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1.
Biochem Biophys Res Commun ; 645: 71-78, 2023 02 19.
Article in English | MEDLINE | ID: mdl-36680939

ABSTRACT

Carbohydrate-binding modules (CBMs) constitute independently folded domains typically associated with carbohydrate-active enzymes (CAZymes). These modules are considered to have a rigid structure without notable conformational changes upon ligand binding, exhibiting a complementary topography in relation to the target carbohydrate. Herein, the high-resolution SAD-solved structure of a CBM from family 3 (BsCBM3) that binds to crystalline cellulose is reported in two crystalline forms. This module showed molecular plasticity with structural differences detected between the two crystalline forms and high RMSD values when compared to NMR ensemble of models. Pronounced structural variances were observed in the cellulose binding interface between NMR and XTAL structures, which were corroborated by molecular dynamics simulations. These findings support that family 3 CBMs targeting to cellulose are rather structurally dynamic modules than rigid entities, suggesting a potential role of conformational changes in polysaccharide recognition and modulation of enzyme activity.


Subject(s)
Carbohydrates , Cellulose , Cellulose/chemistry , Carbohydrates/chemistry , Polysaccharides , Molecular Dynamics Simulation , Protein Binding , Crystallography, X-Ray
2.
Mem Inst Oswaldo Cruz ; 116: e210209, 2022.
Article in English | MEDLINE | ID: mdl-35019070

ABSTRACT

BACKGROUND: Leishmaniasis is a neglected tropical disease caused by the parasite Leishmania braziliensis, commonly found in Brazil and associated with cutaneous and visceral forms of this disease. Like other organisms, L. braziliensis has an enzyme called glutamine synthetase (LbGS) that acts on the synthesis of glutamine from glutamate. This enzyme plays an essential role in the metabolism of these parasites and can be a potential therapeutic target for treating this disease. OBJECTIVES: Investigate LbGS structure and generate structural models of the protein. METHODS: We use the method of crosslinking mass spectrometry (XLMS) and generate structural models in silico using I-TASSER. FINDINGS: 42 XLs peptides were identified, of which 37 are explained in a monomeric model with the other five indicating LbGS dimerization and pentamers interaction region. The comparison of 3D models generated in the presence and absence of XLMS restrictions probed the benefits of modeling with XLMS highlighting the inappropriate folding due to the absence of spatial restrictions. MAIN CONCLUSIONS: In conclusion, we disclose the conservation of the active site and interface regions, but also unique features of LbGS showing the potential of XLMS to probe structural information and explore new drugs.


Subject(s)
Glutamate-Ammonia Ligase/chemistry , Leishmania braziliensis , Protozoan Proteins/chemistry , Leishmania braziliensis/enzymology , Mass Spectrometry , Skin
3.
J Biol Chem ; 295(15): 5012-5021, 2020 04 10.
Article in English | MEDLINE | ID: mdl-32139511

ABSTRACT

ß-Mannanases from the glycoside hydrolase 26 (GH26) family are retaining hydrolases that are active on complex heteromannans and whose genes are abundant in rumen metagenomes and metatranscriptomes. These enzymes can exhibit distinct modes of substrate recognition and are often fused to carbohydrate-binding modules (CBMs), resulting in a molecular puzzle of mechanisms governing substrate preference and mode of action that has not yet been pieced together. In this study, we recovered a novel GH26 enzyme with a CBM35 module linked to its N terminus (CrMan26) from a cattle rumen metatranscriptome. CrMan26 exhibited a preference for galactomannan as substrate and the crystal structure of the full-length protein at 1.85 Å resolution revealed a unique orientation of the ancillary domain relative to the catalytic interface, strategically positioning a surface aromatic cluster of the ancillary domain as an extension of the substrate-binding cleft, contributing to galactomannan preference. Moreover, systematic investigation of nonconserved residues in the catalytic interface unveiled that residues Tyr195 (-3 subsite) and Trp234 (-5 subsite) from distal negative subsites have a key role in galactomannan preference. These results indicate a novel and complex mechanism for substrate recognition involving spatially remote motifs, distal negative subsites from the catalytic domain, and a surface-associated aromatic cluster from the ancillary domain. These findings expand our molecular understanding of the mechanisms of substrate binding and recognition in the GH26 family and shed light on how some CBMs and their respective orientation can contribute to substrate preference.


