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1.
Proc Natl Acad Sci U S A ; 120(22): e2221483120, 2023 05 30.
Article in English | MEDLINE | ID: mdl-37216508

ABSTRACT

The enzymatic decarboxylation of fatty acids (FAs) represents an advance toward the development of biological routes to produce drop-in hydrocarbons. The current mechanism for the P450-catalyzed decarboxylation has been largely established from the bacterial cytochrome P450 OleTJE. Herein, we describe OleTPRN, a poly-unsaturated alkene-producing decarboxylase that outrivals the functional properties of the model enzyme and exploits a distinct molecular mechanism for substrate binding and chemoselectivity. In addition to the high conversion rates into alkenes from a broad range of saturated FAs without dependence on high salt concentrations, OleTPRN can also efficiently produce alkenes from unsaturated (oleic and linoleic) acids, the most abundant FAs found in nature. OleTPRN performs carbon-carbon cleavage by a catalytic itinerary that involves hydrogen-atom transfer by the heme-ferryl intermediate Compound I and features a hydrophobic cradle at the distal region of the substrate-binding pocket, not found in OleTJE, which is proposed to play a role in the productive binding of long-chain FAs and favors the rapid release of products from the metabolism of short-chain FAs. Moreover, it is shown that the dimeric configuration of OleTPRN is involved in the stabilization of the A-A' helical motif, a second-coordination sphere of the substrate, which contributes to the proper accommodation of the aliphatic tail in the distal and medial active-site pocket. These findings provide an alternative molecular mechanism for alkene production by P450 peroxygenases, creating new opportunities for biological production of renewable hydrocarbons.


Subject(s)
Alkenes , Fatty Acids , Fatty Acids/metabolism , Alkenes/chemistry , Decarboxylation , Cytochrome P-450 Enzyme System/metabolism , Oxidation-Reduction
2.
Nat Chem Biol ; 19(2): 218-229, 2023 02.
Article in English | MEDLINE | ID: mdl-36443572

ABSTRACT

Bifidobacteria are early colonizers of the human gut and play central roles in human health and metabolism. To thrive in this competitive niche, these bacteria evolved the capacity to use complex carbohydrates, including mammalian N-glycans. Herein, we elucidated pivotal biochemical steps involved in high-mannose N-glycan utilization by Bifidobacterium longum. After N-glycan release by an endo-ß-N-acetylglucosaminidase, the mannosyl arms are trimmed by the cooperative action of three functionally distinct glycoside hydrolase 38 (GH38) α-mannosidases and a specific GH125 α-1,6-mannosidase. High-resolution cryo-electron microscopy structures revealed that bifidobacterial GH38 α-mannosidases form homotetramers, with the N-terminal jelly roll domain contributing to substrate selectivity. Additionally, an α-glucosidase enables the processing of monoglucosylated N-glycans. Notably, the main degradation product, mannose, is isomerized into fructose before phosphorylation, an unconventional metabolic route connecting it to the bifid shunt pathway. These findings shed light on key molecular mechanisms used by bifidobacteria to use high-mannose N-glycans, a perennial carbon and energy source in the intestinal lumen.


Subject(s)
Bifidobacterium longum , Mannose , Animals , Humans , Mannose/metabolism , Bifidobacterium longum/metabolism , Cryoelectron Microscopy , Polysaccharides/chemistry , Mannosidases/metabolism , Glycoside Hydrolases/chemistry , Bifidobacterium/metabolism , Mammals
3.
Photochem Photobiol Sci ; 22(4): 893-904, 2023 Apr.
Article in English | MEDLINE | ID: mdl-36681778

