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1.
Ecotoxicol Environ Saf ; 273: 116130, 2024 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-38394761

RESUMEN

The manganese peroxidase (MnP) can degrade multiple mycotoxins including deoxynivalenol (DON) efficiently; however, the lignin components abundant in foods and feeds were discovered to interfere with DON catalysis. Herein, using MnP from Ceriporiopsis subvermispora (CsMnP) as a model, it was demonstrated that desired catalysis of DON, but not futile reactions with lignin, in the reaction systems containing feeds could be achieved by engineering MnP and supplementing with a boosting reactant. Specifically, two successive strategies (including the fusion of CsMnP to a DON-recognizing ScFv and identification of glutathione as a specific targeting enhancer) were combined to overcome the lignin competition, which together resulted into elevation of the degradation rate from 2.5% to as high as 82.7% in the feeds. The method to construct a targeting MnP and fortify it with an additional enhancer could be similarly applied to catalyze the many other mycotoxins with yet unknown responsive biocatalysts.


Asunto(s)
Lignina , Micotoxinas , Tricotecenos , Lignina/metabolismo , Peroxidasas/metabolismo
2.
J Struct Biol ; 215(2): 107966, 2023 06.
Artículo en Inglés | MEDLINE | ID: mdl-37100101

RESUMEN

Cortisol is a steroid hormone that is produced by the adrenal gland. It is a primary stress hormone that increases glucose levels in the blood stream. High concentrations of cortisol in the body can be used as a biomarker for acute and chronic stress and related mental and physiological disorders. Therefore, the accurate quantification of cortisol levels in body fluids is essential for clinical diagnosis. In this article, we describe the isolation of recombinant anti-cortisol antibodies with high affinity for cortisol and discover their cross-reactivity with other glucocorticoids. To describe the cortisol binding site and elucidate the structural basis for the binding specificity, the high-resolution crystal structures of the anti-cortisol (17) Fab fragment in the absence of glucocorticoid (2.00 Å) and the presence of cortisol (2.26 Å), corticosterone (1.86 Å), cortisone (1.85 Å) and prednisolone (2.00 Å) were determined. To our knowledge, this is the first determined crystal structure of a cortisol-specific antibody. The recognition of cortisol is driven by hydrophobic interactions and hydrogen bonding at the protein-ligand interface coupled with a conformational transition. Comparison of ligand-free and ligand-bound structures showed that the side chains of residues Tyr58-H and Arg56-H can undergo local conformational changes at the binding site, most likely prior to the binding event via a conformational selection mechanism. Compared to other anti-steroid antibody-antigen complexes, (17) Fab possesses a structurally unique steroid binding site, as the H3 loop from the CDR area has only a minor contribution, but framework residues have a prominent contribution to hapten binding.


Asunto(s)
Glucocorticoides , Fragmentos Fab de Inmunoglobulinas , Fragmentos Fab de Inmunoglobulinas/química , Secuencia de Aminoácidos , Hidrocortisona , Modelos Moleculares , Cristalografía por Rayos X , Conformación Proteica
3.
Biochemistry ; 60(41): 3046-3049, 2021 10 19.
Artículo en Inglés | MEDLINE | ID: mdl-34633186

RESUMEN

Caulobacter crescentus xylonolactonase (Cc XylC, EC 3.1.1.68) catalyzes an intramolecular ester bond hydrolysis over a nonenzymatic acid/base catalysis. Cc XylC is a member of the SMP30 protein family, whose members have previously been reported to be active in the presence of bivalent metal ions, such as Ca2+, Zn2+, and Mg2+. By native mass spectrometry, we studied the binding of several bivalent metal ions to Cc XylC and observed that it binds only one of them, namely, the Fe2+ cation, specifically and with a high affinity (Kd = 0.5 µM), pointing out that Cc XylC is a mononuclear iron protein. We propose that bivalent metal cations also promote the reaction nonenzymatically by stabilizing a short-lived bicyclic intermediate on the lactone isomerization reaction. An analysis of the reaction kinetics showed that Cc XylC complexed with Fe2+ can speed up the hydrolysis of d-xylono-1,4-lactone by 100-fold and that of d-glucono-1,5-lactone by 10-fold as compared to the nonenzymatic reaction. To our knowledge, this is the first discovery of a nonheme mononuclear iron-binding enzyme that catalyzes an ester bond hydrolysis reaction.