Subject(s)
Mannans/metabolism , Mannosidases/chemistry , Mannosidases/metabolism , Metagenome , Mutation , Rumen/metabolism , Amino Acid Sequence , Animals , Catalysis , Catalytic Domain , Cattle , Crystallography, X-Ray , Galactose/analogs & derivatives , Hydrolysis , Mannosidases/genetics , Models, Molecular , Mutagenesis, Site-Directed , Phylogeny , Protein Binding , Sequence Homology , Substrate Specificity
4.
J Biol Chem ; 293(35): 13636-13649, 2018 08 31.
Article in English | MEDLINE | ID: mdl-29997257

ABSTRACT

The classical microbial strategy for depolymerization of ß-mannan polysaccharides involves the synergistic action of at least two enzymes, endo-1,4-ß-mannanases and ß-mannosidases. In this work, we describe the first exo-ß-mannanase from the GH2 family, isolated from Xanthomonas axonopodis pv. citri (XacMan2A), which can efficiently hydrolyze both manno-oligosaccharides and ß-mannan into mannose. It represents a valuable process simplification in the microbial carbon uptake that could be of potential industrial interest. Biochemical assays revealed a progressive increase in the hydrolysis rates from mannobiose to mannohexaose, which distinguishes XacMan2A from the known GH2 ß-mannosidases. Crystallographic analysis indicates that the active-site topology of XacMan2A underwent profound structural changes at the positive-subsite region, by the removal of the physical barrier canonically observed in GH2 ß-mannosidases, generating a more open and accessible active site with additional productive positive subsites. Besides that, XacMan2A contains two residue substitutions in relation to typical GH2 ß-mannosidases, Gly439 and Gly556, which alter the active site volume and are essential to its mode of action. Interestingly, the only other mechanistically characterized mannose-releasing exo-ß-mannanase so far is from the GH5 family, and its mode of action was attributed to the emergence of a blocking loop at the negative-subsite region of a cleft-like active site, whereas in XacMan2A, the same activity can be explained by the removal of steric barriers at the positive-subsite region in an originally pocket-like active site. Therefore, the GH2 exo-ß-mannanase represents a distinct molecular route to this rare activity, expanding our knowledge about functional convergence mechanisms in carbohydrate-active enzymes.


Subject(s)
Bacterial Proteins/metabolism , Xanthomonas/metabolism , beta-Mannosidase/metabolism , Amino Acid Sequence , Bacterial Proteins/chemistry , Catalytic Domain , Crystallography, X-Ray , Hydrolysis , Kinetics , Mannans/metabolism , Mannose/metabolism , Models, Molecular , Protein Conformation , Scattering, Small Angle , Sequence Alignment , Substrate Specificity , X-Ray Diffraction , Xanthomonas/chemistry , Xanthomonas/enzymology , beta-Mannosidase/chemistry
5.
Biotechnol Bioeng ; 116(4): 734-744, 2019 04.
Article in English | MEDLINE | ID: mdl-30556897

ABSTRACT

Rational design is an important tool for sculpting functional and stability properties of proteins and its potential can be much magnified when combined with in vitro and natural evolutionary diversity. Herein, we report the structure-guided design of a xylose-releasing exo-ß-1,4-xylanase from an inactive member of glycoside hydrolase family 43 (GH43). Structural analysis revealed a nonconserved substitution (Lys247 ) that results in the disruption of the hydrogen bond network that supports catalysis. The mutation of this residue to a conserved serine restored the catalytic activity and crystal structure elucidation of the mutant confirmed the recovery of the proper orientation of the catalytically relevant histidine. Interestingly, the tailored enzyme can cleave both xylooligosaccharides and xylan, releasing xylose as the main product, being the first xylose-releasing exo-ß-1,4-xylanase reported in the GH43 family. This enzyme presents a unique active-site topology when compared with closely related ß-xylosidases, which is the absence of a hydrophobic barrier at the positive-subsite region, allowing the accommodation of long substrates. Therefore, the combination of rational design for catalytic activation along with naturally occurring differences in the substrate binding interface led to the discovery of a novel activity within the GH43 family. In addition, these results demonstrate the importance of solvation of the ß-propeller hollow for GH43 catalytic function and expand our mechanistic understanding about the diverse modes of action of GH43 members, a key and polyspecific carbohydrate-active enzyme family abundant in most plant cell-wall-degrading microorganisms.


