ABSTRACT
Cyclomaltohexaicosaose (CA26) is folded into two 1(2)/(3) turns long V-helices that are oriented antiparallel. Crystals of complexes of CA26 with NH(4)I(3) and Ba(I(3))(2) are brown and X-ray analyses show that I(3)(-) units are located in the approximately 5 A wide central channels of the V-helices. In the complex with NH(4)I(3), two CA26 molecules are stacked to form 2 x 1(2)/(3) turns long channels harbouring 3 I(3)(-) at 3.66-3.85 A inter I(3)(-) distance (shorter than van der Waals distance, 4.3 A), whereas in the Ba(I(3))(2) complex, CA26 are not stacked and only one I(3)(-) each fills the V-helices. Glucose...I contacts are formed with C5-H, C3-H, C6-H and (at the ends of the V-helices) with O6 in (+) gauche orientation. By contrast, O2, O3, O4 and O6 in the preferred (-) gauche orientation do not interact with I because these distances are >/=4.01 A and exceed the van der Waals I...O sum of radii by about 0.5 A except for one O2...I distance of 3.68 A near the end of one V-helix. Raman spectra indicate that the complexes share the presence of I(3)(-) with blue amylose-iodine.
Subject(s)
Amylose/chemistry , Cyclodextrins/chemistry , Iodine Compounds/chemistry , Carbohydrate Conformation , Carbohydrate Sequence , Crystallography, X-Ray , Models, Molecular , Molecular Sequence Data , Oxygen/chemistryABSTRACT
A peptide named apisimin was found in honeybee (Apis mellifera L.) royal jelly (RJ). N-terminal sequencing showed that this peptide corresponded to the sequence of a cDNA clone isolated from an expression cDNA library prepared from heads of nurse honeybees. No homology was found between the protein sequence of apisimin with a molecular mass of 5540.4 Da and sequences deposited in the Swiss-Prot database. The 54 amino acids of apisimin do not include Cys, Met, Pro, Arg, His, Tyr, and Trp residues. The peptide shows a well-defined secondary structure as observed by CD spectroscopy, and has the tendency to form oligomers. Isoelectrofocusing showed apisimin to be an acidic peptide.
Subject(s)
Bees/chemistry , Fatty Acids/chemistry , Insect Proteins/isolation & purification , Amino Acid Sequence , Animals , Base Sequence , Bees/genetics , Circular Dichroism , DNA, Complementary/genetics , Insect Proteins/chemistry , Insect Proteins/genetics , Molecular Sequence Data , Molecular Weight , Protein Structure, Secondary , Serine/analysis , Valine/analysisABSTRACT
The 71 amino acid residue omega protein encoded by the Streptococcus pyogenes non-conjugative plasmid pSM19035 is a transcriptional repressor that regulates expression of genes for copy number control and stable maintenance of plasmids. The crystal structure of omega protein has been determined by multiple isomorphous replacement, including anomalous scattering and refined to an R-factor of 21.1 % (R(free)=23.2 %) at 1.5 A resolution. Two monomers related by a non-crystallographic 2-fold axis form a homodimer that occupies the asymmetric unit. Each polypeptide chain is folded into two alpha-helices and one beta-strand forming an antiparallel beta-ribbon in the homodimer. The N-terminal regions (1-23 and 1-22 in subunits I and II, respectively) are not defined in the electron density due to proteolysis of the N-terminal 20 amino acid residues during crystallisation and partial disorder. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognizing the major groove of operator DNA; according to a modelled omega protein-DNA complex, residues Arg31 and Arg31' on the beta-ribbon are in positions to interact with a nucleobase, especially guanine.