Asunto(s)
Proteínas Bacterianas/química , Hidrolasas de Éster Carboxílico/química , Caulobacter crescentus/enzimología , Proteínas Bacterianas/metabolismo , Hidrolasas de Éster Carboxílico/metabolismo , Gluconatos/química , Hidrólisis , Hierro/química , Hierro/metabolismo , Cinética , Lactonas/química , Espectrometría de Masas/métodos , Unión Proteica
4.
Appl Microbiol Biotechnol ; 105(16-17): 6215-6228, 2021 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-34410440

RESUMEN

Deoxyribose-5-phosphate aldolases (DERAs, EC 4.1.2.4) are acetaldehyde-dependent, Class I aldolases catalyzing in nature a reversible aldol reaction between an acetaldehyde donor (C2 compound) and glyceraldehyde-3-phosphate acceptor (C3 compound, C3P) to generate deoxyribose-5-phosphate (C5 compound, DR5P). DERA enzymes have been found to accept also other types of aldehydes as their donor, and in particular as acceptor molecules. Consequently, DERA enzymes can be applied in C-C bond formation reactions to produce novel compounds, thus offering a versatile biocatalytic alternative for synthesis. DERA enzymes, found in all kingdoms of life, share a common TIM barrel fold despite the low overall sequence identity. The catalytic mechanism is well-studied and involves formation of a covalent enzyme-substrate intermediate. A number of protein engineering studies to optimize substrate specificity, enzyme efficiency, and stability of DERA aldolases have been published. These have employed various engineering strategies including structure-based design, directed evolution, and recently also machine learning-guided protein engineering. For application purposes, enzyme immobilization and usage of whole cell catalysis are preferred methods as they improve the overall performance of the biocatalytic processes, including often also the stability of the enzyme. Besides single-step enzymatic reactions, DERA aldolases have also been applied in multi-enzyme cascade reactions both in vitro and in vivo. The DERA-based applications range from synthesis of commodity chemicals and flavours to more complicated and high-value pharmaceutical compounds. KEY POINTS: • DERA aldolases are versatile biocatalysts able to make new C-C bonds. • Synthetic utility of DERAs has been improved by protein engineering approaches. • Computational methods are expected to speed up the future DERA engineering efforts.


Asunto(s)
Aldehído-Liasas , Ribosamonofosfatos , Aldehído-Liasas/genética , Aldehído-Liasas/metabolismo , Fructosa-Bifosfato Aldolasa , Especificidad por Sustrato
5.
Appl Microbiol Biotechnol ; 104(24): 10515-10529, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33147349

RESUMEN

In this work, deoxyribose-5-phosphate aldolase (Ec DERA, EC 4.1.2.4) from Escherichia coli was chosen as the protein engineering target for improving the substrate preference towards smaller, non-phosphorylated aldehyde donor substrates, in particular towards acetaldehyde. The initial broad set of mutations was directed to 24 amino acid positions in the active site or in the close vicinity, based on the 3D complex structure of the E. coli DERA wild-type aldolase. The specific activity of the DERA variants containing one to three amino acid mutations was characterised using three different substrates. A novel machine learning (ML) model utilising Gaussian processes and feature learning was applied for the 3rd mutagenesis round to predict new beneficial mutant combinations. This led to the most clear-cut (two- to threefold) improvement in acetaldehyde (C2) addition capability with the concomitant abolishment of the activity towards the natural donor molecule glyceraldehyde-3-phosphate (C3P) as well as the non-phosphorylated equivalent (C3). The Ec DERA variants were also tested on aldol reaction utilising formaldehyde (C1) as the donor. Ec DERA wild-type was shown to be able to carry out this reaction, and furthermore, some of the improved variants on acetaldehyde addition reaction turned out to have also improved activity on formaldehyde. KEY POINTS: • DERA aldolases are promiscuous enzymes. • Synthetic utility of DERA aldolase was improved by protein engineering approaches. • Machine learning methods aid the protein engineering of DERA.


