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1.
J Biol Chem ; 300(3): 105749, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38354778

RESUMEN

Protein engineering and screening of processive fungal cellobiohydrolases (CBHs) remain challenging due to limited expression hosts, synergy-dependency, and recalcitrant substrates. In particular, glycoside hydrolase family 7 (GH7) CBHs are critically important for the bioeconomy and typically difficult to engineer. Here, we target the discovery of highly active natural GH7 CBHs and engineering of variants with improved activity. Using experimentally assayed activities of genome mined CBHs, we applied sequence and structural alignments to top performers to identify key point mutations linked to improved activity. From ∼1500 known GH7 sequences, an evolutionarily diverse subset of 57 GH7 CBH genes was expressed in Trichoderma reesei and screened using a multiplexed activity screening assay. Ten catalytically enhanced natural variants were identified, produced, purified, and tested for efficacy using industrially relevant conditions and substrates. Three key amino acids in CBHs with performance comparable or superior to Penicillium funiculosum Cel7A were identified and combinatorially engineered into P. funiculosum cel7a, expressed in T. reesei, and assayed on lignocellulosic biomass. The top performer generated using this combined approach of natural diversity genome mining, experimental assays, and computational modeling produced a 41% increase in conversion extent over native P. funiculosum Cel7A, a 55% increase over the current industrial standard T. reesei Cel7A, and 10% improvement over Aspergillus oryzae Cel7C, the best natural GH7 CBH previously identified in our laboratory.


Asunto(s)
Celulosa 1,4-beta-Celobiosidasa , Pruebas de Enzimas , Genoma Fúngico , Mutación , Ingeniería de Proteínas , Aspergillus oryzae/enzimología , Aspergillus oryzae/genética , Celulosa 1,4-beta-Celobiosidasa/química , Celulosa 1,4-beta-Celobiosidasa/clasificación , Celulosa 1,4-beta-Celobiosidasa/genética , Celulosa 1,4-beta-Celobiosidasa/metabolismo , Genoma Fúngico/genética , Ingeniería de Proteínas/métodos , Especificidad por Sustrato , Talaromyces/enzimología , Talaromyces/genética , Trichoderma/enzimología , Trichoderma/genética , Trichoderma/metabolismo , Biocatálisis
2.
Microb Cell Fact ; 23(1): 190, 2024 Jul 02.
Artículo en Inglés | MEDLINE | ID: mdl-38956607

RESUMEN

BACKGROUND: Carbonic anhydrase (CA) enzymes facilitate the reversible hydration of CO2 to bicarbonate ions and protons. Identifying efficient and robust CAs and expressing them in model host cells, such as Escherichia coli, enables more efficient engineering of these enzymes for industrial CO2 capture. However, expression of CAs in E. coli is challenging due to the possible formation of insoluble protein aggregates, or inclusion bodies. This makes the production of soluble and active CA protein a prerequisite for downstream applications. RESULTS: In this study, we streamlined the process of CA expression by selecting seven top CA candidates and used two bioinformatic tools to predict their solubility for expression in E. coli. The prediction results place these enzymes in two categories: low and high solubility. Our expression of high solubility score CAs (namely CA5-SspCA, CA6-SazCAtrunc, CA7-PabCA and CA8-PhoCA) led to significantly higher protein yields (5 to 75 mg purified protein per liter) in flask cultures, indicating a strong correlation between the solubility prediction score and protein expression yields. Furthermore, phylogenetic tree analysis demonstrated CA class-specific clustering patterns for protein solubility and production yields. Unexpectedly, we also found that the unique N-terminal, 11-amino acid segment found after the signal sequence (not present in its homologs), was essential for CA6-SazCA activity. CONCLUSIONS: Overall, this work demonstrated that protein solubility prediction, phylogenetic tree analysis, and experimental validation are potent tools for identifying top CA candidates and then producing soluble, active forms of these enzymes in E. coli. The comprehensive approaches we report here should be extendable to the expression of other heterogeneous proteins in E. coli.


