scholarly journals A forty-year journey in plant research: original contributions to flavonoid biochemistry

2005 ◽  
Vol 83 (5) ◽  
pp. 433-450 ◽  
Author(s):  
Ragai K Ibrahim
Keyword(s):  
Three Dimensional ◽  
Biological Significance ◽  
Flavonoid Biosynthesis ◽  
Dimensional Structure ◽  
Enzymatic Reactions ◽  
Research Career ◽  
Substrate Preferences ◽  
Genes Encoding ◽  
The Common ◽  
New Compounds

This review highlights original contributions by the author to the field of flavonoid biochemistry during his research career of more than four decades. These include elucidation of novel aspects of some of the common enzymatic reactions involved in the later steps of flavonoid biosynthesis, with emphasis on methyltransferases, glucosyltransferases, sulfotransferases, and an oxoglutarate-dependent dioxygenase, as well as cloning, and inferences about phylogenetic relationships, of the genes encoding some of these enzymes. The three-dimensional structure of a flavonol O-methyltransferase was studied through homology-based modeling, using a caffeic acid O-methyltransferase as a template, to explain their strict substrate preferences. In addition, the biological significance of enzymatic prenylation of isoflavones, as well as their role as phytoanticipins and inducers of nodulation genes, are emphasized. Finally, the potential application of knowledge about the genes encoding these enzyme reactions is discussed in terms of improving plant productivity and survival, modification of flavonoid profiles, and the search for new compounds with pharmaceutical and (or) nutraceutical value.Key words: flavonoid enzymology, metabolite localization, gene cloning, 3-D structure, phylogeny.

scholarly journals Crystal structure of the MIF4G domain of the Trypanosoma cruzi translation initiation factor EIF4G5

2019 ◽  
Vol 75 (12) ◽  
pp. 738-743
Author(s):  
Lucca Pietro Camillo dos Santos ◽  
Bruno Moisés de Matos ◽  
Brenda Cecilia de Maman Ribeiro ◽  
Nilson Ivo Tonin Zanchin ◽  
Beatriz Gomes Guimarães
Keyword(s):  
Crystal Structure ◽  
Translation Initiation ◽  
Specific Interaction ◽  
Three Dimensional ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Dimensional Structure ◽  
Initiation Factors ◽  
Genes Encoding ◽  
Rna Complexes

Kinetoplastida, a class of early-diverging eukaryotes that includes pathogenic Trypanosoma and Leishmania species, display key differences in their translation machinery compared with multicellular eukaryotes. One of these differences involves a larger number of genes encoding eIF4E and eIF4G homologs and the interaction pattern between the translation initiation factors. eIF4G is a scaffold protein which interacts with the mRNA cap-binding factor eIF4E, the poly(A)-binding protein, the RNA helicase eIF4A and the eIF3 complex. It contains the so-called middle domain of eIF4G (MIF4G), a multipurpose adaptor involved in different protein–protein and protein–RNA complexes. Here, the crystal structure of the MIF4G domain of T. cruzi EIF4G5 is described at 2.4 Å resolution, which is the first three-dimensional structure of a trypanosomatid MIF4G domain to be reported. Structural comparison with IF4G homologs from other eukaryotes and other MIF4G-containing proteins reveals differences that may account for the specific interaction mechanisms of MIF4G despite its highly conserved overall fold.

scholarly journals Streptococcal phosphotransferase system imports unsaturated hyaluronan disaccharide derived from host extracellular matrices

2018 ◽  
Author(s):  
Sayoko Oiki ◽  
Yusuke Nakamichi ◽  
Yukie Maruyama ◽  
Bunzo Mikami ◽  
Kousaku Murata ◽  
...  
Keyword(s):  
Abc Transporter ◽  
Molecular System ◽  
Bacterial Species ◽  
Three Dimensional ◽  
Amino Sugar ◽  
Extracellular Matrices ◽  
Dimensional Structure ◽  
Phosphotransferase System ◽  
Streptobacillus Moniliformis ◽  
Genes Encoding

