cristalografía por Rayos X , Electroforesis en Gel de Poliacrilamida , Enlace de Hidrógeno , Modelos Moleculares , Datos de Secuencia Molecular , Unión Proteica , Conformación Proteica , Pliegue de Proteína , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Pseudomonas/química , Pseudomonas/enzimología , Alineación de Secuencia
20.
J Biol Chem ; 270(40): 23540-5, 1995 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-7559518

RESUMEN

L-Tryptophan 2',3'-oxidase, an amino acid alpha,beta-dehydrogenase isolated from Chromobacterium violaceum, catalyzes the formation of a double bond between the C alpha and C beta carbons of various tryptophan derivatives provided that they possess: (i) a L-enantiomeric configuration, (ii) an alpha-carbonyl group, and (iii) an unsubstituted and unmodified indole nucleus. Kinetic parameters were evaluated for a series of tryptophan analogues, providing information on the contribution of each chemical group to substrate binding. The stereochemistry of the dehydro product was determined to be a Z-configuration from proton nuclear magnetic resonance assignments. No reaction can be observed in the presence of other aromatic beta-substituted alanyl residues which behave neither as substrates nor as inhibitors and therefore do not compete against this reaction. The enzymatic synthesis of alpha,beta-dehydrotryptophanyl peptides from 5 to 24 residues was successfully achieved without side product formation, irrespective of the position of the tryptophan residue in the amino acid sequence. A reactional mechanism involving a direct alpha,beta-dehydrogenation of the tryptophan side chain is proposed.


Asunto(s)
Chromobacterium/enzimología , Oxidorreductasas/metabolismo , Secuencia de Aminoácidos , Sitios de Unión , Indoles/química , Indoles/metabolismo , Cinética , Datos de Secuencia Molecular , Péptidos/química , Péptidos/metabolismo , Estereoisomerismo , Especificidad por Sustrato , Triptófano/análogos & derivados , Triptófano/química , Triptófano/metabolismo
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