Subject(s)
DNA-Binding Proteins/chemistry , Plasmids/genetics , Repressor Proteins/chemistry , Streptococcus pyogenes/chemistry , Streptococcus pyogenes/genetics , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Base Sequence , Circular Dichroism , Crystallography, X-Ray , DNA/chemistry , DNA/genetics , DNA/metabolism , DNA Replication , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Dimerization , Gene Dosage , Hydrogen Bonding , Models, Molecular , Molecular Sequence Data , Nucleic Acid Conformation , Protein Structure, Quaternary , Protein Structure, Secondary , Repressor Proteins/genetics , Repressor Proteins/metabolism , Sequence Alignment , Solvents , Static ElectricityABSTRACT
The molecular structures of peracylated beta-cyclodextrins (CDs)--heptakis(2,3,6-tri-O-acetyl)-beta-CD (TA), heptakis(2,3,6-tri-O-propanoyl)-beta-CD (TP), and heptakis(2,3,6-tri-O-butanoyl)-beta-CD (TB)--have been determined by single crystal X-ray structure analysis. Due to the lack of O2...O3' hydrogen bonds between adjacent glucose units of the peracylated CDs, the macrocycles are elliptically distorted into nonplanar boat-shaped structures. The glucose units are tilted with respect to the O4 plane to relieve steric hindrance between adjacent acyl chains. In TB, all glucose units adopt the common (4)C(1)-chair conformation and one butanoyl chain intramolecularly penetrates the cavity, whereas, in TA and TP, one glucose unit each occurs in (O)S(2)-skew-boat conformation and one acyl chain closes the O6 side like a lid. In each of the three homologous molecules the intramolecular self-inclusion and lidlike orientation of acyl chains forces the associated O5-C5-C6-O6 torsion angle into a trans-conformation never observed before for unsubstituted CD; the inclusion behavior of TA, TP, and TB in solution has been studied by circular dichroism spectroscopy with the drug molsidomine and several organic compounds. No inclusion complexes are formed, which is attributed to the intramolecular closure of the molecular cavity by one of the acyl chains.
Subject(s)
Cyclodextrins/chemistry , beta-Cyclodextrins , Acetylation , Crystallization , Crystallography, X-Ray , Hydrogen Bonding , Models, Molecular , Molecular Conformation , Molecular StructureABSTRACT
Cycloamylose containing 26 glucose residues (cyclohexaicosaose, CA26) crystallized from water and 30% (v/v) polyethyleneglycol 400 in the orthorhombic space group P2(1)2(1)2(1) in the highly hydrated form CA26.32.59 H(2)O. X-ray analysis of the crystals at 0.85 A resolution shows that the macrocycle of CA26 is folded into two short left-handed V-amylose helices in antiparallel arrangement and related by a twofold rotational pseudosymmetry as reported recently for the (CA26)(2).76.75 H(2)O triclinic crystal form [Gessler, K. et al. Proc. Natl. Acad. Sci. USA 1999, 96, 4246-4251]. In the orthorhombic crystal form, CA26 molecules are packed in motifs reminiscent of V-amylose in hydrated and anhydrous forms. The intramolecular interface between the V-helices in CA26 is dictated by formation of an extended network of interhelical C-H...O hydrogen bonds; a comparable molecular arrangement is also evident for the intermolecular packing, suggesting that it is a characteristic feature of V-amylose interaction. The hydrophobic channels of CA26 are filled with disordered water molecules arranged in chains and held in position by multiple C-H...O hydrogen bonds. In the orthorhombic and triclinic crystal forms, the structures of CA26 molecules are equivalent but the positions of the individual water molecules are different, suggesting that the patterns of water chains are perturbed even by small structural changes associated with differences in packing arrangements in the two crystal lattices rather than with differences in the CA26 geometry.
Subject(s)
Cyclodextrins/chemistry , Water/chemistry , Carbohydrate Conformation , Crystallization , Crystallography, X-Ray , Hydrogen Bonding , Molecular Conformation , Molecular StructureABSTRACT
A single-crystal neutron diffraction study of cyclodecaamylose (CA10) was carried out at 20 K. CA10 crystallizes with 27.18 water molecules [(C(6)H(10)O(5))(10).27.18H(2)O] in space group C2 with unit-cell constants a = 29.31 (5), b = 9.976 (10), c = 19.34 (2) A, beta = 121.07 (2) degrees. The asymmetric unit contains a half molecule of CA10 and 13.59 water molecules, the other half being related by a crystallographic twofold rotation axis. All H atoms except two water H atoms could be located from difference neutron-density maps; structure refinement converged at R = 0.635. Two of the five CH(2)-O6 groups and one of the 15 O2, O3 hydroxyl groups of CA10 are twofold orientationally disordered. A total of 13.59 water molecules in the asymmetric unit are distributed over 23 positions; 20 of which are in the CA10 cavity, and the other three occupy intermolecular interstices. Of the 123 symmetry-independent hydrogen bonds, 25 (= 20%) are three-centered and 7 (= 6%) are four-centered. Water molecules and O-H groups of CA10 form an extended network with cooperative O-H...O-H...O-H hydrogen bonds. They are arranged in 11 polygons with three, four, five, six and eight O-H bonds and in homodromic, antidromic and heterodromic arrangements. Nine polygons are located within the cavity and the others are outside.