Asunto(s)
Escherichia coli , Fructosa-Bifosfato Aldolasa , Aldehído-Liasas/genética , Aldehído-Liasas/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Fructosa-Bifosfato Aldolasa/genética , Aprendizaje Automático , Ingeniería de Proteínas , Especificidad por Sustrato
6.
J Biol Chem ; 292(47): 19315-19327, 2017 11 24.
Artículo en Inglés | MEDLINE | ID: mdl-28974575

RESUMEN

Bifunctional glycoside hydrolases have potential for cost-savings in enzymatic decomposition of plant cell wall polysaccharides for biofuels and bio-based chemicals. The N-terminal GH10 domain of a bifunctional multimodular enzyme CbXyn10C/Cel48B from Caldicellulosiruptor bescii is an enzyme able to degrade xylan and cellulose simultaneously. However, the molecular mechanism underlying its substrate promiscuity has not been elucidated. Herein, we discovered that the binding cleft of CbXyn10C would have at least six sugar-binding subsites by using isothermal titration calorimetry analysis of the inactive E140Q/E248Q mutant with xylo- and cello-oligosaccharides. This was confirmed by determining the catalytic efficiency of the wild-type enzyme on these oligosaccharides. The free form and complex structures of CbXyn10C with xylose- or glucose-configured oligosaccharide ligands were further obtained by crystallographic analysis and molecular modeling and docking. CbXyn10C was found to have a typical (ß/α)8-TIM barrel fold and "salad-bowl" shape of GH10 enzymes. In complex structures with xylo-oligosaccharides, seven sugar-binding subsites were found, and many residues responsible for substrate interactions were identified. Site-directed mutagenesis indicated that 6 and 10 amino acid residues were key residues for xylan and cellulose hydrolysis, respectively. The most important residues are centered on subsites -2 and -1 near the cleavage site, whereas residues playing moderate roles could be located at more distal regions of the binding cleft. Manipulating the residues interacting with substrates in the distal regions directly or indirectly improved the activity of CbXyn10C on xylan and cellulose. Most of the key residues for cellulase activity are conserved across GH10 xylanases. Revisiting randomly selected GH10 enzymes revealed unreported cellulase activity, indicating that the dual function may be a more common phenomenon than has been expected.


Asunto(s)
Celulosa/metabolismo , Endo-1,4-beta Xilanasas/química , Endo-1,4-beta Xilanasas/metabolismo , Firmicutes/enzimología , Secuencia de Aminoácidos , Biocatálisis , Dominio Catalítico , Cristalografía por Rayos X , Endo-1,4-beta Xilanasas/genética , Hidrólisis , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Mutación , Unión Proteica , Conformación Proteica , Homología de Secuencia , Especificidad por Sustrato
7.
Chembiochem ; 19(22): 2348-2352, 2018 11 16.
Artículo en Inglés | MEDLINE | ID: mdl-30204291

RESUMEN

Catechol oxidases and tyrosinases are coupled binuclear copper enzymes that oxidize various o-diphenolic compounds to corresponding o-quinones. Tyrosinases have an additional monooxygenation ability to hydroxylate monophenol to o-diphenol. It is still not clear what causes the difference in the catalytic activities. We solved a complex structure of Aspergillus oryzae catechol oxidase with resorcinol bound into the active site. Catalytic activity of A. oryzae catechol oxidase was studied, for the first time, by high-resolution FT-ICR mass spectrometry to shed light on the reaction mechanism. The enzyme was also found to catalyze monooxygenation of small phenolics, which provides a novel perspective for the discussion of differences in the catalytic activity between tyrosinases and catechol oxidases. According to the results, two binding modes for resorcinol are suggested and a reaction mechanism for coupled binuclear copper enzymes is discussed.