Subject(s)
Bacillus licheniformis/enzymology , Xylose/metabolism , Xylosidases/genetics , Xylosidases/metabolism , Bacillus licheniformis/chemistry , Bacillus licheniformis/genetics , Bacillus licheniformis/metabolism , Catalytic Domain , Crystallography, X-Ray , Enzyme Activation , Hydrogen Bonding , Models, Molecular , Mutagenesis, Site-Directed , Protein Conformation , Protein Multimerization , Substrate Specificity , Xylosidases/chemistry
6.
Biochim Biophys Acta Proteins Proteom ; 1866(4): 569-579, 2018 Apr.
Article in English | MEDLINE | ID: mdl-29454992

ABSTRACT

The Amazon region holds most of the biological richness of Brazil. Despite their ecological and biotechnological importance, studies related to microorganisms from this region are limited. Metagenomics leads to exciting discoveries, mainly regarding non-cultivable microorganisms. Herein, we report the discovery of a novel ß-glucosidase (glycoside hydrolase family 1) gene from a metagenome from Lake Poraquê in the Amazon region. The gene encodes a protein of 52.9 kDa, named AmBgl-LP, which was recombinantly expressed in Escherichia coli and biochemically and structurally characterized. Although AmBgl-LP hydrolyzed the synthetic substrate p-nitrophenyl-ß-d-glucopyranoside (pNPßG) and the natural substrate cellobiose, it showed higher specificity for pNPßG (kcat/Km = 6 s-1·mM-1) than cellobiose (kcat/Km = 0.6 s-1·mM-1). AmBgl-LP showed maximum activity at 40 °C and pH 6.0 when pNPßG was used as the substrate. Glucose is a competitive inhibitor of AmBgl-LP, presenting a Ki of 14 mM. X-ray crystallography and Small Angle X-ray Scattering were used to determine the AmBgl-LP three-dimensional structure and its oligomeric state. Interestingly, despite sharing similar active site architecture with other structurally characterized GH1 family members which are monomeric, AmBgl-LP forms stable dimers in solution. The identification of new GH1 members by metagenomics might extend our understanding of the molecular mechanisms and diversity of these enzymes, besides enabling us to survey their industrial applications.


Subject(s)
Lakes/microbiology , Metagenome , Water Microbiology , beta-Glucosidase/chemistry , Brazil , beta-Glucosidase/genetics , beta-Glucosidase/metabolism
7.
Biochem Biophys Res Commun ; 488(3): 461-465, 2017 07 01.
Article in English | MEDLINE | ID: mdl-28499874

ABSTRACT

Nucleoside diphosphate kinases (NDKs) are key enzymes in the purine-salvage pathway of trypanosomatids and have been associated with the maintenance of host-cell integrity for the benefit of the parasite, being potential targets for rational drug discovery and design. The NDK from Leishmania major (LmNDK) and mutants were expressed and purified to homogeneity. Thermal shift assays were employed to identify potential inhibitors for LmNDK. Calorimetric experiments, site-directed mutagenesis and molecular docking analysis were performed to validate the interaction and to evaluate the structural basis of ligand recognition. Furthermore, the anti-leishmanial activity of the newly identified and validated compound was tested in vitro against different Leishmania species. The molecule SU11652, a Sunitinib analog, was identified as a potential inhibitor for LmNDK and structural studies indicated that this molecule binds to the active site of LmNDK in a similar conformation to nucleotides, mimicking natural substrates. Isothermal titration calorimetry experiments combined with site-directed mutagenesis revealed that the residues H50 and H117, considered essential for catalysis, play an important role in ligand binding. In vitro cell studies showed that SU11652 had similar efficacy to Amphotericin b against some Leishmania species. Together, our results indicate the pyrrole-indolinone SU11652 as a promising scaffold for the rational design of new drugs targeting the enzyme NDK from Leishmania parasites.