ABSTRACT
At the transcriptional level, the pSM19035-encoded omega protein coordinates the expression of proteins required for control of copy number and maintenance of plasmids. Using circular dichroism, fluorescence spectroscopy, ultracentrifugation and an electrophoretic mobility shift assay, the wild-type omega protein and a variant with a C-terminal hexa-histidine tag (omega-H(6)) were characterized. The omega protein is mainly alpha-helical (42%), occurs as homodimer in solution, unfolds thermally with half transition temperatures, T(m), between approximately 43 and approximately 78 degrees C depending on the ionic strength of the buffer, and binds PcopS-DNA with high affinity. The omega-H(6) protein has a modified conformation with lower alpha-helix content (29%), lower thermal stability, and strongly reduced affinity to PcopS-DNA.
Subject(s)
Bacterial Proteins/metabolism , DNA-Binding Proteins/metabolism , Plasmids , Streptococcus pyogenes/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Circular Dichroism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , DNA-Binding Proteins/isolation & purification , Dimerization , Protein Denaturation , Spectrometry, Fluorescence , Thermodynamics , UltracentrifugationABSTRACT
The heterotrimeric complex of the human major histocompatibity complex (MHC) molecule HLA-A*0201, beta2-microglobulin and the decameric peptide GVYDGREHTV derived from the melanoma antigen (MAGE-A4 protein has been determined by X-ray crystallography at 1.4 A resolution. MAGE-A4 belongs to a family of genes that are specifically expressed in a variety of tumours. MAGE-A4-derived peptides are presented by MHC molecules at the cell surface to cytotoxic T-lymphocytes. As the HLA-A*0201:MAGE-A4 complex occurs only on tumour cells, it is considered to be an appropriate target for immunotherapy. The structure presented here reveals potential epitopes specific to the complex and indicates which peptide residues could be recognised by T-cell receptors. In addition, as the structure could be refined anisotropically, it was possible to describe the movements of the bound peptide in more detail.
Subject(s)
Antigens, Neoplasm/chemistry , Antigens, Neoplasm/metabolism , HLA-A Antigens/chemistry , HLA-A Antigens/metabolism , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Amino Acid Sequence , Antigens, Neoplasm/genetics , Antigens, Neoplasm/immunology , Binding Sites , Circular Dichroism , Crystallography, X-Ray , Epitopes, T-Lymphocyte/chemistry , Epitopes, T-Lymphocyte/immunology , HLA-A Antigens/immunology , Humans , Immunotherapy , Ligands , Models, Molecular , Neoplasm Proteins/chemistry , Neoplasm Proteins/genetics , Neoplasm Proteins/immunology , Neoplasm Proteins/metabolism , Peptide Fragments/immunology , Polyethylene Glycols/chemistry , Polyethylene Glycols/metabolism , Protein Binding , Protein Conformation , Protein Denaturation , Receptors, Antigen, T-Cell/immunology , Temperature , Thermodynamics , beta 2-Microglobulin/chemistry , beta 2-Microglobulin/metabolismABSTRACT
In a series of four racemic phenoxyalkyl-alkyl carbinols, 1-phenoxy-2-hydroxybutane (1) is enantioselectively acetylated by Burkholderia cepacia (formerly Pseudomonas cepacia) lipase with an E value > or = 200, whereas for the other three racemates E was found to be < or = 4. To explain the high preference of B. cepacia lipase for (R)-(+)-1, a precursor of its transition state analogue with a tetrahedral P-atom, (R(P),S(P))-O-(2R)-(1-phenoxybut-2-yl)methylphosphonic acid chloride was prepared and crystallized in complex with B. cepacia lipase. The X-ray structure of the complex was determined, allowing to compare the conformation of the inhibitor with results of molecular modelling.