ABSTRACTCertain bacterial species target the polysaccharide glycosaminoglycans (GAGs) of animal extracellular matrices for colonization and/or infection. GAGs such as hyaluronan and chondroitin sulfate consist of repeating disaccharide units of uronate and amino sugar residues, and are depolymerized to unsaturated disaccharides by bacterial extracellular or cell-surface polysaccharide lyase. The disaccharides are degraded and metabolized by cytoplasmic enzymes such as unsaturated glucuronyl hydrolase, isomerase, and reductase. The genes encoding these enzymes are assembled to form a GAG genetic cluster. Here, we demonstrate theStreptococcus agalactiaephosphotransferase system (PTS) for import of unsaturated hyaluronan disaccharide.S. agalactiaeNEM316 was found to depolymerize and assimilate hyaluronan, whereas its mutant with a disruption in PTS genes included in the GAG cluster was unable to grow on hyaluronan, while retaining the ability to depolymerize hyaluronan. Using toluene-treated wild-type cells, the PTS import activity of unsaturated hyaluronan disaccharide was significantly higher than that observed in the absence of the substrate. In contrast, the PTS mutant was unable to import unsaturated hyaluronan disaccharide, indicating that the corresponding PTS is the only importer of fragmented hyaluronan, which is suitable for PTS to phosphorylate the substrate at the C-6 position. The three-dimensional structure of streptococcal EIIA, one of the PTS components, was found to contain a Rossman-fold motif by X-ray crystallization. Docking of EIIA with another component EIIB by modeling provided structural insights into the phosphate transfer mechanism. This study is the first to identify the substrate (unsaturated hyaluronan disaccharide) recognized and imported by the streptococcal PTS.IMPORTANCE (118/120 words)The PTS identified in this work imports sulfate group-free unsaturated hyaluronan disaccharide as a result of the phosphorylation of the substrate at the C-6 position.S. agalactiaecan be indigenous to animal hyaluronan-rich tissues owing to the bacterial molecular system for fragmentation, import, degradation, and metabolism of hyaluronan. Distinct from hyaluronan, most GAGs, which are sulfated at the C-6 position, are unsuitable for PTS due to its inability to phosphorylate the substrate. More recently, we have identified a solute-binding protein-dependent ABC transporter in a pathogenicStreptobacillus moniliformisas an importer of sulfated and non-sulfated fragmented GAGs without any substrate modification. Our findings regarding PTS and ABC transporter shed light on bacterial clever colonization/infection system targeting various animal GAGs.

scholarly journals Carboxy-Terminal Processing of the Large Subunit of [Fe] Hydrogenase from Desulfovibrio desulfuricans ATCC 7757

1999 ◽  
Vol 181 (9) ◽  
pp. 2947-2952 ◽  
Author(s):  
E. Claude Hatchikian ◽  
Valérie Magro ◽  
Nicole Forget ◽  
Yvain Nicolet ◽  
Juan C. Fontecilla-Camps
Keyword(s):  
Large Subunit ◽  
Three Dimensional ◽  
Desulfovibrio Desulfuricans ◽  
Small Subunit ◽  
Dimensional Structure ◽  
Desulfovibrio Vulgaris ◽  
Closely Related Species ◽  
Genes Encoding ◽  
Reported Data ◽  
Carboxy Terminal

ABSTRACT hydA and hydB, the genes encoding the large (46-kDa) and small (13.5-kDa) subunits of the periplasmic [Fe] hydrogenase from Desulfovibrio desulfuricans ATCC 7757, have been cloned and sequenced. The deduced amino acid sequence of the genes product showed complete identity to the sequence of the well-characterized [Fe] hydrogenase from the closely related speciesDesulfovibrio vulgaris Hildenborough (G. Voordouw and S. Brenner, Eur. J. Biochem. 148:515–520, 1985). The data show that in addition to the well-known signal peptide preceding the NH2 terminus of the mature small subunit, the large subunit undergoes a carboxy-terminal processing involving the cleavage of a peptide of 24 residues, in agreement with the recently reported data on the three-dimensional structure of the enzyme (Y. Nicolet, C. Piras, P. Legrand, E. C. Hatchikian, and J. C. Fontecilla-Camps, Structure 7:13–23, 1999). We suggest that this C-terminal processing is involved in the export of the protein to the periplasm.