Subject(s)
Antiprotozoal Agents/pharmacology , Indoles/pharmacology , Leishmania major/enzymology , Nucleoside-Diphosphate Kinase/antagonists & inhibitors , Protein Kinase Inhibitors/pharmacology , Pyrroles/pharmacology , Calorimetry , Cell Survival/drug effects , Dose-Response Relationship, Drug , Leishmania major/drug effects , Molecular Docking Simulation , Mutagenesis, Site-Directed , Nucleoside-Diphosphate Kinase/genetics , Nucleoside-Diphosphate Kinase/metabolism , Parasitic Sensitivity Tests , Protein Kinase Inhibitors/chemistry , Structure-Activity Relationship
8.
Biochem Biophys Res Commun ; 475(4): 350-5, 2016 07 08.
Article in English | MEDLINE | ID: mdl-27233609

ABSTRACT

The arginine repressor (ArgR) regulates arginine biosynthesis in a number of microorganisms and consists of two domains interlinked by a short peptide; the N-terminal domain is involved in DNA binding and the C-terminal domain binds arginine and forms a hexamer made-up of a dimer of trimers. The crystal structure of the C-terminal domain of ArgR from the pathogenic Corynebacterium pseudotuberculosis determined at 1.9 Å resolution contains a tightly bound tyrosine at the arginine-binding site indicating hitherto unobserved promiscuity. Structural analysis of the binding pocket displays clear molecular adaptations to accommodate tyrosine binding suggesting the possible existence of an alternative regulatory process in this pathogenic bacterium.


Subject(s)
Bacterial Proteins/chemistry , Corynebacterium pseudotuberculosis/chemistry , Repressor Proteins/chemistry , Amino Acid Sequence , Arginine/metabolism , Bacterial Proteins/metabolism , Binding Sites , Corynebacterium Infections/microbiology , Corynebacterium pseudotuberculosis/metabolism , Crystallography, X-Ray , Humans , Models, Molecular , Protein Domains , Repressor Proteins/metabolism , Substrate Specificity , Tyrosine/metabolism
9.
Biochem Biophys Res Commun ; 474(4): 696-701, 2016 Jun 10.
Article in English | MEDLINE | ID: mdl-27154221

ABSTRACT

Plant aldo-keto reductases of the AKR4C subfamily play key roles during stress and are attractive targets for developing stress-tolerant crops. However, these AKR4Cs show little to no activity with previously-envisioned sugar substrates. We hypothesized a structural basis for the distinctive cofactor binding and substrate specificity of these plant enzymes. To test this, we solved the crystal structure of a novel AKR4C subfamily member, the AKR4C7 from maize, in the apo form and in complex with NADP(+). The binary complex revealed an intermediate state of cofactor binding that preceded closure of Loop B, and also indicated that conformational changes upon substrate binding are required to induce a catalytically-favorable conformation of the active-site pocket. Comparative structural analyses of homologues (AKR1B1, AKR4C8 and AKR4C9) showed that evolutionary redesign of plant AKR4Cs weakened interactions that stabilize the closed conformation of Loop B. This in turn decreased cofactor affinity and altered configuration of the substrate-binding site. We propose that these structural modifications contribute to impairment of sugar reductase activity in favor of other substrates in the plant AKR4C subgroup, and that catalysis involves a three-step process relevant to other AKRs.


Subject(s)
Aldehyde Reductase/chemistry , Aldehyde Reductase/ultrastructure , NADP/chemistry , NADP/ultrastructure , Plant Proteins/chemistry , Plant Proteins/ultrastructure , Aldo-Keto Reductases , Binding Sites , Coenzymes/chemistry , Coenzymes/ultrastructure , Enzyme Activation , Molecular Docking Simulation , Protein Binding , Protein Conformation , Substrate Specificity
10.
Biochemistry ; 54(10): 1930-42, 2015 Mar 17.
Article in English | MEDLINE | ID: mdl-25714929