Subject(s)
Burkholderia cepacia/enzymology , Lipase/chemistry , Organophosphorus Compounds/metabolism , Catalysis , Crystallography, X-Ray , Hydrogen Bonding , Lipase/antagonists & inhibitors , Lipase/metabolism , Models, Molecular , Stereoisomerism , Substrate SpecificityABSTRACT
The inclusion complex beta-cyclodextrin.2,7-dihydroxynaphthalene.4.6 H(2)O crystallized in the monoclinic space group P2(1), with a=14.082(3), b=19.079(4), c=12.417(3) A, beta=109.28(3) degrees, V=3149.0(11) A(3), and Z=2. An X-ray study performed at room temperature shows that the crystal packing is of the herringbone type with one 2,7-dihydroxynaphthalene included completely in the beta-CD cavity, its long axis being oriented along the beta-CD molecular axis, and 4.6 water molecules are placed in the interstitial space. The beta-CD macrocycle is elliptically distorted, and the guest molecule is held in the hydrophobic beta-CD cavity by C-H...O and C-H...pi interactions.
Subject(s)
Cyclodextrins/chemistry , Naphthalenes/chemistry , beta-Cyclodextrins , Crystallography, X-Ray , Hydrogen Bonding , Ligands , Molecular Conformation , Molecular Structure , Oligosaccharides/chemistry , WaterABSTRACT
Fluorescence correlation spectroscopy (FCS) was used to characterize the interaction of fluorescence labeled single-stranded DNA (ssDNA) with hexameric RepA DNA-helicase (hRepA) encoded by plasmid RSF1010. The apparent dissociation constants, Kd(app), for the equilibrium binding of 12mer, 30mer, and 45mer ssDNA 5'-labeled with BFL to hRepA dimer in the presence of 0.5 mM ATPgammaS at pH 5.8 and 25 degrees C were determined to be 0.58 +/- 0.12, 0.52 +/- 0.07, and 1.66 +/- 0.32 microM, respectively. Binding curves are compatible with one binding site for ssDNA present on hRepA dimer, with no indication of cooperativity. At pH 7.6 in the presence of ATPgammaS and at pH 5.8 in the absence of ATPgammaS, complex formation between ssDNA and hRepA was too weak for measuring complete binding curves by FCS. Under these conditions, the dissociation constant, Kd(app), is in the range between 10 and 250 microM. The kinetics of complex formation at pH 5.8 are faster than the time resolution (approximately 10-20 s) of FCS experiments under pseudo-first-order conditions, with respect to BFL-ssDNA. Photon correlation spectroscopy (PCS) experiments yielded, within the experimental error range, the same values for the apparent hydrodynamic radii, R(h), of hRepA dimer and its complex with ssDNA as determined by FCS (R(h) = 6.6 +/- 1 nm). hRepA starts to aggregate under acidic conditions (Subject(s)
DNA Helicases/metabolism
, DNA, Bacterial/metabolism
, DNA, Single-Stranded/metabolism
, Fluorescent Dyes/metabolism
, Proteins/metabolism
, Trans-Activators
, Binding Sites
, Boron Compounds/metabolism
, Calorimetry
, Circular Dichroism
, DNA-Binding Proteins/metabolism
, Dimerization
, Escherichia coli
, Lasers
, Photons
, Scattering, Radiation
, Solutions
, Spectrometry, Fluorescence/methods
, Ultracentrifugation
ABSTRACT
Life on Earth depends on photosynthesis, the conversion of light energy from the Sun to chemical energy. In plants, green algae and cyanobacteria, this process is driven by the cooperation of two large protein-cofactor complexes, photosystems I and II, which are located in the thylakoid photosynthetic membranes. The crystal structure of photosystem I from the thermophilic cyanobacterium Synechococcus elongatus described here provides a picture at atomic detail of 12 protein subunits and 127 cofactors comprising 96 chlorophylls, 2 phylloquinones, 3 Fe4S4 clusters, 22 carotenoids, 4 lipids, a putative Ca2+ ion and 201 water molecules. The structural information on the proteins and cofactors and their interactions provides a basis for understanding how the high efficiency of photosystem I in light capturing and electron transfer is achieved.