ABSTRACT

Beetle luciferases were classified into three functional groups: (1) pH-sensitive yellow-green-emitting (fireflies) which change the bioluminescence color to red at acidic pH, high temperatures and presence of heavy metals; (2) the pH-insensitive green-yellow-emitting (click beetles, railroad worms and firefly isozymes) which are not affected by these factors, and (3) pH-insensitive red-emitting. Although the pH-sensing site in firefly luciferases was recently identified, it is unclear why some luciferases are pH-insensitive despite the presence of some conserved pH-sensing residues. Through circular dichroism, we compared the secondary structural changes and unfolding temperature of luciferases of representatives of these three groups: (1) pH-sensitive green-yellow-emitting Macrolampis sp2 (Mac) and Amydetes vivianii (Amy) firefly luciferases; (2) the pH-insensitive green-emitting Pyrearinus termitilluminans larval click beetle (Pte) and Aspisoma lineatum (Al2) larval firefly luciferases, and (3) the pH-insensitive red-emitting Phrixotrix hirtus railroadworm (PxRE) luciferase. The most blue-shifted luciferases, independently of pH sensitivity, are thermally more stable at different pHs than the red-shifted ones. The pH-sensitive luciferases undergo increases of α-helices and thermal stability above pH 6. The pH-insensitive Pte luciferase secondary structure remains stable between pH 6 and 8, whereas the Al2 luciferase displays an increase of the ß-sheet at pH 8. The PxRE luciferase also displays an increase of α-helices at pH 8. The results indicate that green-yellow emission in beetle luciferases can be attained by: (1) a structurally rigid scaffold which stabilizes a single closed active site conformation in the pH-insensitive luciferases, and (2) active site compaction above pH 7.0 in the more flexible pH-sensitive luciferases.


Subject(s)
Coleoptera , Animals , Coleoptera/metabolism , Luciferases, Firefly/metabolism , Amino Acid Sequence , Luciferases/chemistry , Fireflies , Luminescent Measurements
4.
Nat Chem Biol ; 16(8): 920-929, 2020 08.
Article in English | MEDLINE | ID: mdl-32451508

ABSTRACT

The fundamental and assorted roles of ß-1,3-glucans in nature are underpinned on diverse chemistry and molecular structures, demanding sophisticated and intricate enzymatic systems for their processing. In this work, the selectivity and modes of action of a glycoside hydrolase family active on ß-1,3-glucans were systematically investigated combining sequence similarity network, phylogeny, X-ray crystallography, enzyme kinetics, mutagenesis and molecular dynamics. This family exhibits a minimalist and versatile (α/ß)-barrel scaffold, which can harbor distinguishing exo or endo modes of action, including an ancillary-binding site for the anchoring of triple-helical ß-1,3-glucans. The substrate binding occurs via a hydrophobic knuckle complementary to the canonical curved conformation of ß-1,3-glucans or through a substrate conformational change imposed by the active-site topology of some fungal enzymes. Together, these findings expand our understanding of the enzymatic arsenal of bacteria and fungi for the breakdown and modification of ß-1,3-glucans, which can be exploited for biotechnological applications.


Subject(s)
Glucan 1,3-beta-Glucosidase/chemistry , Glycoside Hydrolases/chemistry , beta-Glucans/chemistry , Amino Acid Sequence/genetics , Binding Sites/physiology , Catalytic Domain/physiology , Crystallography, X-Ray/methods , Glucan 1,3-beta-Glucosidase/metabolism , Glucans/chemistry , Glycosides/chemistry , Models, Molecular , Substrate Specificity/physiology
6.
J Enzyme Inhib Med Chem ; 34(1): 310-321, 2019 Dec.
Article in English | MEDLINE | ID: mdl-30734604

ABSTRACT

Loxosceles spiders' venoms consist of a mixture of proteins, including the sphingomyelinases D (SMases D), which are the main toxic components responsible for local and systemic effects in human envenomation. Herein, based on the structural information of SMase D from Loxosceles laeta spider venom and virtual docking-based screening approach, three benzene sulphonate compounds (named 1, 5 and 6) were identified as potential Loxosceles SMase D inhibitors. All compounds inhibited the hydrolysis of the sphingomyelin substrate by both recombinant and native SMases D. Compounds 5 and 6 acted as SMases D uncompetitive inhibitors with Ki values of 0.49 µM and 0.59 µM, respectively. Compound 1 is a mixed type inhibitor, and presented a Ki value of 0.54 µM. In addition, the three compounds inhibited the binding of SMases D to human erythrocytes and the removal of glycophorin C from the cell surface, which are important events in the complement-dependent haemolysis induced by Loxosceles venom. Moreover, compounds 5 and 6 reduced the binding of SMases to human keratinocytes membrane and the venom induced cell death. Importantly, compounds 5 and 6 also controlled the development of the necrotic lesion in an in vivo model of loxoscelism. Together, our findings indicate that the novel SMase D inhibitors presented here are able to suppress both local and systemic reactions induced by Loxosceles venoms. Since the number of Loxosceles envenomation accidents is currently growing worldwide, our results indicate that both inhibitors are promising scaffolds for the rational design of new drugs targeting SMases D from these spiders.