Asunto(s)
Aspergillus oryzae/enzimología , Catecol Oxidasa , Monofenol Monooxigenasa/metabolismo , Sitios de Unión , Catálisis , Dominio Catalítico , Catecol Oxidasa/química , Catecol Oxidasa/metabolismo , Cobre/química , Cristalografía por Rayos X , Modelos Moleculares , Oxidación-Reducción , Conformación Proteica , Especificidad por Sustrato
8.
Appl Microbiol Biotechnol ; 100(17): 7549-63, 2016 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-27102126

RESUMEN

We describe here the identification and characterization of two novel enzymes belonging to the IlvD/EDD protein family, the D-xylonate dehydratase from Caulobacter crescentus, Cc XyDHT, (EC 4.2.1.82), and the L-arabonate dehydratase from Rhizobium leguminosarum bv. trifolii, Rl ArDHT (EC 4.2.1.25), that produce the corresponding 2-keto-3-deoxy-sugar acids. There is only a very limited amount of characterization data available on pentonate dehydratases, even though the enzymes from these oxidative pathways have potential applications with plant biomass pentose sugars. The two bacterial enzymes share 41 % amino acid sequence identity and were expressed and purified from Escherichia coli as homotetrameric proteins. Both dehydratases were shown to accept pentonate and hexonate sugar acids as their substrates and require Mg(2+) for their activity. Cc XyDHT displayed the highest activity on D-xylonate and D-gluconate, while Rl ArDHT functioned best on D-fuconate, L-arabonate and D-galactonate. The configuration of the OH groups at C2 and C3 position of the sugar acid were shown to be critical, and the C4 configuration also contributed substantially to the substrate recognition. The two enzymes were also shown to contain an iron-sulphur [Fe-S] cluster. Our phylogenetic analysis and mutagenesis studies demonstrated that the three conserved cysteine residues in the aldonic acid dehydratase group of IlvD/EDD family members, those of C60, C128 and C201 in Cc XyDHT, and of C59, C127 and C200 in Rl ArDHT, are needed for coordination of the [Fe-S] cluster. The iron-sulphur cluster was shown to be crucial for the catalytic activity (kcat) but not for the substrate binding (Km) of the two pentonate dehydratases.


Asunto(s)
Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Caulobacter crescentus/enzimología , Hidroliasas/genética , Hidroliasas/metabolismo , Rhizobium leguminosarum/enzimología , Secuencia de Aminoácidos , Arabinosa/metabolismo , Clonación Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Gluconatos/metabolismo , Alineación de Secuencia , Xilosa/metabolismo
9.
Biochem J ; 472(3): 297-307, 2015 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-26438878

RESUMEN

Aldose-aldose oxidoreductase (Cc AAOR) is a recently characterized enzyme from the bacterial strain Caulobacter crescentus CB15 belonging to the glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Cc AAOR catalyses the oxidation and reduction of a panel of aldose monosaccharides using a tightly bound NADP(H) cofactor that is regenerated in the catalytic cycle. Furthermore, Cc AAOR can also oxidize 1,4-linked oligosaccharides. In the present study, we present novel crystal structures of the dimeric Cc AAOR in complex with the cofactor and glycerol, D-xylose, D-glucose, maltotriose and D-sorbitol determined to resolutions of 2.0, 1.8, 1.7, 1.9 and 1.8 Å (1 Å=0.1 nm), respectively. These complex structures allowed for a detailed analysis of the ligand-binding interactions. The structures showed that the C1 carbon of a substrate, which is either reduced or oxidized, is close to the reactive C4 carbon of the nicotinamide ring of NADP(H). In addition, the O1 hydroxy group of the substrate, which is either protonated or deprotonated, is unexpectedly close to both Lys(104) and Tyr(189), which may both act as a proton donor or acceptor. This led us to hypothesize that this intriguing feature could be beneficial for Cc AAOR to catalyse the reduction of a linear form of a monosaccharide substrate and the oxidation of a pyranose form of the same substrate in a reaction cycle, during which the bound cofactor is regenerated.