Asunto(s)
Anhidrasas Carbónicas , Biología Computacional , Escherichia coli , Solubilidad , Escherichia coli/genética , Escherichia coli/metabolismo , Escherichia coli/enzimología , Anhidrasas Carbónicas/metabolismo , Anhidrasas Carbónicas/genética , Biología Computacional/métodos , Filogenia , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/genética , Dióxido de Carbono/metabolismo
3.
Plant Cell ; 32(7): 2367-2382, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32354790

RESUMEN

Xylans are a major component of plant cell walls. O-Acetyl moieties are the dominant backbone substituents of glucuronoxylan in dicots and play a major role in the polymer-polymer interactions that are crucial for wall architecture and normal plant development. Here, we describe the biochemical, structural, and mechanistic characterization of Arabidopsis (Arabidopsis thaliana) xylan O-acetyltransferase 1 (XOAT1), a member of the plant-specific Trichome Birefringence Like (TBL) family. Detailed characterization of XOAT1-catalyzed reactions by real-time NMR confirms that it exclusively catalyzes the 2-O-acetylation of xylan, followed by nonenzymatic acetyl migration to the O-3 position, resulting in products that are monoacetylated at both O-2 and O-3 positions. In addition, we report the crystal structure of the catalytic domain of XOAT1, which adopts a unique conformation that bears some similarities to the α/ß/α topology of members of the GDSL-like lipase/acylhydrolase family. Finally, we use a combination of biochemical analyses, mutagenesis, and molecular simulations to show that XOAT1 catalyzes xylan acetylation through formation of an acyl-enzyme intermediate, Ac-Ser-216, by a double displacement bi-bi mechanism involving a Ser-His-Asp catalytic triad and unconventionally uses an Arg residue in the formation of an oxyanion hole.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Polisacáridos/metabolismo , Acetilación , Acetiltransferasas/química , Acetiltransferasas/genética , Acetiltransferasas/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Arginina/metabolismo , Catálisis , Dominio Catalítico , Cristalografía por Rayos X , Células HEK293 , Humanos , Espectroscopía de Resonancia Magnética , Proteínas de la Membrana , Modelos Moleculares , Mutación , Conformación Proteica , Xilanos/metabolismo
4.
Int J Mol Sci ; 23(11)2022 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-35682749

RESUMEN

Microbial conversion of biomass relies on a complex combination of enzyme systems promoting synergy to overcome biomass recalcitrance. Some thermophilic bacteria have been shown to exhibit particularly high levels of cellulolytic activity, making them of particular interest for biomass conversion. These bacteria use varying combinations of CAZymes that vary in complexity from a single catalytic domain to large multi-modular and multi-functional architectures to deconstruct biomass. Since the discovery of CelA from Caldicellulosiruptor bescii which was identified as one of the most active cellulase so far identified, the search for efficient multi-modular and multi-functional CAZymes has intensified. One of these candidates, GuxA (previously Acel_0615), was recently shown to exhibit synergy with other CAZymes in C. bescii, leading to a dramatic increase in growth on biomass when expressed in this host. GuxA is a multi-modular and multi-functional enzyme from Acidothermus cellulolyticus whose catalytic domains include a xylanase/endoglucanase GH12 and an exoglucanase GH6, representing a unique combination of these two glycoside hydrolase families in a single CAZyme. These attributes make GuxA of particular interest as a potential candidate for thermophilic industrial enzyme preparations. Here, we present a more complete characterization of GuxA to understand the mechanism of its activity and substrate specificity. In addition, we demonstrate that GuxA exhibits high levels of synergism with E1, a companion endoglucanase from A. cellulolyticus. We also present a crystal structure of one of the GuxA domains and dissect the structural features that might contribute to its thermotolerance.


Asunto(s)
Actinobacteria , Actinomycetales , Celulasa , Biomasa , Celulasa/química , Celulosa/química , Humanos
5.
Proteins ; 89(12): 1647-1672, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34561912

RESUMEN

The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.