Subject(s)
Phosphodiesterase Inhibitors/pharmacology , Phosphoric Diester Hydrolases/metabolism , Skin Diseases/drug therapy , Small Molecule Libraries/pharmacology , Spider Bites/drug therapy , Animals , Erythrocytes/drug effects , Erythrocytes/metabolism , Humans , Molecular Structure , Phosphodiesterase Inhibitors/chemical synthesis , Phosphodiesterase Inhibitors/chemistry , Rabbits , Small Molecule Libraries/chemical synthesis , Small Molecule Libraries/chemistry , Spiders
7.
J Biol Chem ; 292(17): 7023-7039, 2017 04 28.
Article in English | MEDLINE | ID: mdl-28292930

ABSTRACT

Leishmania parasites have evolved a number of strategies to cope with the harsh environmental changes during mammalian infection. One of these mechanisms involves the functional gain that allows mitochondrial 2-Cys peroxiredoxins to act as molecular chaperones when forming decamers. This function is critical for parasite infectivity in mammals, and its activation has been considered to be controlled exclusively by the enzyme redox state under physiological conditions. Herein, we have revealed that magnesium and calcium ions play a major role in modulating the ability of these enzymes to act as molecular chaperones, surpassing the redox effect. These ions are directly involved in mitochondrial metabolism and participate in a novel mechanism to stabilize the decameric form of 2-Cys peroxiredoxins in Leishmania mitochondria. Moreover, we have demonstrated that a constitutively dimeric Prx1m mutant impairs the survival of Leishmania under heat stress, supporting the central role of the chaperone function of Prx1m for Leishmania parasites during the transition from insect to mammalian hosts.


Subject(s)
Calcium/metabolism , Leishmania/metabolism , Magnesium/metabolism , Mitochondrial Proteins/metabolism , Peroxiredoxins/metabolism , Protozoan Proteins/metabolism , Anisotropy , Chromatography , Disulfides/chemistry , Fluorometry , Gene Expression Regulation , Homeodomain Proteins/metabolism , Humans , Hydrogen-Ion Concentration , Light , Mitochondria/metabolism , Molecular Chaperones/metabolism , Mutagenesis, Site-Directed , Oxidation-Reduction , Oxygen/chemistry , Protein Multimerization , Scattering, Radiation , Temperature
8.
J Cell Biochem ; 118(8): 2053-2063, 2017 08.
Article in English | MEDLINE | ID: mdl-27808444

ABSTRACT

Sphingomyelinases D have only been identified in arachnid venoms, Corynebacteria, Arcanobacterium, Photobacterium and in the fungi Aspergillus and Coccidioides. The arachnid and bacterial enzymes share very low sequence identity and do not contain the HKD sequence motif characteristic of the phospholipase D superfamily, however, molecular modeling and circular dichroism of SMases D from Loxosceles intermedia and Corynebacterium pseudotuberculosis indicate similar folds. The phospholipase, hemolytic and necrotic activities and mice vessel permeabilities were compared and both enzymes possess the ability to hydrolyze phospholipids and also promote similar pathological reactions in the host suggesting the existence of a common underlying mechanism in tissue disruption. J. Cell. Biochem. 118:2053-2063, 2017. © 2016 Wiley Periodicals, Inc.


Subject(s)
Arthropod Proteins/toxicity , Bacterial Proteins/toxicity , Capillary Permeability/drug effects , Corynebacterium pseudotuberculosis/chemistry , Phosphoric Diester Hydrolases/toxicity , Spiders/chemistry , Amino Acid Sequence , Animals , Arthropod Proteins/genetics , Arthropod Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cloning, Molecular , Corynebacterium pseudotuberculosis/enzymology , Corynebacterium pseudotuberculosis/pathogenicity , Erythrocytes/drug effects , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Hemolysis/drug effects , Horses , Humans , Mice , Phosphoric Diester Hydrolases/genetics , Phosphoric Diester Hydrolases/metabolism , Rabbits , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Recombinant Proteins/toxicity , Sequence Alignment , Sequence Homology, Amino Acid , Sheep, Domestic , Skin/drug effects , Skin/pathology , Spiders/enzymology , Spiders/pathogenicity
9.
Biochim Biophys Acta Proteins Proteom ; 1865(4): 395-403, 2017 Apr.
Article in English | MEDLINE | ID: mdl-28088615