Asunto(s)
Caulobacter crescentus/enzimología , Oxidorreductasas/química , Proteínas Bacterianas , Catálisis , Cristalografía por Rayos X , Oxidación-Reducción , Relación Estructura-Actividad
10.
Biochemistry ; 53(51): 8052-60, 2014 Dec 30.
Artículo en Inglés | MEDLINE | ID: mdl-25454257

RESUMEN

Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both d-glucuronic and d-galacturonic acid. The corresponding gene coding for At keto-deoxy-d-galactarate (KDG) dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterized. Here, we present the kinetic characterization and crystal structure of At KDG dehydratase, which catalyzes the next step, the decarboxylating hydrolyase reaction of KDG to produce α-ketoglutaric semialdehyde (α-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 Å, 1.5 Å, and 2.1 Å resolution, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.


Asunto(s)
Agrobacterium tumefaciens/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Hidroliasas/química , Hidroliasas/metabolismo , Agrobacterium tumefaciens/genética , Aldehído-Liasas/química , Aldehído-Liasas/genética , Aldehído-Liasas/metabolismo , Proteínas Arqueales/química , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Proteínas Bacterianas/genética , Dominio Catalítico/genética , Cristalografía por Rayos X , Hidroliasas/genética , Concentración de Iones de Hidrógeno , Cinética , Redes y Vías Metabólicas , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Conformación Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Especificidad por Sustrato , Azúcares Ácidos/química , Azúcares Ácidos/metabolismo , Sulfolobus solfataricus/enzimología , Sulfolobus solfataricus/genética , Espectrometría de Masas en Tándem
11.
ACS Omega ; 9(15): 17089-17096, 2024 Apr 16.
Artículo en Inglés | MEDLINE | ID: mdl-38645339

RESUMEN

In the development of proteins, aptamers, and molecular imprints for diagnostic purposes, a major goal is to obtain a molecule with both a high binding affinity and specificity for the target ligand. Cushing syndrome or Addison's disease can be diagnosed by cortisol level tests. We have previously characterized and solved the crystal structure of an anti-cortisol (17) Fab fragment having a high affinity to cortisol but also significant cross-reactivity to other glucocorticoids, especially the glucocorticoid drug prednisolone. We used native mass spectrometry (MS) to determine the binding affinities of nine steroid hormones to anti-cortisol (17) Fab, including steroidogenic precursors of cortisol. Based on the results, the number of hydroxyl groups in the structure of a steroid ligand plays a key role in the antigen recognition by the Fab fragment as the ligands with three hydroxyl groups, cortisol and prednisolone, had the highest affinities. The antibody affinity toward steroid hormones often decreases with a decrease in the number of hydroxyl groups in the structure. The presence of the hydroxyl group at position C11 increased the affinity more than did the other hydroxyl groups at positions C17 or C21. The binding affinities obtained by native MS were compared to the values determined by surface plasmon resonance (SPR), and the affinities were found to correlate well between these two techniques. Our study demonstrates that native MS with a large dynamic range and high sensitivity is a versatile tool for ligand binding studies of proteins.