Asunto(s)
Modelos Moleculares , Conformación Proteica , Proteínas/química , Programas Informáticos , Secuencia de Aminoácidos , Biología Computacional , Microscopía por Crioelectrón , Cristalografía por Rayos X , Análisis de Secuencia de Proteína
7.
Appl Environ Microbiol ; 85(3)2019 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-30478233

RESUMEN

Genomes of extremely thermophilic Caldicellulosiruptor species encode novel cellulose binding proteins, called tapirins, located proximate to the type IV pilus locus. The C-terminal domain of Caldicellulosiruptor kronotskyensis tapirin 0844 (Calkro_0844) is structurally unique and has a cellulose binding affinity akin to that seen with family 3 carbohydrate binding modules (CBM3s). Here, full-length and C-terminal versions of tapirins from Caldicellulosiruptor bescii (Athe_1870), Caldicellulosiruptor hydrothermalis (Calhy_0908), Caldicellulosiruptor kristjanssonii (Calkr_0826), and Caldicellulosiruptor naganoensis (NA10_0869) were produced recombinantly in Escherichia coli and compared to Calkro_0844. All five tapirins bound to microcrystalline cellulose, switchgrass, poplar, and filter paper but not to xylan. Densitometry analysis of bound protein fractions visualized by SDS-PAGE revealed that Calhy_0908 and Calkr_0826 (from weakly cellulolytic species) associated with the cellulose substrates to a greater extent than Athe_1870, Calkro_0844, and NA10_0869 (from strongly cellulolytic species). Perhaps this relates to their specific needs to capture glucans released from lignocellulose by cellulases produced in Caldicellulosiruptor communities. Calkro_0844 and NA10_0869 share a higher degree of amino acid sequence identity (>80% identity) with each other than either does with Athe_1870 (∼50%). The levels of amino acid sequence identity of Calhy_0908 and Calkr_0826 to Calkro_0844 were only 16% and 36%, respectively, although the three-dimensional structures of their C-terminal binding regions were closely related. Unlike the parent strain, C. bescii mutants lacking the tapirin genes did not bind to cellulose following short-term incubation, suggesting a role in cell association with plant biomass. Given the scarcity of carbohydrates in neutral terrestrial hot springs, tapirins likely help scavenge carbohydrates from lignocellulose to support growth and survival of Caldicellulosiruptor species.IMPORTANCE The mechanisms by which microorganisms attach to and degrade lignocellulose are important to understand if effective approaches for conversion of plant biomass into fuels and chemicals are to be developed. Caldicellulosiruptor species grow on carbohydrates from lignocellulose at elevated temperatures and have biotechnological significance for that reason. Novel cellulose binding proteins, called tapirins, are involved in the way that Caldicellulosiruptor species interact with microcrystalline cellulose, and additional information about the diversity of these proteins across the genus, including binding affinity and three-dimensional structural comparisons, is provided here.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Proteínas Portadoras/química , Proteínas Portadoras/metabolismo , Celulosa/metabolismo , Firmicutes/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Proteínas Portadoras/genética , Celulosa/química , Firmicutes/química , Firmicutes/genética , Genoma Bacteriano , Manantiales de Aguas Termales/microbiología , Calor , Dominios Proteicos
8.
Plant J ; 91(6): 931-949, 2017 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-28670741

RESUMEN

The mechanistic underpinnings of the complex process of plant polysaccharide biosynthesis are poorly understood, largely because of the resistance of glycosyltransferase (GT) enzymes to structural characterization. In Arabidopsis thaliana, a glycosyl transferase family 37 (GT37) fucosyltransferase 1 (AtFUT1) catalyzes the regiospecific transfer of terminal 1,2-fucosyl residues to xyloglucan side chains - a key step in the biosynthesis of fucosylated sidechains of galactoxyloglucan. We unravel the mechanistic basis for fucosylation by AtFUT1 with a multipronged approach involving protein expression, X-ray crystallography, mutagenesis experiments and molecular simulations. Mammalian cell culture expressions enable the sufficient production of the enzyme for X-ray crystallography, which reveals the structural architecture of AtFUT1 in complex with bound donor and acceptor substrate analogs. The lack of an appropriately positioned active site residue as a catalytic base leads us to propose an atypical water-mediated fucosylation mechanism facilitated by an H-bonded network, which is corroborated by mutagenesis experiments as well as detailed atomistic simulations.