ABSTRACT

The cellulases from Glycoside Hydrolyses family 12 (GH12) play an important role in cellulose degradation and plant cell wall deconstruction being widely used in a number of bioindustrial processes. Aiming to contribute toward better comprehension of these class of the enzymes, here we describe a high-yield secretion of a endoglucanase GH12 from Aspegillus terreus (AtGH12), which was cloned and expressed in Aspergillus nidulans strain A773. The purified protein was used for complete biochemical and functional characterization. The optimal temperature and pH of the enzyme were 55°C and 5.0 respectively, which has high activity against ß-glucan and xyloglucan and also is active toward glucomannan and CMC. The enzyme retained activity up to 60°C. AtGH12 is strongly inhibited by Cu2+, Fe2+, Cd2+, Mn2+, Ca2+, Zn2+ and EDTA, whereas K+, Tween, Cs+, DMSO, Triton X-100 and Mg2+ enhanced the enzyme activity. Furthermore, SAXS data reveal that the enzyme has a globular shape and CD analysis demonstrated a prevalence of a ß-strand structure corroborating with typical ß-sheets fold commonly found for other endoglucanases from GH12 family.


Subject(s)
Aspergillus , Cellulase , Cloning, Molecular , Fungal Proteins , Gene Expression , Aspergillus/enzymology , Aspergillus/genetics , Cellulase/biosynthesis , Cellulase/chemistry , Cellulase/genetics , Fungal Proteins/biosynthesis , Fungal Proteins/chemistry , Fungal Proteins/genetics , Recombinant Proteins
10.
J Biol Chem ; 290(13): 8582-90, 2015 Mar 27.
Article in English | MEDLINE | ID: mdl-25666622

ABSTRACT

2-Cys peroxiredoxins belonging to the Prx1 subfamily are Cys-based peroxidases that control the intracellular levels of H2O2 and seem to assume a chaperone function under oxidative stress conditions. The regulation of their peroxidase activity as well as the observed functional switch from peroxidase to chaperone involves changes in their quaternary structure. Multiple factors can modulate the oligomeric transitions of 2-Cys peroxiredoxins such as redox state, post-translational modifications, and pH. However, the molecular basis for the pH influence on the oligomeric state of these enzymes is still elusive. Herein, we solved the crystal structure of a typical 2-Cys peroxiredoxin from Leishmania in the dimeric (pH 8.5) and decameric (pH 4.4) forms, showing that conformational changes in the catalytic loop are associated with the pH-induced decamerization. Mutagenesis and biophysical studies revealed that a highly conserved histidine (His(113)) functions as a pH sensor that, at acidic conditions, becomes protonated and forms an electrostatic pair with Asp(76) from the catalytic loop, triggering the decamerization. In these 2-Cys peroxiredoxins, decamer formation is important for the catalytic efficiency and has been associated with an enhanced sensitivity to oxidative inactivation by overoxidation of the peroxidatic cysteine. In eukaryotic cells, exposure to high levels of H2O2 can trigger intracellular pH variations, suggesting that pH changes might act cooperatively with H2O2 and other oligomerization-modulator factors to regulate the structure and function of typical 2-Cys peroxiredoxins in response to oxidative stress.


Subject(s)
Peroxidases/chemistry , Protozoan Proteins/chemistry , Catalytic Domain , Crystallography, X-Ray , Hydrogen-Ion Concentration , Leishmania braziliensis/enzymology , Mitochondria/enzymology , Models, Molecular , Protein Multimerization , Protein Structure, Quaternary , Protein Structure, Secondary
11.
J Biol Chem ; 289(11): 7362-73, 2014 Mar 14.
Article in English | MEDLINE | ID: mdl-24469445