Die Synthese und Struktur von Clusteraziden: A4[Nb6Cl12(N3)6](H2O)2 mit A=Rb. Cs / Synthesis and Structure of the Cluster Azides: A4Nb6Cl12(N3)6](H2O)2 with A=Rb, Cs

1995 ◽  
Vol 50 (9) ◽  
pp. 1377-1381 ◽  
Author(s):  
Olaf Reckeweg ◽  
H.-Jürgen Meyer
Keyword(s):  
Single Crystal ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Crystal Data ◽  
Mechanical Pressure ◽  
Space Group ◽  
X Ray ◽  
Methanolic Solution ◽  
New Compounds

AbstractThe new compounds A4[Nb6Cl12(N3)6](H2O)2 (A = Rb, Cs) were synthesized from In4[Nb6Cl12Cl6] by substituting six terminal Cl ligands and the In+ ions in methanolic solution. An X-ray structure refinement was performed on single-crystal data of Rb4[Nb6Cl12(N3)6](H2O)2 (1) (space group P1̄, Z = 1, a = 912.5(1) pm, b = 937.2(1) pm, c = 1062.0(1) pm, α = 96.88(2)°, β = 101.89(1)°, γ = 101.44(2)°) and Cs4[Nb6Cl12(N3)6](H2O)2 (2) (space group PI, Z = 1, a = 920.9(5) pm, b = 947.9(7) pm, c = 1091.8(7) pm, α = 96.89(6)°, β = 103.35(5)°, γ = 101.60(5)°. Each of the centrosymmetric [Nb6Cl12(N3)6]4- ions of the isotypic compounds contains six terminal azide groups at the corners of the octahedral niobium cluster (d̄Nb-N = 226(1) pm (1), 225(1) pm (2), bond angles Nb-N-N 120-127°). The [Nb6Cl12(N3)6]4- ions are linked via Rb-N and Rb-Cl interactions of the Rb+ ions to form a three-dimensional structure. Crystals of the compounds react explosively on heating or mechanical pressure.

scholarly journals From the Eukaryotic Molybdenum Cofactor Biosynthesis to the Moonlighting Enzyme mARC

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3287 ◽  
Author(s):  
Manuel Tejada-Jimenez ◽  
Alejandro Chamizo-Ampudia ◽  
Victoria Calatrava ◽  
Aurora Galvan ◽  
Emilio Fernandez ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Cytochrome B5 ◽  
Three Dimensional ◽  
Reducing Power ◽  
Aldehyde Oxidase ◽  
Nitrite Reduction ◽  
Dimensional Structure ◽  
Enzymatic Reactions ◽  
Structural Mechanism ◽  
Cofactor Biosynthesis

All eukaryotic molybdenum (Mo) enzymes contain in their active site a Mo Cofactor (Moco), which is formed by a tricyclic pyranopterin with a dithiolene chelating the Mo atom. Here, the eukaryotic Moco biosynthetic pathway and the eukaryotic Moco enzymes are overviewed, including nitrate reductase (NR), sulfite oxidase, xanthine oxidoreductase, aldehyde oxidase, and the last one discovered, the moonlighting enzyme mitochondrial Amidoxime Reducing Component (mARC). The mARC enzymes catalyze the reduction of hydroxylated compounds, mostly N-hydroxylated (NHC), but as well of nitrite to nitric oxide, a second messenger. mARC shows a broad spectrum of NHC as substrates, some are prodrugs containing an amidoxime structure, some are mutagens, such as 6-hydroxylaminepurine and some others, which most probably will be discovered soon. Interestingly, all known mARC need the reducing power supplied by different partners. For the NHC reduction, mARC uses cytochrome b5 and cytochrome b5 reductase, however for the nitrite reduction, plant mARC uses NR. Despite the functional importance of mARC enzymatic reactions, the structural mechanism of its Moco-mediated catalysis is starting to be revealed. We propose and compare the mARC catalytic mechanism of nitrite versus NHC reduction. By using the recently resolved structure of a prokaryotic MOSC enzyme, from the mARC protein family, we have modeled an in silico three-dimensional structure of a eukaryotic homologue.