Asunto(s)
Arabidopsis/enzimología , Fucosiltransferasas/química , Glucanos/química , Modelos Estructurales , Xilanos/química , Arabidopsis/genética , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Cristalografía por Rayos X , Fucosiltransferasas/genética , Fucosiltransferasas/metabolismo , Glicosilación , Simulación de Dinámica Molecular , Mutagénesis , Agua/metabolismo , Galactósido 2-alfa-L-Fucosiltransferasa
9.
J Biol Chem ; 290(17): 10645-56, 2015 Apr 24.
Artículo en Inglés | MEDLINE | ID: mdl-25720489

RESUMEN

A variety of catalytic and noncatalytic protein domains are deployed by select microorganisms to deconstruct lignocellulose. These extracellular proteins are used to attach to, modify, and hydrolyze the complex polysaccharides present in plant cell walls. Cellulolytic enzymes, often containing carbohydrate-binding modules, are key to this process; however, these enzymes are not solely responsible for attachment. Few mechanisms of attachment have been discovered among bacteria that do not form large polypeptide structures, called cellulosomes, to deconstruct biomass. In this study, bioinformatics and proteomics analyses identified unique, discrete, hypothetical proteins ("tapirins," origin from Maori: to join), not directly associated with cellulases, that mediate attachment to cellulose by species in the noncellulosomal, extremely thermophilic bacterial genus Caldicellulosiruptor. Two tapirin genes are located directly downstream of a type IV pilus operon in strongly cellulolytic members of the genus, whereas homologs are absent from the weakly cellulolytic Caldicellulosiruptor species. Based on their amino acid sequence, tapirins are specific to these extreme thermophiles. Tapirins are also unusual in that they share no detectable protein domain signatures with known polysaccharide-binding proteins. Adsorption isotherm and trans vivo analyses demonstrated the carbohydrate-binding module-like affinity of the tapirins for cellulose. Crystallization of a cellulose-binding truncation from one tapirin indicated that these proteins form a long ß-helix core with a shielded hydrophobic face. Furthermore, they are structurally unique and define a new class of polysaccharide adhesins. Strongly cellulolytic Caldicellulosiruptor species employ tapirins to complement substrate-binding proteins from the ATP-binding cassette transporters and multidomain extracellular and S-layer-associated glycoside hydrolases to process the carbohydrate content of lignocellulose.


Asunto(s)
Bacterias/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Celulosa/metabolismo , Adsorción , Bacterias/genética , Bacterias/ultraestructura , Adhesión Bacteriana/fisiología , Proteínas Bacterianas/genética , Sitios de Unión , Fimbrias Bacterianas/metabolismo , Genes Bacterianos , Modelos Moleculares , Filogenia , Plantas/microbiología , Estructura Terciaria de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
10.
Proteins ; 84(3): 295-304, 2016 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-26572060

RESUMEN

Family 48 cellobiohydrolases are some of the most abundant glycoside hydrolases in nature. They are able to degrade cellulosic biomass and therefore serve as good enzyme candidates for biofuel production. Family 48 cellulases hydrolyze cellulose chains via a processive mechanism, and produce end products composed primarily of cellobiose as well as other cellooligomers (dp ≤ 4). The challenge of utilizing cellulases in biofuel production lies in their extremely slow turnover rate. A factor contributing to the low enzyme activity is suggested to be product binding to enzyme and the resulting performance inhibition. In this study, we quantitatively evaluated the product inhibitory effect of four family 48 glycoside hydrolases using molecular dynamics simulations and product expulsion free-energy calculations. We also suggested a series of single mutants of the four family 48 glycoside hydrolases with theoretically reduced level of product inhibition. The theoretical calculations provide a guide for future experimental studies designed to produce mutant cellulases with enhanced activity.