ABSTRACT

GH5 is one of the largest glycoside hydrolase families, comprising at least 20 distinct activities within a common structural scaffold. However, the molecular basis for the functional differentiation among GH5 members is still not fully understood, principally for xyloglucan specificity. In this work, we elucidated the crystal structures of two novel GH5 xyloglucanases (XEGs) retrieved from a rumen microflora metagenomic library, in the native state and in complex with xyloglucan-derived oligosaccharides. These results provided insights into the structural determinants that differentiate GH5 XEGs from parental cellulases and a new mode of action within the GH5 family related to structural adaptations in the -1 subsite. The oligosaccharide found in the XEG5A complex, permitted the mapping, for the first time, of the positive subsites of a GH5 XEG, revealing the importance of the pocket-like topology of the +1 subsite in conferring the ability of some GH5 enzymes to attack xyloglucan. Complementarily, the XEG5B complex covered the negative subsites, completing the subsite mapping of GH5 XEGs at high resolution. Interestingly, XEG5B is, to date, the only GH5 member able to cleave XXXG into XX and XG, and in the light of these results, we propose that a modification in the -1 subsite enables the accommodation of a xylosyl side chain at this position. The stereochemical compatibility of the -1 subsite with a xylosyl moiety was also reported for other structurally nonrelated XEGs belonging to the GH74 family, indicating it to be an essential attribute for this mode of action.


Subject(s)
Bacteria/enzymology , Bacterial Proteins/chemistry , Cellulase/chemistry , Glucans/chemistry , Oligosaccharides/chemistry , Xylans/chemistry , Bacteria/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Catalytic Domain , Cellulase/genetics , Cellulase/metabolism , Glucans/genetics , Glucans/metabolism , Oligosaccharides/genetics , Oligosaccharides/metabolism , Structure-Activity Relationship , Substrate Specificity , Xylans/genetics , Xylans/metabolism
11.
J Struct Biol ; 192(3): 336-341, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26410384

ABSTRACT

Nucleoside diphosphate kinase (NDK) is a housekeeping enzyme that plays key roles in nucleotide recycling and homeostasis in trypanosomatids. Moreover, it is secreted by the intracellular parasite Leishmania to modulate the host response. These functions make NDK an attractive target for drug design and for studies aiming at a better understanding of the mechanisms mediating host-pathogen interactions. Here, we report the crystal structures of three mutants of the NDK from Leishmania major (LmNDK) that affects the stability of the hexameric biological assembly including P95S, Δ5Ct (lacking the last five residues) and the double mutant P100S/Δ5Ct. Although P95S and Δ5Ct variants conserve the hexameric structure of the wild-type protein, the double mutant becomes a dimer as shown by in solution studies. Free energy calculation of dimer-dimer interfaces and enzymatic assays indicate that P95S, Δ5Ct and P100S/Δ5Ct mutations progressively decrease the hexamer stability and enzyme activity. These results demonstrate that the mutated regions play a role in protein function through stabilizing the quaternary arrangement.


Subject(s)
Leishmania major/enzymology , Nucleoside-Diphosphate Kinase/genetics , Nucleoside-Diphosphate Kinase/ultrastructure , Protein Structure, Quaternary/genetics , Amino Acid Sequence , Crystallography, X-Ray , Host-Pathogen Interactions , Models, Molecular
12.
J Biol Chem ; 289(46): 32186-32200, 2014 Nov 14.
Article in English | MEDLINE | ID: mdl-25266726

ABSTRACT

Xanthomonas pathogens attack a variety of economically relevant plants, and their xylan CUT system (carbohydrate utilization with TonB-dependent outer membrane transporter system) contains two major xylanase-related genes, xynA and xynB, which influence biofilm formation and virulence by molecular mechanisms that are still elusive. Herein, we demonstrated that XynA is a rare reducing end xylose-releasing exo-oligoxylanase and not an endo-ß-1,4-xylanase as predicted. Structural analysis revealed that an insertion in the ß7-α7 loop induces dimerization and promotes a physical barrier at the +2 subsite conferring this unique mode of action within the GH10 family. A single mutation that impaired dimerization became XynA active against xylan, and high endolytic activity was achieved when this loop was tailored to match a canonical sequence of endo-ß-1,4-xylanases, supporting our mechanistic model. On the other hand, the divergent XynB proved to be a classical endo-ß-1,4-xylanase, despite the low sequence similarity to characterized GH10 xylanases. Interestingly, this enzyme contains a calcium ion bound nearby to the glycone-binding region, which is required for catalytic activity and structural stability. These results shed light on the molecular basis for xylan degradation by Xanthomonas and suggest how these enzymes synergistically assist infection and pathogenesis. Our findings indicate that XynB contributes to breach the plant cell wall barrier, providing nutrients and facilitating the translocation of effector molecules, whereas the exo-oligoxylanase XynA possibly participates in the suppression of oligosaccharide-induced immune responses.