12.
J Biol Inorg Chem ; 18(8): 917-29, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-24043469

RESUMEN

Catechol oxidases (EC 1.10.3.1) catalyse the oxidation of o-diphenols to their corresponding o-quinones. These oxidases contain two copper ions (CuA and CuB) within the so-called coupled type 3 copper site as found in tyrosinases (EC 1.14.18.1) and haemocyanins. The crystal structures of a limited number of bacterial and fungal tyrosinases and plant catechol oxidases have been solved. In this study, we present the first crystal structure of a fungal catechol oxidase from Aspergillus oryzae (AoCO4) at 2.5-Å resolution. AoCO4 belongs to the newly discovered family of short-tyrosinases, which are distinct from other tyrosinases and catechol oxidases because of their lack of the conserved C-terminal domain and differences in the histidine pattern for CuA. The sequence identity of AoCO4 with other structurally known enzymes is low (less than 30 %), and the crystal structure of AoCO4 diverges from that of enzymes belonging to the conventional tyrosinase family in several ways, particularly around the central α-helical core region. A diatomic oxygen moiety was identified as a bridging molecule between the two copper ions CuA and CuB separated by a distance of 4.2-4.3 Å. The UV/vis absorption spectrum of AoCO4 exhibits a distinct maximum of absorbance at 350 nm, which has been reported to be typical of the oxy form of type 3 copper enzymes.


Asunto(s)
Aspergillus oryzae/enzimología , Catecol Oxidasa/química , Secuencia de Aminoácidos , Aspergillus oryzae/química , Dominio Catalítico , Catecol Oxidasa/metabolismo , Cristalografía por Rayos X , Modelos Moleculares , Datos de Secuencia Molecular , Oxidación-Reducción , Oxidorreductasas/química , Oxidorreductasas/metabolismo , Conformación Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Alineación de Secuencia
13.
Bioresour Technol ; 372: 128695, 2023 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-36731612

RESUMEN

The efficient degradation of plant polysaccharides in agricultural waste requires xylanases with high catalytic activity. In this study, the C-terminal proline-rich GH10 xylanase XynA from sheep rumen was investigated using product analysis, structural characterization, truncated and site-directed mutagenesis, molecular dynamics simulation, and application evaluation, revealing that the proline-rich C-terminus contributes to the interaction at the substrate-binding pocket to reduce the binding free energy. Compared to the C-terminally truncated enzyme XynA-Tr, XynA has a more favorable conformation for proton transfer and affinity attack, facilitating the degradation of oligomeric and beechwood xylan without altering the hydrolysis pattern. Moreover, both the reduced sugar yield and weight loss of the pretreated wheat bran, corn cob, and corn stalk hydrolyzed by XynA for 12 h increased by more than 30 %. These findings are important to better understand the relationship between enzyme activities and their terminal regions and suggest candidate materials for lignocellulosic biomass utilization.


Asunto(s)
Endo-1,4-beta Xilanasas , Lignina , Animales , Ovinos , Endo-1,4-beta Xilanasas/metabolismo , Biomasa , Lignina/metabolismo , Polisacáridos , Xilanos/metabolismo
14.
Biotechnol Biofuels Bioprod ; 15(1): 147, 2022 Dec 28.
Artículo en Inglés | MEDLINE | ID: mdl-36578086

RESUMEN

Platform chemicals and polymer precursors can be produced via enzymatic pathways starting from lignocellulosic waste materials. The hemicellulose fraction of lignocellulose contains aldopentose sugars, such as D-xylose and L-arabinose, which can be enzymatically converted into various biobased products by microbial non-phosphorylated oxidative pathways. The Weimberg and Dahms pathways convert pentose sugars into α-ketoglutarate, or pyruvate and glycolaldehyde, respectively, which then serve as precursors for further conversion into a wide range of industrial products. In this review, we summarize the known three-dimensional structures of the enzymes involved in oxidative non-phosphorylative pathways of pentose catabolism. Key structural features and reaction mechanisms of a diverse set of enzymes responsible for the catalytic steps in the reactions are analysed and discussed.