Asunto(s)
Proteínas Bacterianas/química , Glicósido Hidrolasas/química , Sustitución de Aminoácidos , Proteínas Bacterianas/genética , Dominio Catalítico , Inhibidores Enzimáticos/química , Glicósido Hidrolasas/genética , Simulación de Dinámica Molecular , Estructura Secundaria de Proteína , Homología Estructural de Proteína , Termodinámica
11.
Photosynth Res ; 128(1): 45-57, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26526668

RESUMEN

The green alga Chlamydomonas reinhardtii contains six plastidic [2Fe2S]-cluster ferredoxins (FDXs), with FDX1 as the predominant isoform under photoautotrophic growth. FDX2 is highly similar to FDX1 and has been shown to interact with specific enzymes (such as nitrite reductase), as well as to share interactors with FDX1, such as the hydrogenases (HYDA), ferredoxin:NAD(P) reductase I (FNR1), and pyruvate:ferredoxin oxidoreductase (PFR1), albeit performing at low catalytic rates. Here we report the FDX2 crystal structure solved at 1.18 Å resolution. Based on differences between the Chlorella fusca FDX1 and C. reinhardtii FDX2 structures, we generated and purified point-mutated versions of the FDX2 protein and assayed them in vitro for their ability to catalyze hydrogen and NADPH photo-production. The data show that structural differences at two amino acid positions contribute to functional differences between FDX1 and FDX2, suggesting that FDX2 might have evolved from FDX1 toward a different physiological role in the cell. Moreover, we demonstrate that the mutations affect both the midpoint potentials of the FDX and kinetics of the FNR reaction, possibly due to altered binding between FDX and FNR. An effect on H2 photo-production rates was also observed, although the kinetics of the reaction were not further characterized.


Asunto(s)
Chlamydomonas reinhardtii/química , Ferredoxinas/química , Ferredoxinas/metabolismo , Sitios de Unión , Dominio Catalítico , Cristalografía por Rayos X , Escherichia coli/genética , Ferredoxina-NADP Reductasa/metabolismo , Ferredoxinas/genética , Hidrógeno/metabolismo , Modelos Moleculares , Mutagénesis Sitio-Dirigida , NADP/metabolismo , Oxidación-Reducción , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Homología de Secuencia de Aminoácido , Homología Estructural de Proteína
12.
Biotechnol Bioeng ; 111(4): 664-73, 2014 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-24264519

RESUMEN

Lignocellulosic biomass is a potential source of sustainable transportation fuels, but efficient enzymatic saccharification of cellulose is a key challenge in its utilization. Cellulases from the glycoside hydrolase (GH) family 48 constitute an important component of bacterial biomass degrading systems and structures of three enzymes from this family have been previously published. We report a new crystal structure of TfCel48A, a reducing end directed exocellulase from Thermobifida fusca, which shows that this enzyme shares important structural features with the other members of the GH48 family. The active site tunnel entrance of the known GH48 exocellulases is enriched in aromatic residues, which are known to interact well with anhydroglucose units of cellulose. We carried out site-directed mutagenesis studies of these aromatic residues (Y97, F195, Y213, and W313) along with two non-aromatic residues (N212 and S311) also located around the tunnel entrance and a W315 residue inside the active site tunnel. Only the aromatic residues located around the tunnel entrance appear to be important for the ability of TfCel48A to access individual cellulose chains on bacterial cellulose (BC), a crystalline substrate. Both Trp residues were found to be important for the processivity of TfCel48A on BC and phosphoric acid swollen cellulose (PASC), but only W313 appears to play a role in the ability of the enzyme to access individual cellulose chains in BC. When acting on BC, reduced processivity was found to correlate with reduced enzyme activity. The reverse, however, is true when PASC is the substrate. Presumably, higher density of available cellulose chain ends and the amorphous nature of PASC explain the increased initial activity of mutants with lower processivity.