ABSTRACT

Arabinanases (ABNs, EC 3.2.1.99) are promising catalysts for environmentally friendly biomass conversion into energy and chemicals. These enzymes catalyze the hydrolysis of the α-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans releasing arabino-oligosaccharides and arabinose, the second most abundant pentose in nature. In this work, new findings about the molecular mechanisms governing activation, functional differentiation, and catalysis of GH43 ABNs are presented. Biophysical, mutational, and biochemical studies with the hyperthermostable two-domain endo-acting ABN from Thermotoga petrophila (TpABN) revealed how some GH43 ABNs are activated by calcium ions via hyperpolarization of the catalytically relevant histidine and the importance of the ancillary domain for catalysis and conformational stability. On the other hand, the two GH43 ABNs from rumen metagenome, ARN2 and ARN3, presented a calcium-independent mechanism in which sodium is the most likely substituent for calcium ions. The crystal structure of the two-domain endo-acting ARN2 showed that its ability to efficiently degrade branched substrates is due to a larger catalytic interface with higher accessibility than that observed in other ABNs with preference for linear arabinan. Moreover, crystallographic characterization of the single-domain exo-acting ARN3 indicated that its cleavage pattern producing arabinose is associated with the chemical recognition of the reducing end of the substrate imposed by steric impediments at the aglycone-binding site. By structure-guided rational design, ARN3 was converted into a classical endo enzyme, confirming the role of the extended Arg(203)-Ala(230) loop in determining its action mode. These results reveal novel molecular aspects concerning the functioning of GH43 ABNs and provide new strategies for arabinan degradation.


Subject(s)
Arabinose/chemistry , Bacterial Proteins/metabolism , Catalysis , Glycoside Hydrolases/metabolism , Gram-Negative Anaerobic Straight, Curved, and Helical Rods/enzymology , Amino Acid Sequence , Animals , Binding Sites , Biotechnology , Calcium/chemistry , Cattle , Cloning, Molecular , Crystallography, X-Ray , DNA Mutational Analysis , Hydrolysis , Ions/chemistry , Kinetics , Ligands , Metagenome , Metals/chemistry , Models, Molecular , Molecular Sequence Data , Mutagenesis , Protein Engineering , Protein Structure, Tertiary , Rumen/microbiology , Sequence Homology, Amino Acid , Solvents/chemistry
12.
Biochim Biophys Acta ; 1844(7): 1260-7, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24726393

ABSTRACT

The substrate specificity of TcoCBc1 was evaluated using two internally quenched fluorescent peptide libraries with randomized sequences designed to detect carboxydipeptidase (Abz-GXXZXK(Dnp)-OH) and endopeptidase (Abz-GXXZXXQ-EDDnp) activities at acidic and neutral pHs, respectively. All the data obtained with TcoCBc1 were compared with those of human cathepsin B, including the pH profiles of the hydrolytic reactions. The most relevant observation is the preference of TcoCBc1 for substrates with a pair of acidic amino acids at positions P(2) and P(1) for its carboxydipeptidase activity and the well acceptance for E and D at P(1) position for endopeptidase activity. These peculiar preferences for negatively charged groups of TcoCBc1 and its requirements for carboxydipeptidase activity were also observed on Abz labeled analogues of bradykinin (Abz-RPPG(↓)FSAFR-OH, Abz-RPPG(↓)FS(↓)AF-OH, Abz-RPPG(↓)DE(↓)AF-OH) and angiotensin I (Abz-DR(↓)VYIHAFHL-OH), where (↓) indicates the cleavage site. TcoCBc1 was modeled based on the atomic coordinates of the cathepsin B from Trypanosoma brucei and the positively charged environment in TcoCBc1 catalytic site contrasts with the negatively charged environment in human cathepsin B. The preferences of S1 and S2 subsites of TcoCBc1 for acidic amino acids have to be taken into consideration for future studies of physiological roles of TcoCBc1 as for instance in apoptotic processes of Trypanosoma congolense.


Subject(s)
Angiotensin I/metabolism , Bradykinin/metabolism , Cathepsin B/metabolism , Peptide Fragments/metabolism , Trypanosoma congolense/enzymology , Catalytic Domain , Cathepsin B/chemistry , Fluorescence Resonance Energy Transfer , Humans , Hydrogen-Ion Concentration , Hydrolysis , Kinetics , Models, Molecular , Peptide Library , Protein Conformation , Recombinant Proteins/metabolism , Substrate Specificity
13.
Biochim Biophys Acta ; 1844(3): 545-52, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24373874