15.
Protein Sci ; 31(2): 371-383, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-34761460

RESUMEN

Xylonolactonase Cc XylC from Caulobacter crescentus catalyzes the hydrolysis of the intramolecular ester bond of d-xylonolactone. We have determined crystal structures of Cc XylC in complex with d-xylonolactone isomer analogues d-xylopyranose and (r)-(+)-4-hydroxy-2-pyrrolidinone at high resolution. Cc XylC has a 6-bladed ß-propeller architecture, which contains a central open channel having the active site at one end. According to our previous native mass spectrometry studies, Cc XylC is able to specifically bind Fe2+ . The crystal structures, presented here, revealed an active site bound metal ion with an octahedral binding geometry. The side chains of three amino acid residues, Glu18, Asn146, and Asp196, which participate in binding of metal ion are located in the same plane. The solved complex structures allowed suggesting a reaction mechanism for intramolecular ester bond hydrolysis in which the major contribution for catalysis arises from the carbonyl oxygen coordination of the xylonolactone substrate to the Fe2+ . The structure of Cc XylC was compared with eight other ester hydrolases of the ß-propeller hydrolase family. The previously published crystal structures of other ß-propeller hydrolases contain either Ca2+ , Mg2+ , or Zn2+ and show clear similarities in ligand and metal ion binding geometries to that of Cc XylC. It would be interesting to reinvestigate the metal binding specificity of these enzymes and clarify whether they are also able to use Fe2+ as a catalytic metal. This could further expand our understanding of utilization of Fe2+ not only in oxidative enzymes but also in hydrolases.


Asunto(s)
Hidrolasas de Éster Carboxílico , Caulobacter crescentus , Hidrolasas de Éster Carboxílico/química , Hidrolasas de Éster Carboxílico/metabolismo , Dominio Catalítico , Caulobacter crescentus/enzimología , Cristalografía por Rayos X , Hidrolasas , Hidrólisis , Hierro , Lactonas/química , Lactonas/metabolismo
16.
Bioresour Technol ; 358: 127434, 2022 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-35680086

RESUMEN

The recalcitrance of cellulosic biomass greatly hinders its enzymatic degradation. Expansins induce cell wall loosening and promote efficient cellulose utilization; however, the molecular mechanism underlying their action is not well understood. In this study, TlEXLX1, a fungal expansin from Talaromyces leycettanus JCM12802, was characterized in terms of phylogeny, synergy, structure, and mechanism of action. TlEXLX1 displayed varying degrees of synergism with commercial cellulase in the pretreatment of corn straw and filter paper. TlEXLX1 binds to cellulose via domain 2, mediated by CH-π interactions with residues Tyr291, Trp292, and Tyr327. Residues Asp237, Glu238, and Asp248 in domain 1 form hydrogen bonds with glucose units and break the inherent hydrogen bonding within the cellulose matrix. This study identified the expansin amino acid residues crucial for cellulose binding, and elucidated the structure and function of expansins in cell wall networks; this has potential applications in biomass utilization.


Asunto(s)
Celulasa , Celulosa , Proteínas Bacterianas/metabolismo , Pared Celular/metabolismo , Celulasa/metabolismo , Celulosa/química , Hidrólisis
17.
Toxins (Basel) ; 14(7)2022 06 29.
Artículo en Inglés | MEDLINE | ID: mdl-35878178

RESUMEN

The fungal secondary metabolite patulin is a mycotoxin widespread in foods and beverages which poses a serious threat to human health. However, no enzyme was known to be able to degrade this mycotoxin. For the first time, we discovered that a manganese peroxidase (MrMnP) from Moniliophthora roreri can efficiently degrade patulin. The MrMnP gene was cloned into pPICZα(A) and then the recombinant plasmid was transformed into Pichia pastoris X-33. The recombinant strain produced extracellular manganese peroxidase with an activity of up to 3659.5 U/L. The manganese peroxidase MrMnP was able to rapidly degrade patulin, with hydroascladiol appearing as a main degradation product. Five mg/L of pure patulin were completely degraded within 5 h. Moreover, up to 95% of the toxin was eliminated in a simulated patulin-contaminated apple juice after 24 h. Using Escherichia coli as a model, it was demonstrated that the deconstruction of patulin led to detoxification. Collectively, these traits make MrMnP an intriguing candidate useful in enzymatic detoxification of patulin in foods and beverages.