Subject(s)
Cyanobacteria/chemistry , Photosynthetic Reaction Center Complex Proteins/chemistry , Carotenoids/chemistry , Carotenoids/physiology , Chlorophyll/physiology , Crystallography, X-Ray , Cyanobacteria/physiology , Electron Transport , Light-Harvesting Protein Complexes , Lipids/chemistry , Lipids/physiology , Macromolecular Substances , Models, Molecular , Peptides/chemistry , Peptides/physiology , Photosynthetic Reaction Center Complex Proteins/metabolism , Photosystem I Protein Complex , Protein ConformationABSTRACT
The proteins encoded by the Streptococcus pyogenes broad-host range and low copy-number plasmid pSM19035 form a toxin-antitoxin module that secures stable maintenance by causing the death of plasmid-free segregants. The epsilonzeta protein complex was crystallized in four different forms at pH 5.0 and pH 7.0 using the vapour-diffusion method with PEG 3350 and ethylene glycol as precipitants. Three of the crystal forms were obtained in the same droplet under identical conditions at pH 5.0. One form belongs to the enantiomorphic space groups P4(3)2(1)2 or P4(1)2(1)2. For the other two, the X-ray reflection conditions match those of space group P2(1)2(1)2(1), one representing a superlattice of the other. A crystal form growing at pH 7.0 also belongs to space group P2(1)2(1)2(1), but there is no indication of a structural relationship to the other orthorhombic forms. Initially, the crystals diffracted to 2.9 A resolution and diffracted to 1.95 A after soaking at pH 7.0. A preparation of selenomethionyl epsilonzeta protein complex yielded single crystals suitable for X-ray diffraction experiments using synchrotron sources.
Subject(s)
Bacterial Proteins/chemistry , Plasmids , Streptococcus pyogenes/genetics , Bacterial Proteins/isolation & purification , Crystallization , Crystallography, X-Ray , Protein Conformation , Streptococcus pyogenes/chemistryABSTRACT
Unwinding of double-stranded DNA into single-stranded intermediates required for various fundamental life processes is catalyzed by helicases, a family of mono-, di- or hexameric motor proteins fueled by nucleoside triphosphate hydrolysis. The three-dimensional crystal structure of the hexameric helicase RepA encoded by plasmid RSF1010 has been determined by X-ray diffraction at 2.4 A resolution. The hexamer shows an annular structure with 6-fold rotational symmetry and a approximately 17 A wide central hole, suggesting that single-stranded DNA may be threaded during unwinding. Homologs of all five conserved sequence motifs of the DnaB-like helicase family are found in RepA, and the topography of the monomer resembles RecA and the helicase domain of the bacteriophage T7 gp4 protein. In a modeled complex, ATP molecules are located at the subunit interfaces and clearly define adenine-binding and ATPase catalytic sites formed by amino acid residues located on adjacent monomers; most remarkable is the "arginine finger" Arg207 contributing to the active site in the adjacent monomer. This arrangement of active-site residues suggests cooperativity between monomers in ATP hydrolysis and helicase activity of RepA. The mechanism of DNA unwinding remains elusive, as RepA is 6-fold symmetric, contrasting the recently published asymmetric structure of the bacteriophage T7 gp4 helicase domain.
Subject(s)
DNA Helicases/chemistry , DNA-Binding Proteins , Gram-Negative Bacteria/enzymology , Gram-Negative Bacteria/genetics , Plasmids/genetics , Proteins/chemistry , Trans-Activators , Adenosine Triphosphatases/metabolism , Adenosine Triphosphate/metabolism , Amino Acid Motifs , Amino Acid Sequence , Arginine/chemistry , Binding Sites , Conserved Sequence , Crystallography, X-Ray , DNA Helicases/genetics , DNA Helicases/metabolism , DNA Primase/chemistry , Dimerization , Models, Molecular , Molecular Sequence Data , Protein Structure, Quaternary , Protein Structure, Tertiary , Protein Subunits , Proteins/genetics , Proteins/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence AlignmentABSTRACT
The usage of standard 96 well microplates for the screening of crystallization conditions of recombinant proteins offers several advantages when compared to commonly used crystallization plate formats. The adoption of robotic technology for plate and glass slide preparation within a "hanging drop" vapour diffusion crystallization experiment enables to work with an increased throughput at reduced costs. In addition to commercial pipetting devices with a 96-channel aspirator/dispenser, solenoid ink-jet technology was applied to form 250 nl droplets with a diameter of approximately 1 mm. This allows miniaturization of crystallization screening set-ups with an estimated ten-fold cost reduction when compared to commonly used 24 well plates.
