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J Yariv

Publications and source records attributed to J Yariv.

At least 19 recordsLinked to original sources
PubMed1998

Structure of a monoclinic crystal from of cyctochrome b1 (Bacterioferritin) from E. coli.

Crystals of E. coli cytochrome b1, alias bacterioferritin, were grown fr om a low ionic strength solution. The resulting monoclniic P21 structure was solved by molecular replacement and refined using noncrystallographi c symmetries applied to the fundamental unit, consisting of two protein subunits and a single haem. From the Patterson self-rotation results it was shown that the asymmetric unit of the monoclinic crystal consists of 12 such dimers and corresponds to a complete, nearly spherical, molecule of bacterioferritin (M4 = 450 kDa) of 432 point-group symmetry. It is thus the most symmetrical cytochrome. As previously determined for the tetragonal form, the haem is located in a special position on a local twofold axis of the dimer. A bimetal centre is also observed within the four-helix bundle of each monomer; a metal-binding site is located on the fourfold axis.

Amino Acid Sequence↗
PubMed1996

Circumstantial evidence for cytochrome b1 involvement in the functioning of lac-permease in respiring Escherichia coli.

The structure of the haem-binding site of cytochrome b1 and particularly the fact that the two protein ligands of the haem are methionines could explain a correlation found between loss of lac-permease activity and replacement of methionine by norleucine in the protein of aerobically respiring E. coli. If cytochrome b1 is essential for lac-permease mediated transport in whole bacteria as this correlation suggests, translocation of substrate by this permease must be coupled to electron transport. Such a dependence would invalidate the chemiosmotic interpretation of lactose transport in E. coli in its present form and would be in variance with the coupling-by-energy theories of lactose transport that exempted translocation from dependence on energy yielding processes.

Bacterial Proteins↗
PubMed1994

Structure of a unique twofold symmetric haem-binding site.

Bacterioferritin of Escherichia coli, also known as cytochrome b1, is a hollow, nearly spherical shell made up of 24 identical protein subunits and 12 haems. We have solved this structure in a tetragonal crystal form at 2.9 A resolution. We find that each haem is bound in a pocket formed by the interface between a pair of symmetry-related subunits. The quasi-twofold axis of the haem is closely aligned with the local twofold axis relating these subunits. The axial ligands of the haem are sulphurs of two equivalent methionyl residues (Met 52) from the symmetry-related subunits. A cluster of four water molecules is trapped in the gap between the upper edge of the haem and two extended protein loops which close off the haem from the outer aqueous environment. This is the first structure of a bis-methionine ligated haem-binding site and the first case of a twofold symmetric haem-binding site.

Bacterial Proteins↗
PubMed1989

Molecular size and symmetry of the bacterioferritin of Escherichia coli. X-ray crystallographic characterization of four crystal forms.

X-ray crystallographic data from four crystal forms of Escherichia coli bacterioferritin show that the molecule has a diameter in the range 119 to 128 A. Molecules are composed of 24 subunits arranged in 432 symmetry. In both size and symmetry the molecule resembles ferritin from eukaryotes. The four crystal forms are monoclinic, space group P2(1) with unit cell dimensions a = 118.7 A, b = 211.6 A, c = 123.3 A and beta = 119.1 degrees; orthorhombic, C222(1), a = 128.7 A, b = 197.1 A, c = 202.8 A; tetragonal, P4(2)2(1)2, a = b = 210.6 A, c = 145.0 A and cubic, I432, a = 146.9 A.

Bacterial Proteins↗
PubMed1989

The structure of the saccharide-binding site of concanavalin A.