ABSTRACT

Snake venom metalloproteinases (SVMPs) belonging to P-I class are able to hydrolyze extracellular matrix proteins and coagulation factors triggering local and systemic reactions by multiple molecular mechanisms that are not fully understood. BmooMPα-I, a P-I class SMVP from Bothrops moojeni venom, was active upon neuro- and vaso-active peptides including angiotensin I, bradykinin, neurotensin, oxytocin and substance P. Interestingly, BmooMPα-I showed a strong bias towards hydrolysis after proline residues, which is unusual for most of characterized peptidases. Moreover, the enzyme showed kininogenase activity similar to that observed in plasma and cells by kallikrein. FRET peptide assays indicated a relative promiscuity at its S2-S'2 subsites, with proline determining the scissile bond. This unusual post-proline cleaving activity was confirmed by the efficient hydrolysis of the synthetic combinatorial library MCA-GXXPXXQ-EDDnp, described as resistant for canonical peptidases, only after Pro residues. Structural analysis of the tripeptide LPL complexed with BmooMPα-I, generated by molecular dynamics simulations, assisted in defining the subsites and provided the structural basis for subsite preferences such as the restriction of basic residues at the S2 subsite due to repulsive electrostatic effects and the steric impediment for large aliphatic or aromatic side chains at the S1 subsite. These new functional and structural findings provided a further understanding of the molecular mechanisms governing the physiological effects of this important class of enzymes in envenomation process.


Subject(s)
Crotalid Venoms/enzymology , Kallikreins/metabolism , Metalloproteases/metabolism , Serine Endopeptidases/metabolism , Amino Acid Sequence , Animals , Bothrops , Hydrolysis , Kinetics , Molecular Dynamics Simulation , Peptides/chemistry , Peptides/metabolism , Prolyl Oligopeptidases , Radioimmunoassay , Substrate Specificity
14.
Biochem Biophys Res Commun ; 467(1): 171-7, 2015 Nov 06.
Article in English | MEDLINE | ID: mdl-26299923

ABSTRACT

Exfoliative toxins are serine proteases secreted by Staphylococcus aureus that are associated with toxin-mediated staphylococcal syndromes. To date, four different serotypes of exfoliative toxins have been identified and 3 of them (ETA, ETB, and ETD) are linked to human infection. Among these toxins, only the ETD structure remained unknown, limiting our understanding of the structural determinants for the functional differentiation between these toxins. We recently identified an ETD-like protein associated to S. aureus strains involved in mild mastitis in sheep. The crystal structure of this ETD-like protein was determined at 1.95 Å resolution and the structural analysis provide insights into the oligomerization, stability and specificity and enabled a comprehensive structural comparison with ETA and ETB. Despite the highly conserved molecular architecture, significant differences in the composition of the loops and in both the N- and C-terminal α-helices seem to define ETD-like specificity. Molecular dynamics simulations indicate that these regions defining ET specificity present different degrees of flexibility and may undergo conformational changes upon substrate recognition and binding. DLS and AUC experiments indicated that the ETD-like is monomeric in solution whereas it is present as a dimer in the asymmetric unit indicating that oligomerization is not related to functional differentiation among these toxins. Differential scanning calorimetry and circular dichroism assays demonstrated an endothermic transition centered at 52 °C, and an exothermic aggregation in temperatures up to 64 °C. All these together provide insights about the mode of action of a toxin often secreted in syndromes that are not associated with either ETA or ETB.


Subject(s)
Exfoliatins/chemistry , Exfoliatins/toxicity , Staphylococcus aureus/chemistry , Staphylococcus aureus/pathogenicity , Animals , Crystallography, X-Ray , Exfoliatins/classification , Female , Humans , Models, Molecular , Molecular Dynamics Simulation , Protein Conformation , Sheep , Staphylococcal Infections/etiology , Staphylococcal Infections/microbiology , Static Electricity , Structural Homology, Protein , Syndrome
15.
Appl Microbiol Biotechnol ; 99(12): 5095-107, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25605422

ABSTRACT

Xyloglucan-specific endo-ß-1,4-glucanases (Xegs, EC 3.2.1.151) exhibit high catalytic specificity for ß-1,4 linkages of xyloglucan, a branched hemicellulosic polysaccharide abundant in dicot primary cell walls and present in many monocot species. In nature, GH12 Xegs are not associated with carbohydrate-binding modules (CBMs), and here, we have investigated the effect of the fusion of the xyloglucan-specific CBM44 on the structure and function of a GH12 Xeg from Aspergillus niveus (XegA). This fusion presented enhanced catalytic properties and conferred superior thermal stability on the XegA. An increased k cat (chimera, 177.03 s(-1); XegA, 144.31 s(-1)) and reduced KM (chimera, 1.30 mg mL(-1); XegA, 1.50 mg mL(-1)) resulted in a 1.3-fold increase in catalytic efficiency of the chimera over the parental XegA. Although both parental and chimeric enzymes presented catalytic optima at pH 5.5 and 60 °C, the thermostabilitiy of the chimera at 60 °C was greater than the parental XegA. Moreover, the crystallographic structure of XegA together with small-angle X-ray scattering (SAXS) and molecular dynamics simulations revealed that the spatial arrangement of the domains in the chimeric enzyme resulted in the formation of an extended binding cleft that may explain the improved kinetic properties of the CBM44-XegA chimera.