Asunto(s)
Malus , Patulina , Agaricales , Bebidas/análisis , Contaminación de Alimentos/análisis , Humanos , Malus/microbiología , Patulina/metabolismo , Peroxidasas , Saccharomycetales
18.
Biochemistry ; 50(21): 4396-8, 2011 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-21524088

RESUMEN

Laccases catalyze the oxidation of phenolic substrates and the concominant reduction of dioxygen to water. We used xenon as an oxygen probe in search of routes for the entry of dioxygen into the catalytic center. Two xenon-pressurized crystal structures of recombinant Melanocarpus albomyces laccase were determined, showing three hydrophobic Xe-binding sites located in domain C. The analysis of hydrophobic cavities in other laccase structures further suggested the preference of domain C for binding of hydrophobic species such as dioxygen, thus suggesting that the hydrophobic core of domain C could function as a channel through which dioxygen can enter the trinuclear copper center.


Asunto(s)
Ascomicetos/enzimología , Lacasa/metabolismo , Sondas Moleculares , Oxígeno/metabolismo , Xenón , Sitios de Unión , Dominio Catalítico , Gases , Modelos Moleculares , Proteínas Recombinantes/metabolismo
19.
J Struct Biol ; 174(1): 156-63, 2011 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-21130883

RESUMEN

We have determined the crystal structure of Trichoderma reesei (Hypocrea jecorina) ß-galactosidase (Tr-ß-gal) at a 1.2Å resolution and its complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4Å resolutions, respectively. Tr-ß-gal is a potential enzyme for lactose hydrolysis in the dairy industry and belongs to family 35 of the glycoside hydrolases (GH-35). The high resolution crystal structures of this six-domain enzyme revealed interesting features about the structure of Tr-ß-gal. We discovered conformational changes in the two loop regions in the active site, implicating a conformational selection-mechanism for the enzyme. In addition, the Glu200, an acid/base catalyst showed two different conformations which undoubtedly affect the pK(a) value of this residue and the catalytic mechanism. The electron density showed extensive glycosylation, suggesting a structure stabilizing role for glycans. The longest glycan showed an electron density that extends to the eighth monosaccharide unit in the extended chain. The Tr-ß-gal structure also showed a well-ordered structure for a unique octaserine motif on the surface loop of the fifth domain.


Asunto(s)
Cristalografía por Rayos X/métodos , Trichoderma/enzimología , beta-Galactosidasa/química , beta-Galactosidasa/metabolismo , Dominio Catalítico , Glicerol/metabolismo , Modelos Moleculares , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , beta-Galactosidasa/genética
20.
Artículo en Inglés | MEDLINE | ID: mdl-21636908

RESUMEN

Catechol oxidase is an enzyme that catalyzes the oxidation of o-diphenols to the corresponding o-quinones. It is a copper-containing enzyme with a binuclear copper active site. Here, the crystallization and multiple-wavelength anomalous dispersion data collection of catechol oxidase from the mould fungus Aspergillus oryzae are described. During the purification, three forms of the enzyme (39.3, 40.5 and 44.3 kDa) were obtained. A mixture of these three forms was initially crystallized and gave crystals that diffracted to 2.5 Šresolution and belonged to space group P3(2)21, with unit-cell parameters a = b = 118.9, c = 84.5 Å, α = ß = 90, γ = 120°. A preparation containing only the shorter form (39.3 kDa) produced crystals that diffracted to 2.9 Šresolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.8, b = 95.3, c = 139.5 Å, α = ß = γ = 90°.


Asunto(s)
Aspergillus oryzae/enzimología , Catecol Oxidasa/química , Cristalización , Cristalografía por Rayos X
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