scholarly journals Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases

2001 ◽  
Vol 183 (2) ◽  
pp. 680-686 ◽  
Author(s):  
Kathryn A. Buss ◽  
David R. Cooper ◽  
Cheryl Ingram-Smith ◽  
James G. Ferry ◽  
David Avram Sanders ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Acetate Kinase ◽  
Active Site Residues ◽  
Methanosarcina Thermophila ◽  
The Core ◽  
Binding Domains ◽  
The Common ◽  
Actin Superfamily

ABSTRACT Acetate kinase, an enzyme widely distributed in theBacteria and Archaea domains, catalyzes the phosphorylation of acetate. We have determined the three-dimensional structure of Methanosarcina thermophila acetate kinase bound to ADP through crystallography. As we previously predicted, acetate kinase contains a core fold that is topologically identical to that of the ADP-binding domains of glycerol kinase, hexokinase, the 70-kDa heat shock cognate (Hsc70), and actin. Numerous charged active-site residues are conserved within acetate kinases, but few are conserved within the phosphotransferase superfamily. The identity of the points of insertion of polypeptide segments into the core fold of the superfamily members indicates that the insertions existed in the common ancestor of the phosphotransferases. Another remarkable shared feature is the unusual, epsilon conformation of the residue that directly precedes a conserved glycine residue (Gly-331 in acetate kinase) that binds the α-phosphate of ADP. Structural, biochemical, and geochemical considerations indicate that an acetate kinase may be the ancestral enzyme of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases.

scholarly journals Selfish: discovery of differential chromatin interactions via a self-similarity measure

2019 ◽  
Vol 35 (14) ◽  
pp. i145-i153 ◽  
Author(s):  
Abbas Roayaei Ardakany ◽  
Ferhat Ay ◽  
Stefano Lonardi
Keyword(s):  
Comparative Analysis ◽  
Similarity Measure ◽  
Fundamental Problem ◽  
Three Dimensional ◽  
Biological Significance ◽  
Real Data ◽  
Dimensional Structure ◽  
Self Similarity ◽  
Contact Maps ◽  
Chromatin Interactions

AbstractMotivationHigh-throughput conformation capture experiments, such as Hi-C provide genome-wide maps of chromatin interactions, enabling life scientists to investigate the role of the three-dimensional structure of genomes in gene regulation and other essential cellular functions. A fundamental problem in the analysis of Hi-C data is how to compare two contact maps derived from Hi-C experiments. Detecting similarities and differences between contact maps are critical in evaluating the reproducibility of replicate experiments and for identifying differential genomic regions with biological significance. Due to the complexity of chromatin conformations and the presence of technology-driven and sequence-specific biases, the comparative analysis of Hi-C data is analytically and computationally challenging.ResultsWe present a novel method called Selfish for the comparative analysis of Hi-C data that takes advantage of the structural self-similarity in contact maps. We define a novel self-similarity measure to design algorithms for (i) measuring reproducibility for Hi-C replicate experiments and (ii) finding differential chromatin interactions between two contact maps. Extensive experimental results on simulated and real data show that Selfish is more accurate and robust than state-of-the-art methods.Availability and implementationhttps://github.com/ucrbioinfo/Selfish

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of theEscherichia colicommon pilus chaperone EcpB

2015 ◽  
Vol 71 (6) ◽  
pp. 676-679 ◽  
Author(s):  
James A. Garnett ◽  
Mamou Diallo ◽  
Steve J. Matthews
Keyword(s):  
Heavy Atom ◽  
Three Dimensional ◽  
Solid Surfaces ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
The Common ◽  
First Time

Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. InEscherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.4 Å resolution. These crystals belonged to the trigonal space groupP3121 orP3221, with unit-cell parametersa=b= 62.65,c= 121.14 Å and one monomer in the asymmetric unit. Molecular replacement was unsuccessful, but selenomethionine-substituted protein and heavy-atom derivatives are being prepared for phasing. The three-dimensional structure of EcpB will provide invaluable information on the subtle mechanistic differences in biogenesis between the alternative and classical CU pathways. Furthermore, this is the first time that this refolding strategy has been used to purify CU chaperones, and it could be implemented in similar systems where it has not been possible to obtain highly ordered crystals.

scholarly journals The N Terminus of the Escherichia coli Transcription Activator MalT Is the Domain of Interaction with MalY

2002 ◽  
Vol 184 (11) ◽  
pp. 3069-3077 ◽  
Author(s):  
Anja Schlegel ◽  
Olivier Danot ◽  
Evelyne Richet ◽  
Thomas Ferenci ◽  
Winfried Boos
Keyword(s):  
Escherichia Coli ◽  
Gel Filtration ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structural Domain ◽  
Transcription Activator ◽  
Acetyl Esterase ◽  
Regulatory Circuits ◽  
Genes Encoding

ABSTRACT The maltose system of Escherichia coli consists of a number of genes encoding proteins involved in the uptake and metabolism of maltose and maltodextrins. The system is positively regulated by MalT, its transcriptional activator. MalT activity is controlled by two regulatory circuits: a positive one with maltotriose as effector and a negative one involving several proteins. MalK, the ATP-hydrolyzing subunit of the cognate ABC transporter, MalY, an enzyme with the activity of a cystathionase, and Aes, an acetyl esterase, phenotypically act as repressors of MalT activity. By in vivo titration assays, we have shown that the N-terminal 250 amino acids of MalT contain the interaction site for MalY but not for MalK. This was confirmed by gel filtration analysis, where MalY was shown to coelute with the N-terminal MalT structural domain. Mutants in MalT causing elevated mal gene expression in the absence of exogenous maltodextrins were tested in their response to the three repressors. The different MalT mutations exhibited a various degree of sensitivity towards these repressors, but none was resistant to all of them. Some of them became nearly completely resistant to Aes while still being sensitive to MalY. These mutations are located at positions 38, 220, 243, and 359, most likely defining the interaction patch with Aes on the three-dimensional structure of MalT.

scholarly journals Three-dimensional structure and ligand binding properties of trichosurin, a metatherian lipocalin from the milk whey of the common brushtail possum Trichosurus vulpecula

2007 ◽  
Vol 408 (1) ◽  
pp. 29-38 ◽  
Author(s):  
Randall P. Watson ◽  
Jerome Demmer ◽  
Edward N. Baker ◽  
Vickery L. Arcus
Keyword(s):  
Three Dimensional ◽  
Extracellular Proteins ◽  
Dimensional Structure ◽  
Brushtail Possum ◽  
Trichosurus Vulpecula ◽  
Three Dimensional Structure ◽  
Milk Whey ◽  
Ph Values ◽  
The Common ◽  
Common Brushtail Possum

Lipocalins are extracellular proteins (17–25 kDa) that bind and transport small lipophilic molecules. The three-dimensional structure of the first lipocalin from a metatherian has been determined at different values of pH both with and without bound ligands. Trichosurin, a protein from the milk whey of the common brushtail possum, Trichosurus vulpecula, has been recombinantly expressed in Escherichia coli, refolded from inclusion bodies, purified and crystallized at two different pH values. The three-dimensional structure of trichosurin was solved by X-ray crystallography in two different crystal forms to 1.9 Å (1 Å=0.1 nm) and 2.6 Å resolution, from crystals grown at low and high pH values respectively. Trichosurin has the typical lipocalin fold, an eight-stranded anti-parallel β-barrel but dimerizes in an orientation that has not been seen previously. The putative binding pocket in the centre of the β-barrel is well-defined in both high and low pH structures and is occupied by water molecules along with isopropanol molecules from the crystallization medium. Trichosurin was also co-crystallized with a number of small molecule ligands and structures were determined with 2-naphthol and 4-ethylphenol bound in the centre of the β-barrel. The binding of phenolic compounds by trichosurin provides clues to the function of this important marsupial milk protein, which is highly conserved across metatherians.

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