Asunto(s)
Actinomycetales/enzimología , Proteínas Bacterianas/química , Celulasas/química , Actinomycetales/genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Celulasas/genética , Celulasas/metabolismo , Cristalografía por Rayos X , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Conformación Proteica
13.
J Biol Chem ; 287(49): 41068-77, 2012 Nov 30.
Artículo en Inglés | MEDLINE | ID: mdl-23055526

RESUMEN

Currently, the cost of cellulase enzymes remains a key economic impediment to commercialization of biofuels. Enzymes from glycoside hydrolase family 48 (GH48) are a critical component of numerous natural lignocellulose-degrading systems. Although computational mining of large genomic data sets is a promising new approach for identifying novel cellulolytic activities, current computational methods are unable to distinguish between cellulases and enzymes with different substrate specificities that belong to the same protein family. We show that by using a robust computational approach supported by experimental studies, cellulases and non-cellulases can be effectively identified within a given protein family. Phylogenetic analysis of GH48 showed non-monophyletic distribution, an indication of horizontal gene transfer. Enzymatic function of GH48 proteins coded by horizontally transferred genes was verified experimentally, which confirmed that these proteins are cellulases. Computational and structural studies of GH48 enzymes identified structural elements that define cellulases and can be used to computationally distinguish them from non-cellulases. We propose that the structural element that can be used for in silico discrimination between cellulases and non-cellulases belonging to GH48 is an ω-loop located on the surface of the molecule and characterized by highly conserved rare amino acids. These markers were used to screen metagenomics data for "true" cellulases.


Asunto(s)
Celulasa/química , Glicósido Hidrolasas/química , Celulosa/química , Dicroismo Circular , Clonación Molecular , Clostridium/enzimología , Biología Computacional/métodos , Secuencia Conservada , Evolución Molecular , Transferencia de Gen Horizontal , Genómica , Modelos Genéticos , Filogenia , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Análisis de Secuencia de ADN , Programas Informáticos
14.
Acta Crystallogr D Biol Crystallogr ; 69(Pt 4): 534-9, 2013 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-23519661

RESUMEN

The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase catalytic module (PL3-cat) has been structurally described and synergistic digestion studies with C. bescii cellulase A have been performed on unpretreated biomass. The X-ray structure of PL3-cat was determined at 1.6 Å resolution (PDB entry 4ew9) in complex with the products of trigalacturonic acid. Comparison with family 1 pectate lyase (PL1) structures shows that the active site of the PL3 catalytic module is considerably different. However, on superimposing the identical sugar rings at the -2 subsites conserved interactions could be identified. Interestingly, only one catalytic residue, the lysine that donates the proton to the carboxylate group in the ß-elimination reaction of PL1 (Lys108 in PL3-cat), is conserved in PL3 and there is no arginine to abstract the proton from the C5 carbon of the galactouronate ring. This suggests that the reaction mechanism of PL3 requires different catalytic residues. Most interestingly, comparison with other proton-abstraction reactions reveals that in PL3 the α-proton is abstracted by a lysine, in a striking similarity to enolases. These observations led us to propose that in PL3-cat Lys108 is the catalytic base, Glu84 is the catalytic acid and an acidified water molecule completes the anti ß-elimination reaction by protonating the O4 atom of the substrate. Also, our digestion experiments with unpretreated switchgrass show that the loadings of C. bescii cellobiohydrolase A (CelA) can be lowered by the addition of PL3 to the reaction mixture. This result suggests that PL3 can significantly improve the deconstruction of unpretreated biomass by allowing other enzymes to better access their preferred substrates.


Asunto(s)
Bacillales/enzimología , Polisacárido Liasas/química , Biocatálisis , Celulasa/química , Cristalografía por Rayos X , Pectinas/química , Pectinas/metabolismo , Polisacárido Liasas/metabolismo , Relación Estructura-Actividad , Especificidad por Sustrato
15.
Artículo en Inglés | MEDLINE | ID: mdl-24316824

RESUMEN

Here, a 1.82 Šresolution X-ray structure of a glycoside hydrolase family 74 (GH74) enzyme from Acidothermus cellulolyticus is reported. The resulting structure was refined to an R factor of 0.150 and an Rfree of 0.196. Structural analysis shows that five related structures have been reported with a secondary-structure similarity of between 75 and 89%. The five similar structures were all either Clostridium thermocellum or Geotrichum sp. M128 GH74 xyloglucanases. Structural analysis indicates that the A. cellulolyticus GH74 enzyme is an endoxyloglucanase, as it lacks a characteristic loop that blocks one end of the active site in exoxyloglucanases. Superimposition with the C. thermocellum GH74 shows that Asp451 and Asp38 are the catalytic residues.