Subject(s)
Aspergillus/enzymology , Endo-1,3(4)-beta-Glucanase/chemistry , Endo-1,3(4)-beta-Glucanase/metabolism , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Glucans/metabolism , Xylans/metabolism , Amino Acid Sequence , Aspergillus/chemistry , Aspergillus/genetics , Endo-1,3(4)-beta-Glucanase/genetics , Fungal Proteins/genetics , Glucans/chemistry , Kinetics , Molecular Dynamics Simulation , Molecular Sequence Data , Protein Engineering , Protein Structure, Tertiary , Scattering, Small Angle , Substrate Specificity , X-Ray Diffraction , Xylans/chemistry
16.
J Biol Chem ; 288(47): 34131-34145, 2013 Nov 22.
Article in English | MEDLINE | ID: mdl-24097982

ABSTRACT

Myosin V (MyoV) motors have been implicated in the intracellular transport of diverse cargoes including vesicles, organelles, RNA-protein complexes, and regulatory proteins. Here, we have solved the cargo-binding domain (CBD) structures of the three human MyoV paralogs (Va, Vb, and Vc), revealing subtle structural changes that drive functional differentiation and a novel redox mechanism controlling the CBD dimerization process, which is unique for the MyoVc subclass. Moreover, the cargo- and motor-binding sites were structurally assigned, indicating the conservation of residues involved in the recognition of adaptors for peroxisome transport and providing high resolution insights into motor domain inhibition by CBD. These results contribute to understanding the structural requirements for cargo transport, autoinhibition, and regulatory mechanisms in myosin V motors.


Subject(s)
Myosin Type V/chemistry , Binding Sites , Biological Transport, Active/physiology , Humans , Myosin Type V/genetics , Myosin Type V/metabolism , Peroxisomes/chemistry , Peroxisomes/genetics , Peroxisomes/metabolism , Protein Structure, Quaternary , Protein Structure, Tertiary , Structural Homology, Protein
17.
Biochim Biophys Acta ; 1834(8): 1492-500, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23459129

ABSTRACT

Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (kcat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes.


Subject(s)
Bacillus subtilis/enzymology , Endo-1,4-beta Xylanases/chemistry , Glycoside Hydrolases/chemistry , Molecular Dynamics Simulation , Recombinant Fusion Proteins/chemistry , Computer Simulation , Endo-1,4-beta Xylanases/genetics , Endo-1,4-beta Xylanases/metabolism , Glycoside Hydrolases/genetics , Glycoside Hydrolases/metabolism , Models, Molecular , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Scattering, Small Angle
18.
Biochim Biophys Acta ; 1824(3): 461-7, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22230786

ABSTRACT

Xyloglucan is a major structural polysaccharide of the primary (growing) cell wall of higher plants. It consists of a cellulosic backbone (beta-1,4-linked glucosyl residues) that is frequently substituted with side chains. This report describes Aspergillus nidulans strain A773 recombinant secretion of a dimeric xyloglucan-specific endo-ß-1,4-glucanohydrolase (XegA) cloned from Aspergillus niveus. The ORF of the A. niveus xegA gene is comprised of 714 nucleotides, and encodes a 238 amino acid protein with a calculated molecular weight of 23.5kDa and isoelectric point of 4.38. The optimal pH and temperature were 6.0 and 60°C, respectively. XegA generated a xyloglucan-oligosaccharides (XGOs) pattern similar to that observed for cellulases from family GH12, i.e., demonstrating that its mode of action includes hydrolysis of the glycosidic linkages between glucosyl residues that are not branched with xylose. In contrast to commercial lichenase, mixed linkage beta-glucan (lichenan) was not digested by XegA, indicating that the enzyme did not cleave glucan ß-1,3 or ß-1,6 bonds. The far-UV CD spectrum of the purified enzyme indicated a protein rich in ß-sheet structures as expected for GH12 xyloglucanases. Thermal unfolding studies displayed two transitions with mid-point temperatures of 51.3°C and 81.3°C respectively, and dynamic light scattering studies indicated that the first transition involves a change in oligomeric state from a dimeric to a monomeric form. Since the enzyme is a predominantly a monomer at 60°C, the enzymatic assays demonstrated that XegA is more active in its monomeric state.