Subject(s)
Crystallography/instrumentation , Crystallography/methods , Miniaturization/instrumentation , Miniaturization/methods , Recombinant Proteins/chemistry , Concanavalin A/chemistry , Crystallization , Indicators and Reagents , Muramidase/chemistry , SolutionsABSTRACT
Oxygenic photosynthesis is the principal energy converter on earth. It is driven by photosystems I and II, two large protein-cofactor complexes located in the thylakoid membrane and acting in series. In photosystem II, water is oxidized; this event provides the overall process with the necessary electrons and protons, and the atmosphere with oxygen. To date, structural information on the architecture of the complex has been provided by electron microscopy of intact, active photosystem II at 15-30 A resolution, and by electron crystallography on two-dimensional crystals of D1-D2-CP47 photosystem II fragments without water oxidizing activity at 8 A resolution. Here we describe the X-ray structure of photosystem II on the basis of crystals fully active in water oxidation. The structure shows how protein subunits and cofactors are spatially organized. The larger subunits are assigned and the locations and orientations of the cofactors are defined. We also provide new information on the position, size and shape of the manganese cluster, which catalyzes water oxidation.
Subject(s)
Cyanobacteria/chemistry , Photosynthetic Reaction Center Complex Proteins/chemistry , Chlorophyll/chemistry , Chlorophyll A , Crystallography, X-Ray , Light-Harvesting Protein Complexes , Manganese/chemistry , Models, Molecular , Photosystem II Protein Complex , Protein ConformationABSTRACT
The calf spleen purine nucleoside phosphorylase (PNP) ternary complex with an N(7)-acycloguanosine inhibitor and a phosphate ion has been crystallized in the cubic space group P2(1)3, with unit-cell parameter a = 94.11 A and one monomer per asymmetric unit. X-ray diffraction data were collected using synchrotron radiation (Station X31, EMBL Outstation, DESY, Hamburg). The crystal structure was refined to a resolution of 2.2 A and R and R(free) values of 17.5 and 24.5%, respectively. The acyclonucleoside inhibitor is bound in the active site in an inverted ('upside-down') orientation of the purine base compared with natural substrates. The side chain of Asp243 forms two hydrogen bonds with the base ring: N(delta) donates a hydrogen to N(3) and O(delta) accepts a hydrogen from the guanine N(2)-amino group. N(1)--H of the base is hydrogen bonded to O(epsilon) of Glu201, while N(9) accepts a hydrogen bond from Thr242 O(gamma). In addition, a water molecule (W417) bridges the N(2)-amino group of the base and O(epsilon) of Glu201. In the phosphate-binding site, a phosphate ion is bound to Ser33, His64, Arg84, His86, Ala116 and Ser220. The acyclic chain of the N(7)-acycloguanosine inhibitor is in a folded conformation and together with a water molecule (W388) occupies the pentose-binding site, with possible hydrogen bonds to Tyr88 O(eta) and His257 N(delta 1). This new binding mode fully accounts for the previously observed substrate properties of 7-beta-D-ribofuranosides of hypoxanthine and guanine. It also provides a new starting point for the design of inhibitors of PNP for therapeutic and other applications.
Subject(s)
Guanosine/chemistry , Phosphates/chemistry , Purine-Nucleoside Phosphorylase/chemistry , Spleen/enzymology , Animals , Anions , Binding Sites , Cattle , Crystallography, X-Ray , Models, Molecular , Protein Conformation , Purine-Nucleoside Phosphorylase/antagonists & inhibitors , Substrate SpecificityABSTRACT
Helicases couple the hydrolysis of nucleoside triphosphates (NTPs) to the unwinding of double-stranded nucleic acids and are essential in DNA metabolism. Thus far, no inhibitors are known for helicases except heliquinomycin isolated from Streptomyces sp. As the three-dimensional structure of the hexameric replicative DNA helicase RepA encoded by the broad host-range plasmid RSF1010 is known, this protein served as a model helicase to search for inhibitory compounds. The commercially available flavone derivatives luteolin, morin, myricetin and dimyricetin (an oxidation product of myricetin) inhibited the ATPase and double-stranded DNA unwinding activities of RepA. Dimyricetin was the most effective inhibitor for both activities. Single-stranded DNA-dependent RepA ATPase activity is inhibited non-competitively by all four compounds. This finding contrasts the inhibition of phosphoinositide 3-kinase by flavones that fit into the ATP binding pocket of this enzyme. Myricetin also inhibited the growth of a Gram-positive and a Gram-negative bacterial species. As we found other hexameric and non-hexameric prokaryotic helicases to be differentially sensitive to myricetin, flavones may provide substructures for the design of molecules helpful for unraveling the mechanism of helicase action and of novel pharmacologically useful molecules.