A complex of concanavalin A with methyl alpha-D-mannopyranoside has been crystallized in space group P212121 with a = 123.9 A, b = 129.1 A and c = 67.5 A. X-ray diffraction intensities to 2.9 A resolution have been collected on a Xentronics/Nicolet area detector. The structure has been solved by molecular replacement where the starting model was based on refined coordinates of an I222 crystal of saccharide-free concanavalin A. The structure of the saccharide complex was refined by restrained least-squares methods to an R-factor value of 0.19. In this crystal form, the asymmetric unit contains four protein subunits, to each of which a molecule of mannoside is bound in a shallow crevice near the surface of the protein. The methyl alpha-D-mannopyranoside molecule is bound in the C1 chair conformation 8.7 A from the calcium-binding site and 12.8 A from the transition metal-binding site. A network of seven hydrogen bonds connects oxygen atoms O-3, O-4, O-5 and O-6 of the mannoside to residues Asn14, Leu99, Tyr100, Asp208 and Arg228. O-2 and O-1 of the mannoside extend into the solvent. O-2 is hydrogen-bonded through a water molecule to an adjacent asymmetric unit. O-1 is not involved in any hydrogen bond and there is no fixed position for its methyl substituent.

Binding Sites↗
PubMed1988

Chemical and Mössbauer spectroscopic evidence that iron-containing concanavalin A is a ferritin.

We report here the preparation of iron-containing concanavalin A. It has a protein-to-iron ratio of 2.0, and the iron compound it contains is particulate with an average diameter of 85 A. Iron-containing concanavalin A interacts reversibly with dextran and with methyl alpha-D-glucoside. The molecular basis of these findings is discussed and a possible mechanism suggested where one of the molecular forms of concanavalin A has the structure of an apoferritin into which iron is deposited in the form of ferrihydrite.

Chemical Phenomena↗
PubMed1987

Properties of a new crystal form of the complex of concanavalin A with methyl alpha-D-glucopyranoside.

The complex of concanavalin A with methyl alpha-D-glucopyranoside crystallizes as regular rhombic dodecahedra containing 35% protein by weight. The crystal is of space group I23 with a = 167.8 A (1 A = 0.1 nm) and contains one concanavalin A dimer per asymmetric unit. It diffracts to a resolution of 1.9 A and is suitable for crystallographic investigation of the structure of the saccharide-binding site.

Binding Sites↗
PubMed1985

Preliminary results for the primary structure of bacterioferritin of Escherichia coli.

Bacterioferritins are type-b cytochromes which resemble ferritin. Amino acid analysis combined with chemical modification and partial sequence analysis characterize bacterioferritin of Escherichia coli in terms of its primary structure. It is a protein composed of one kind of polypeptide chain that commences with methionine and terminates with glutamic acid. The length of the polypeptide chain is, tentatively, 146 residues. Besides the N-terminal methionine residue there are three more methionine residues, which yield four CNBr peptides, which have been aligned. The identity of the following positions in the sequence has been ascertained: residues 1-25, 30-37, 83-88, 127-132 and 143-146. No homology with ferritin was found.

Amino Acid Sequence↗
PubMed1984

Ferritin: design and formation of an iron-storage molecule.

Although essential for most forms of life, too much iron is harmful. To cope with these antagonistic phenomena an iron-storage molecule, ferritin, has evolved. The structure of horse spleen apoferritin, which has recently been refined, consists of 24 symmetrically related subunits forming a near-spherical hollow shell. In ferritin the central cavity is occupied by an iron core of 'ferrihydrite', a geologically ephemeral mineral found in hot or cold springs and in mine workings, or produced in the laboratory by heating solutions of ferric salts. Ferritin itself forms most readily from apoferritin, in the presence of dioxygen, from FeII, not FeIII. Access to its interior is through small intersubunit channels, and the protein influences both the rate of FeII-oxidation and the form of oxide produced.

Animals↗
PubMed1983

Dynamics of heme iron in crystals of metmyoglobin and deoxymyoglobin.