Subject(s)
Bacterial Proteins/metabolism , Endo-1,4-beta Xylanases/metabolism , Plants/microbiology , Xanthomonas/enzymology , Xylans/metabolism , beta-Glucosidase/metabolism , Amino Acid Sequence , Calcium/metabolism , Calorimetry , Carbohydrate Metabolism , Cell Wall/enzymology , Cloning, Molecular , Crystallography, X-Ray , Glycoside Hydrolases/metabolism , Ions , Molecular Sequence Data , Oligosaccharides/metabolism , Protein Engineering , Protein Multimerization , Sequence Homology, Amino Acid , Temperature
13.
BMC Evol Biol ; 15: 290, 2015 Dec 21.
Article in English | MEDLINE | ID: mdl-26690570

ABSTRACT

BACKGROUND: Sphingomyelinase D is the main toxin present in the venom of Loxosceles spiders. Several isoforms present in these venoms can be structurally classified in two groups. Class I Sphingomyelinase D contains a single disulphide bridge and variable loop. Class II Sphingomyelinase D presents an additional intrachain disulphide bridge that links a flexible loop with a catalytic loop. These classes exhibit differences in their toxic potential. In this paper we address the distribution of the structural classes of SMase D within and among species of spiders and also their evolutionary origin by means of phylogenetic analyses. We also conducted tests to assess the action of natural selection in their evolution combined to structural modelling of the affected sites. RESULTS: The majority of the Class I enzymes belong to the same clade, which indicates a recent evolution from a single common ancestor. Positively selected sites are located on the catalytic interface, which contributes to a distinct surface charge distribution between the classes. Sites that may prevent the formation of an additional bridge were found in Class I enzymes. CONCLUSIONS: The evolution of Sphingomyelinase D has been driven by natural selection toward an increase in noxiousness, and this might help explain the toxic variation between classes.


Subject(s)
Evolution, Molecular , Phosphoric Diester Hydrolases/genetics , Spider Venoms/enzymology , Spiders/classification , Spiders/genetics , Animals , Models, Molecular , Phosphoric Diester Hydrolases/chemistry , Phylogeny , Selection, Genetic , Spider Venoms/genetics , Spiders/enzymology
14.
Biochem Biophys Res Commun ; 468(1-2): 365-71, 2015.
Article in English | MEDLINE | ID: mdl-26505799

ABSTRACT

2S albumins, the seed storage proteins, are the primary sources of carbon and nitrogen and are involved in plant defense. The mature form of Moringa oleifera (M. oleifera), a chitin binding protein isoform 3-1 (mMo-CBP3-1) a thermostable antifungal, antibacterial, flocculating 2S albumin is widely used for the treatment of water and is potentially interesting for the development of both antifungal drugs and transgenic crops. The crystal structure of mMo-CBP3-1 determined at 1.7 Å resolution demonstrated that it is comprised of two proteolytically processed α-helical chains, stabilized by four disulfide bridges that is stable, resistant to pH changes and has a melting temperature (TM) of approximately 98 °C. The surface arginines and the polyglutamine motif are the key structural factors for the observed flocculating, antibacterial and antifungal activities. This represents the first crystal structure of a 2S albumin and the model of the pro-protein indicates the structural changes that occur upon formation of mMo-CBP3-1 and determines the structural motif and charge distribution patterns for the diverse observed activities.


Subject(s)
2S Albumins, Plant/chemistry , Moringa oleifera/chemistry , Seeds/chemistry , Amino Acid Sequence , Crystallography, X-Ray , Models, Molecular , Molecular Sequence Data , Protein Conformation
15.
BMC Struct Biol ; 15: 2, 2015 Feb 03.
Article in English | MEDLINE | ID: mdl-25643978