Asunto(s)
Actinomycetales/química , Proteínas Bacterianas/química , Glicósido Hidrolasas/química , Modelos Moleculares , Actinomycetales/enzimología , Actinomycetales/genética , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Clostridium thermocellum/química , Clostridium thermocellum/enzimología , Clostridium thermocellum/genética , Cristalografía por Rayos X , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Geotrichum/química , Geotrichum/enzimología , Geotrichum/genética , Glicósido Hidrolasas/genética , Glicósido Hidrolasas/metabolismo , Datos de Secuencia Molecular , Dominios y Motivos de Interacción de Proteínas , Estructura Secundaria de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia , Homología Estructural de Proteína
16.
J Biol Chem ; 286(39): 34023-35, 2011 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-21840996

RESUMEN

The CYTH superfamily of proteins is named after its two founding members, the CyaB adenylyl cyclase from Aeromonas hydrophila and the human 25-kDa thiamine triphosphatase. Because these proteins often form a closed ß-barrel, they are also referred to as triphosphate tunnel metalloenzymes (TTM). Functionally, they are characterized by their ability to bind triphosphorylated substrates and divalent metal ions. These proteins exist in most organisms and catalyze different reactions depending on their origin. Here we investigate structural and catalytic properties of the recombinant TTM protein from Nitrosomonas europaea (NeuTTM), a 19-kDa protein. Crystallographic data show that it crystallizes as a dimer and that, in contrast to other TTM proteins, it has an open ß-barrel structure. We demonstrate that NeuTTM is a highly specific inorganic triphosphatase, hydrolyzing tripolyphosphate (PPP(i)) with high catalytic efficiency in the presence of Mg(2+). These data are supported by native mass spectrometry analysis showing that the enzyme binds PPP(i) (and Mg-PPP(i)) with high affinity (K(d) < 1.5 µm), whereas it has a low affinity for ATP or thiamine triphosphate. In contrast to Aeromonas and Yersinia CyaB proteins, NeuTTM has no adenylyl cyclase activity, but it shares several properties with other enzymes of the CYTH superfamily, e.g. heat stability, alkaline pH optimum, and inhibition by Ca(2+) and Zn(2+) ions. We suggest a catalytic mechanism involving a catalytic dyad formed by Lys-52 and Tyr-28. The present data provide the first characterization of a new type of phosphohydrolase (unrelated to pyrophosphatases or exopolyphosphatases), able to hydrolyze inorganic triphosphate with high specificity.


Asunto(s)
Proteínas Bacterianas/química , Hidrolasas/química , Metaloproteínas/química , Nitrosomonas europaea/enzimología , Proteínas Bacterianas/genética , Catálisis , Hidrolasas/genética , Metaloproteínas/genética , Nitrosomonas europaea/genética , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Relación Estructura-Actividad
17.
Acta Crystallogr D Biol Crystallogr ; 68(Pt 3): 292-9, 2012 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-22349231

RESUMEN

The efficient deconstruction of lignocellulosic biomass remains a significant barrier to the commercialization of biofuels. Whereas most commercial plant cell-wall-degrading enzyme preparations used today are derived from fungi, the cellulosomal enzyme system from Clostridium thermocellum is an equally effective catalyst, yet of considerably different structure. A key difference between fungal enzyme systems and cellulosomal enzyme systems is that cellulosomal enzyme systems utilize self-assembled scaffolded multimodule enzymes to deconstruct biomass. Here, the possible function of the X1 modules in the complex multimodular enzyme system cellobiohydrolase A (CbhA) from C. thermocellum is explored. The crystal structures of the two X1 modules from C. thermocellum CbhA have been solved individually and together as one construct. The role that calcium may play in the stability of the X1 modules has also been investigated, as well as the possibility that they interact with each other. Furthermore, the results show that whereas the X1 modules do not seem to act as cellulose disruptors, they do aid in the thermostability of the CbhA complex, effectively allowing it to deconstruct cellulose at a higher temperature.