Subject(s)
Aspergillus/chemistry , Cell Wall/chemistry , Cellulase/chemistry , Fungal Proteins/chemistry , Glucans/chemistry , Xylans/chemistry , Amino Acid Sequence , Aspergillus/enzymology , Aspergillus nidulans/genetics , Cell Wall/enzymology , Cellulase/genetics , Cellulase/metabolism , Circular Dichroism , Fungal Proteins/genetics , Fungal Proteins/metabolism , Glucans/metabolism , Glycoside Hydrolases/chemistry , Glycoside Hydrolases/metabolism , Hydrogen-Ion Concentration , Isoelectric Point , Kinetics , Light , Molecular Sequence Data , Molecular Weight , Protein Multimerization , Protein Structure, Secondary , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Scattering, Radiation , Substrate Specificity , Temperature , Xylans/metabolism
19.
Acta Crystallogr D Biol Crystallogr ; 69(Pt 10): 1958-64, 2013 Oct.
Article in English | MEDLINE | ID: mdl-24100315

ABSTRACT

The crystal structure of the myotoxic, cell-penetrating, basic polypeptide crotamine isolated from the venom of Crotalus durissus terrificus has been determined by single-wavelength anomalous dispersion techniques and refined at 1.7 Šresolution. The structure reveals distinct cationic and hydrophobic surface regions that are located on opposite sides of the molecule. This surface-charge distribution indicates its possible mode of interaction with negatively charged phospholipids and other molecular targets to account for its diverse pharmacological activities. Although the sequence identity between crotamine and human ß-defensins is low, the three-dimensional structures of these functionally related peptides are similar. Since crotamine is a leading member of a large family of myotoxic peptides, its structure will provide a basis for the design of novel cell-penetrating molecules.


Subject(s)
Crotalid Venoms/chemistry , Peptides/chemistry , Amino Acid Sequence , Animals , Brazil , Crotalid Venoms/toxicity , Crotalus , Crystallography, X-Ray , Humans , Molecular Sequence Data , Neurotoxins/chemistry , Neurotoxins/toxicity , Peptides/toxicity , Reptilian Proteins/chemistry , Reptilian Proteins/toxicity
20.
Biochem J ; 441(1): 95-104, 2012 Jan 01.
Article in English | MEDLINE | ID: mdl-21880019

ABSTRACT

Cellulases participate in a number of biological events, such as plant cell wall remodelling, nematode parasitism and microbial carbon uptake. Their ability to depolymerize crystalline cellulose is of great biotechnological interest for environmentally compatible production of fuels from lignocellulosic biomass. However, industrial use of cellulases is somewhat limited by both their low catalytic efficiency and stability. In the present study, we conducted a detailed functional and structural characterization of the thermostable BsCel5A (Bacillus subtilis cellulase 5A), which consists of a GH5 (glycoside hydrolase 5) catalytic domain fused to a CBM3 (family 3 carbohydrate-binding module). NMR structural analysis revealed that the Bacillus CBM3 represents a new subfamily, which lacks the classical calcium-binding motif, and variations in NMR frequencies in the presence of cellopentaose showed the importance of polar residues in the carbohydrate interaction. Together with the catalytic domain, the CBM3 forms a large planar surface for cellulose recognition, which conducts the substrate in a proper conformation to the active site and increases enzymatic efficiency. Notably, the manganese ion was demonstrated to have a hyper-stabilizing effect on BsCel5A, and by using deletion constructs and X-ray crystallography we determined that this effect maps to a negatively charged motif located at the opposite face of the catalytic site.


Subject(s)
Bacillus subtilis/enzymology , Bacterial Proteins/metabolism , Cellulases/metabolism , Bacillus subtilis/genetics , Bacillus subtilis/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Calcium/metabolism , Cellulases/chemistry , Cellulases/genetics , Cloning, Molecular , Gene Expression Regulation, Bacterial/physiology , Hot Temperature , Kinetics , Manganese/chemistry , Models, Molecular , Protein Conformation , Protein Structure, Tertiary , Substrate Specificity
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