Subject(s)
DNA Helicases/metabolism , DNA-Binding Proteins , Flavonoids/pharmacology , Proteins/metabolism , Trans-Activators , Adenosine Triphosphatases/antagonists & inhibitors , Adenosine Triphosphatases/metabolism , Bacillus subtilis/drug effects , Bacillus subtilis/growth & development , Cell Division/drug effects , DNA Helicases/antagonists & inhibitors , Dose-Response Relationship, Drug , Escherichia coli/drug effects , Escherichia coli/growth & development , Flavonoids/chemistry , Kinetics , Oligonucleotides/genetics , Oligonucleotides/metabolism , Proteins/antagonists & inhibitors , Structure-Activity RelationshipABSTRACT
As a member of the alpha-amylase superfamily of enzymes, amylomaltase catalyzes either the transglycosylation from one alpha-1,4 glucan to another or an intramolecular cyclization. The latter reaction is typical for cyclodextrin glucanotransferases. In contrast to these enzymes, amylomaltase catalyzes the formation of cyclic glucans with a degree of polymerization larger than 22. To characterize the factors that determine the size of the synthesized cycloamyloses, we have analyzed the X-ray structure of amylomaltase from Thermus aquaticus in complex with the inhibitor acarbose, a maltotetraose derivative, at 1.9 A resolution. Two acarbose molecules are bound to the enzyme, one in the active site groove at subsite -3 to +1 and a second one approximately 14 A away from the nonreducing end of the acarbose bound to the catalytic site. The inhibitor bound to the catalytic site occupies subsites -3 to +1. Unlike the situation in other enzymes of the alpha-amylase family, the inhibitor is not processed and the inhibitory cyclitol ring of acarbose, which mimicks the half chair conformation of the transition state, does not bind to catalytic subsite -1. The minimum ring size of cycloamyloses produced by this enzyme is proposed to be determined by the distance of the specific substrate binding sites at the active site and near Tyr54 and by the size of the 460s loop. The 250s loop might be involved in binding of the substrate at the reducing end of the scissile bond.
Subject(s)
Acarbose/chemistry , Acarbose/metabolism , Glycogen Debranching Enzyme System/chemistry , Glycogen Debranching Enzyme System/metabolism , Thermus/enzymology , Binding Sites , Carbohydrate Sequence , Crystallography, X-Ray , Cyclodextrins/metabolism , Glucans/chemical synthesis , Models, Molecular , Molecular Sequence Data , Protein Binding , Protein Conformation , Protein Folding , Protein Structure, SecondaryABSTRACT
Octakis(2,3,6-tri-O-methyl)-gamma-CD (TRIMEG) cocrystallized at 18 degrees C with 4.5 water molecules in the orthorhombic space group P2(1)2(1)2(1), unit cell dimensions a = 10.7879(3), b = 29.0580(9), c = 32.2909(11) A. The TRIMEG macrocycle is in a 'round' form with all glucose units oriented syn, and one O-6-CH3 methoxy group points 'toward' the molecular cavity. The TRIMEG x 4.5 H2O molecules are stacked to form infinite cylinders with the central cavities aligned into channels filled for each TRIMEG by 4.5 water molecules distributed over 15 partially occupied sites. This structure differs from the two known structures of TRIMEG in which two diametrically opposed glucoses are oriented anti to yield an 'elliptical' form, and their O-6-CH3 groups are directed 'toward' the cavity and close it at this side to form a bowl-shaped molecule.