Asunto(s)
Celulosa 1,4-beta-Celobiosidasa/química , Celulosa/química , Celulosomas/enzimología , Clostridium thermocellum/enzimología , Complejos Multienzimáticos/química , Sitios de Unión , Biomasa , Celulosa 1,4-beta-Celobiosidasa/metabolismo , Cristalografía por Rayos X , Estructura Terciaria de Proteína
18.
Nature ; 440(7085): 833-7, 2006 Apr 06.
Artículo en Inglés | MEDLINE | ID: mdl-16598263

RESUMEN

The magnesium ion, Mg2+, is essential for myriad biochemical processes and remains the only major biological ion whose transport mechanisms remain unknown. The CorA family of magnesium transporters is the primary Mg2+ uptake system of most prokaryotes and a functional homologue of the eukaryotic mitochondrial magnesium transporter. Here we determine crystal structures of the full-length Thermotoga maritima CorA in an apparent closed state and its isolated cytoplasmic domain at 3.9 A and 1.85 A resolution, respectively. The transporter is a funnel-shaped homopentamer with two transmembrane helices per monomer. The channel is formed by an inner group of five helices and putatively gated by bulky hydrophobic residues. The large cytoplasmic domain forms a funnel whose wide mouth points into the cell and whose walls are formed by five long helices that are extensions of the transmembrane helices. The cytoplasmic neck of the pore is surrounded, on the outside of the funnel, by a ring of highly conserved positively charged residues. Two negatively charged helices in the cytoplasmic domain extend back towards the membrane on the outside of the funnel and abut the ring of positive charge. An apparent Mg2+ ion was bound between monomers at a conserved site in the cytoplasmic domain, suggesting a mechanism to link gating of the pore to the intracellular concentration of Mg2+.


Asunto(s)
Proteínas Bacterianas/química , Proteínas de Transporte de Catión/química , Cationes Bivalentes/metabolismo , Magnesio/metabolismo , Thermotoga maritima/química , Proteínas Bacterianas/metabolismo , Proteínas de Transporte de Catión/metabolismo , Cristalización , Cristalografía por Rayos X , Canales Iónicos/química , Canales Iónicos/metabolismo , Modelos Moleculares , Estructura Secundaria de Proteína , Electricidad Estática
19.
Artículo en Inglés | MEDLINE | ID: mdl-21543854

RESUMEN

Here, a 2.0 Å resolution X-ray structure of Clostridium thermocellum cellulase K family 4 carbohydrate-binding module (CelK CBM4) is reported. The resulting structure was refined to an R factor of 0.212 and an R(free) of 0.274. Structural analysis shows that this new structure is very similar to the previously solved structure of C. thermocellum CbhA CBM4. Most importantly, these data support the previously proposed notion of an extended binding pocket using a novel tryptophan-containing loop that may be highly conserved in clostridial CBM4 proteins.


Asunto(s)
Celulasa/química , Clostridium thermocellum/enzimología , Cristalografía por Rayos X , Modelos Moleculares , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína
20.
Acta Crystallogr Sect F Struct Biol Cryst Commun ; 67(Pt 12): 1498-500, 2011 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-22139151

RESUMEN

A 1.5 Å resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase is reported (PDB entry 3t9g). The resulting structure was refined to an R factor of 0.143 and an R(free) of 0.178. Structural analysis shows that this new structure is very similar to the previously solved structure of a family 3 pectate lyase from Bacillus sp. strain KSM-P15 (PDB entry 1ee6), with a root-mean-square deviation of 0.93 Å and a sequence identity of 53%. This structural similarity is significant considering that C. bescii is a hyperthermophile and Bacillus sp. is a mesophile.


Asunto(s)
Bacillaceae/enzimología , Biocatálisis , Polisacárido Liasas/química , Cristalografía por Rayos X , Modelos Moleculares , Estructura Terciaria de Proteína
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