ABSTRACT

BACKGROUND: Nucleoside diphosphate kinase (NDK) is a housekeeping enzyme that plays key roles in nucleotide recycling and homeostasis in trypanosomatids. It is also secreted by the intracellular parasite Leishmania to modulate the host response. These functions make NDK an attractive target for drug design and for studies aiming at a better understanding of the mechanisms mediating host-pathogen interactions. RESULTS: We report the crystal structure and biophysical characterization of the NDK from Leishmania braziliensis (LbNDK). The subunit consists of six α-helices along with a core of four ß-strands arranged in a ß2ß3ß1ß4 antiparallel topology order. In contrast to the NDK from L. major, the LbNDK C-terminal extension is partially unfolded. SAXS data showed that LbNDK forms hexamers in solution in the pH range from 7.0 to 4.0, a hydrodynamic behavior conserved in most eukaryotic NDKs. However, DSF assays show that acidification and alkalization decrease the hexamer stability. CONCLUSIONS: Our results support that LbNDK remains hexameric in pH conditions akin to that faced by this enzyme when secreted by Leishmania amastigotes in the parasitophorous vacuoles (pH 4.7 to 5.3). The unusual unfolded conformation of LbNDK C-terminus decreases the surface buried in the trimer interface exposing new regions that might be explored for the development of compounds designed to disturb enzyme oligomerization, which may impair the important nucleotide salvage pathway in these parasites.


Subject(s)
Leishmania braziliensis/enzymology , Nucleoside-Diphosphate Kinase/chemistry , Protozoan Proteins/chemistry , Crystallography, X-Ray , Enzyme Stability , Hydrogen-Ion Concentration , Leishmania braziliensis/chemistry , Models, Molecular , Nucleoside-Diphosphate Kinase/genetics , Protein Multimerization , Protein Structure, Secondary , Protein Structure, Tertiary , Protein Unfolding , Protozoan Proteins/genetics , Scattering, Small Angle
16.
Molecules ; 20(1): 1176-91, 2015 Jan 13.
Article in English | MEDLINE | ID: mdl-25591119

ABSTRACT

Human Neks are a conserved protein kinase family related to cell cycle progression and cell division and are considered potential drug targets for the treatment of cancer and other pathologies. We screened the activation loop mutant kinases hNek1 and hNek2, wild-type hNek7, and five hNek6 variants in different activation/phosphorylation statesand compared them against 85 compounds using thermal shift denaturation. We identified three compounds with significant Tm shifts: JNK Inhibitor II for hNek1(Δ262-1258)-(T162A), Isogranulatimide for hNek6(S206A), andGSK-3 Inhibitor XIII for hNek7wt. Each one of these compounds was also validated by reducing the kinases activity by at least 25%. The binding sites for these compounds were identified by in silico docking at the ATP-binding site of the respective hNeks. Potential inhibitors were first screened by thermal shift assays, had their efficiency tested by a kinase assay, and were finally analyzed by molecular docking. Our findings corroborate the idea of ATP-competitive inhibition for hNek1 and hNek6 and suggest a novel non-competitive inhibition for hNek7 in regard to GSK-3 Inhibitor XIII. Our results demonstrate that our approach is useful for finding promising general and specific hNekscandidate inhibitors, which may also function as scaffolds to design more potent and selective inhibitors.


Subject(s)
Cell Cycle Proteins/antagonists & inhibitors , Protein Kinase Inhibitors/pharmacology , Protein Serine-Threonine Kinases/antagonists & inhibitors , Cell Cycle Proteins/metabolism , Humans , Molecular Docking Simulation , NIMA-Related Kinase 1 , NIMA-Related Kinases , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/metabolism , Protein Serine-Threonine Kinases/metabolism , Recombinant Proteins/drug effects , Recombinant Proteins/metabolism , Substrate Specificity
17.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 6): 1631-9, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24914974