The 57Fe gamma-ray resonance absorption spectra have been measured in crystals of metmyoglobin and deoxymyoglobin over a wide range of temperatures. Above a critical temperature common to both proteins (220 K), the dynamics of heme iron display a dramatic change, in that two kinds of thermal fluctuations come into play--a fast fluctuation associated with a steep decrease of the total fluctuation of characteristic time 10(-8) sec, associated with bounded diffusive motion. By using both discrete jump and continuous diffusion models, the latter based on the Brownian motion of an overdamped harmonic oscillator, the essential parameters of the iron motion (mean square displacement and jump frequency or diffusion constant) can be derived as a function of temperature. Thus, for deoxy Mb at 288 K, the mean square displacement for the fast fluctuation is about 6 X 10(-2) A2 and for the diffusive motion is 1.6 X 10(-2) A2; the diffusion constant is 4 X 10(-10) cm2/sec. The diffusive process is associated with an activation energy of about 0.75 kcal/mol. Although the same general kinds of phenomena are observed in crystals of MetMb and deoxy Mb, significant differences in behavior are found, which suggest that the main dynamical phenomenon observed reflects internal large-scale motions of the protein.

Animals↗
PubMed1982

The molecular composition of the volutin granule of yeast.

The volutin granule was isolated from yeast by disruption of freeze-dried cells in an organic solvent and density-gradient-gradient centrifugation. The granule is composed of two types of macromolecule, a linear-chain polyphosphate and four basic proteins, of molecular weights ranging from 10 000 to 20 000. In the dissolved granule these macromolecules are in a complex that is uniform by hydrodynamic criteria (s20,w = 22.3 S). The polyphosphate separated from this complex gives a single 31P n.m.r. resonance and in the analytical ultracentrifuge behaves as a monodisperse solute of molecular weight 245 000 +/- 1000. In the 31P n.m.r. spectrum of yeast used for its isolation, this polyphosphate accounts for 14% of total cell polyphosphate.

Amino Acids↗
PubMed1981

The composition and the structure of bacterioferritin of Escherichia coli.

Bacterioferritin isolated from Escherichia coli is of two kinds: a protein containing a polynuclear iron compound, the bacterioferritin proper and a protein free of the polynuclear iron compound, the apo-bacterioferritin. Bacterioferritin of both kinds is characterized by absorption maxima at 417,530 and 560 nm, contributed by protohaem IX. Single crystals of bacterioferritin of the space group I432 suggest that the molecule is made up of 24 identical subunits related by a cubic point symmetry. The molecular weight of the protein subunit, as determined by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis, is 15000. In the electron microscope the bacterioferritin molecule appears to be a sphere of 9.5 nm (95 A) diameter composed of a negatively staining outer shell and an inner electron-dense core of 6 nm (60 A) diameter.

Apoproteins↗
PubMed1980

Mössbauer spectroscopy of Escherichia coli and its iron-storage protein.

57Fe Mössbauer spectra of whole frozen Escherichia coli cells and of an iron storage protein isolated from iron-rich cells of E. coli have been measured over a range of temperatures down to 0.08 K. The spectra of E. coli cells with high iron content and of the iron storage protein were found to be very similar. Above 4 K these spectra consist of a quadrupole split doublet characteristic of Fe3+. Below 3.5 K, the spectra display magnetic hyperfine splitting which is temperature dependent, and point to the existence of an ordered magnetic phase associated with a saturation magnetic hyperfine field of 43 tesla in both samples. The results indicate that the bulk of iron in the iron-rich cells is in the form of aggregates similar in nature to the iron cores in the isolated protein, although the latter account for not more than 1% of the total iron in the cells. The Mössbauer spectra of the isolated protein are different from those observed in ferritin, the iron-storage protein of plants and higher animals, showing that the iron cores in these two proteins are different.

Escherichia coli↗
PubMed1979

13C NMR analysis of methionine sulfoxide in protein.

The 13C epsilon NMR signal of methionine sulfoxide is 22.6 ppm downfield from that of methionine. This affords a method by which the extent of methionine oxidation can be determined in intact protein. We demonstrate the utility of this approach with beta-galactosidase enriched with 13C in its methionine methyls.

Chloramines↗
PubMed1977

beta-Galactosidase.

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Acetylgalactosamine↗