ABSTRACT

Product inhibition of ß-glucosidases (BGs) by glucose is considered to be a limiting step in enzymatic technologies for plant-biomass saccharification. Remarkably, some ß-glucosidases belonging to the GH1 family exhibit unusual properties, being tolerant to, or even stimulated by, high glucose concentrations. However, the structural basis for the glucose tolerance and stimulation of BGs is still elusive. To address this issue, the first crystal structure of a fungal ß-glucosidase stimulated by glucose was solved in native and glucose-complexed forms, revealing that the shape and electrostatic properties of the entrance to the active site, including the +2 subsite, determine glucose tolerance. The aromatic Trp168 and the aliphatic Leu173 are conserved in glucose-tolerant GH1 enzymes and contribute to relieving enzyme inhibition by imposing constraints at the +2 subsite that limit the access of glucose to the -1 subsite. The GH1 family ß-glucosidases are tenfold to 1000-fold more glucose tolerant than GH3 BGs, and comparative structural analysis shows a clear correlation between active-site accessibility and glucose tolerance. The active site of GH1 BGs is located in a deep and narrow cavity, which is in contrast to the shallow pocket in the GH3 family BGs. These findings shed light on the molecular basis for glucose tolerance and indicate that GH1 BGs are more suitable than GH3 BGs for biotechnological applications involving plant cell-wall saccharification.


Subject(s)
Cellulases/chemistry , Glucose/chemistry , Amino Acid Sequence , Catalytic Domain , Crystallization , Crystallography, X-Ray , Molecular Sequence Data , Protein Conformation , Scattering, Small Angle , Sequence Homology, Amino Acid
18.
Plant Physiol ; 162(3): 1311-23, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23709667

ABSTRACT

The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism.


Subject(s)
Citrus sinensis/metabolism , Cyclophilins/chemistry , Cyclophilins/metabolism , Cysteine/metabolism , RNA Polymerase II/metabolism , Amino Acid Sequence , Binding Sites , Catalytic Domain , Conserved Sequence , Crystallography, X-Ray , Cyclophilins/genetics , Cyclosporine/chemistry , Cyclosporine/metabolism , Disulfides/metabolism , Glutamic Acid/metabolism , Models, Molecular , Molecular Sequence Data , Oxidation-Reduction , Protein Conformation , Thioredoxins/metabolism , Zinc/metabolism
19.
NPJ Biofilms Microbiomes ; 10(1): 105, 2024 Oct 14.
Article in English | MEDLINE | ID: mdl-39397008

ABSTRACT

Gut microbiota members from the Bacteroidota phylum play a pivotal role in mammalian health and metabolism. They thrive in this diverse ecosystem due to their notable ability to cope with distinct recalcitrant dietary glycans via polysaccharide utilization loci (PULs). Our study reveals that a PUL from an herbivore gut bacterium belonging to the Bacteroidota phylum, with a gene composition similar to that in the human gut, exhibits extended functionality. While the human gut PUL targets mixed-linkage ß-glucans specifically, the herbivore gut PUL also efficiently processes linear and substituted ß-1,3-glucans. This gain of function emerges from molecular adaptations in recognition proteins and carbohydrate-active enzymes, including a ß-glucosidase specialized for ß(1,6)-glucosyl linkages, a typical substitution in ß(1,3)-glucans. These findings broaden the existing model for non-cellulosic ß-glucans utilization by gut bacteria, revealing an additional layer of functional and evolutionary complexity within the gut microbiota, beyond conventional gene insertions/deletions to intricate biochemical interactions.


Subject(s)
Bacteroidetes , Gastrointestinal Microbiome , Herbivory , beta-Glucans , beta-Glucans/metabolism , Animals , Bacteroidetes/genetics , Humans , Phylogeny , Carbohydrate Metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism
20.
Article in English | MEDLINE | ID: mdl-23545647

ABSTRACT

Tryparedoxin peroxidase (TXNPx) is an essential constituent of the main enzymatic scavenger system for reactive oxygen species (ROS) in trypanosomatids. Genetic studies have demonstrated the importance of this system for the development and virulence of these parasites, representing a potential target for the discovery of new trypanocidal drugs. In this work, the mitochondrial TXNPx from Leishmania braziliensis was cloned, overexpressed, purified and crystallized. The crystals diffracted to 3.3 Å resolution and belonged to space group P4(2)2(1)2, with unit-cell parameters a = b = 131.8, c = 44.4 Å. These studies will contribute to a better understanding of the molecular mechanisms involved in ROS detoxification by trypanosomatids.


Subject(s)
Leishmania braziliensis/enzymology , Peroxidases/chemistry , Protozoan Proteins/chemistry , Cloning, Molecular , Crystallization , Crystallography, X-Ray , Gene Expression , Mitochondria/enzymology , Peroxidases/isolation & purification , Protozoan Proteins/isolation & purification
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