Refined crystal structure of Cd, Zn metallothionein at 2.0 A resolution

The crystal structure of Cd5,Zn2-metallothionein from rat liver has been refined at 2.0 A resolution of a R-value of 0.176 for all observed data. The five Cd positions in the asymmetric unit of the crystal create a pseudo-centrosymmetric constellation about a crystallographic 2-fold axis. Consequently, the distribution of anomalous differences is almost ideally centrosymmetric. Therefore, the previously reported metal positions and the protein model derived therefrom are incorrect. Direct methods were applied to the protein amplitudes to locate the Cd positions. The new positions were used to calculate a new electron density map based on the Cd anomalous scattering and partial structure to model the metal clusters and the protein. Phases calculated from this model predict the positions of three sites in a (NH4)2WS4 derivative. Single isomorphous replacement phases calculated with these tungsten sites confirm the positions of the Cd sites from the new direct methods calculations. The refined metallothionein structure has a root-mean-square deviation of 0.016 A from ideality of bonds and normal stereochemistry of phi, phi and chi torsion angles. The metallothionein crystal structure is in agreement with the structures for the alpha and beta domains in solution derived by nuclear magnetic resonance methods. The overall chain folds and all metal to cysteine bonds are the same in the two structure determinations. The handedness of a short helix in the alpha-domain (residues 41 to 45) is the same in both structures. The crystal structure provides information concerning the metal cluster geometry and cysteine solvent accessibility and side-chain stereochemistry. Short cysteine peptide sequences repeated in the structure adopt restricted conformations which favor the formation of amide to sulfur hydrogen bonds. The crystal packing reveals intimate association of molecules about the diagonal 2-fold axes and trapped ions of crystallization (modeled as phosphate and sodium). Variation in the chemical and structural environments of the metal sites is in accord with data for metal exchange reactions in metallothioneins.

Circular dichroism and magnetic circular dichroism of Azotobacter vinelandii ferredoxin I

Room temperature circular dichroism (CD) and low temperature magnetic circular dichroism (MCD) spectra of air-oxidized and dithionite-reduced Azotobacter vinelandii ferredoxin I (FdI), a [( 4Fe-4S]2+/1+, [3Fe-4S]1+/0) protein, are reported. Unlike the CD of oxidized FdI, the CD of dithionite-reduced FdI exhibits significant pH dependence, consistent with protonation-deprotonation at or near the cluster reduced: the [3Fe-4S] cluster. The MCD of reduced FdI, which originates in the paramagnetic reduced [3Fe-4S]0 cluster, is also pH-dependent. Detailed studies of the field dependence and temperature dependence of the MCD of oxidized and reduced FdI, in the latter case at pH 6.0 and 8.3, are reported. The low-field temperature dependence of the MCD of oxidized FdI, which originates in the paramagnetic oxidized [3Fe-4S]1+ cluster, establishes the absence of a significant population of excited electronic states of this cluster up to 60 K. The low-field temperature dependence of the MCD of reduced FdI establishes that the ground-state manifold of the reduced [3Fe-4S]0 cluster possesses S greater than or equal to 2 at both pH 6.0 and 8.3. Analysis, assuming S = 2 and an axial zero-field splitting Hamiltonian, leads to D = -2.0 and -3.5 cm-1 at pH 6.0 and 8.3, respectively. The site of the (de)protonation affecting the spectroscopic properties of the [3Fe-4S] cluster remains unknown.

Species-specific sequences of abalone lysin, the sperm protein that creates a hole in the egg envelope

Abalone eggs are contained within a rigid, elevated vitelline envelope through which the sperm must pass before reaching the egg cell membrane. Abalone spermatozoa possess an acrosomal protein called lysin that creates a hole in the egg vitelline envelope by a nonenzymatic mechanism. Lysins from two species of abalone, termed pink and red, which share the same habitat, exhibit species specificity in the dissolution of isolated egg envelopes. Cloning and sequencing the cDNAs for pink and red abalone lysins reveal transcript lengths of approximately 660 nucleotides. The open reading frames of 465 (pink) and 462 (red) nucleotides show a 13% difference. The 3' untranslated regions before the poly(A) tails are 170 (pink) and 165 (red) nucleotides long and differ from each other by about 7%. The protein sequences show nearly identical signal sequences of 18 amino acids for both lysins. The mature protein is 137 amino acids in the pink abalone and 136 in the red abalone; the two mature lysins differ in 29 of 137 amino acids (21%). The most variable region, which may account for lysin's species specificity, is at the NH2 terminus, where 11 of the 15 amino acids differ between the two species. Predictions of secondary structure indicate that both lysins contain four homologous amphiphilic alpha-helices.

Diffraction quality crystals of lysin from spermatozoa of the red abalone (Haliotis rufescens)

Single crystals of the protein lysin (Mr = 16,070) from the spermatozoa of the red abalone (Haliotis rufescens) have been obtained by the vapor diffusion technique, using as precipitants a 32.5% saturated solution of (NH4)2SO4 (incubation at 18 degrees C) or a 5% w/v polyethyleneglycol 8000 solution (incubation at 29 degrees C), both in Bis-Tris-iminodiacetic acid buffers of pH 7.0. The addition to the droplets of EDTA, other carboxylate-containing polyanions, and/or organic solvents improved the size and quality of the crystals and, especially with (NH4)2SO4, addition of EDTA, and/or organic solvents produced a change in crystal habit which resulted in crystals more elongated in the b direction. The crystals belong to the orthorhombic space group P2(1)2(1)2(1) with a = 52.3 A, b = 46.0 A, and c = 81.5 A and one molecule per asymmetric unit. The crystals diffract to 2.3 A resolution. The molecular structure of lysin is relevant to the nonenzymatic mechanism by which the protein dissolves a hole in the egg vitelline layer during fertilization.

Site-directed mutagenesis of Azotobacter vinelandii ferredoxin I: [Fe-S] cluster-driven protein rearrangement

Azotobacter vinelandii ferredoxin I is a small protein that contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. Recently the x-ray crystal structure has been redetermined and the fdxA gene, which encodes the protein, has been cloned and sequenced. Here we report the site-directed mutation of Cys-20, which is a ligand of the [4Fe-4S] cluster in the native protein, to alanine and the characterization of the protein product by x-ray crystallographic and spectroscopic methods. The data show that the mutant protein again contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. The new [4Fe-4S] cluster obtains its fourth ligand from Cys-24, a free cysteine in the native structure. The formation of this [4Fe-4S] cluster drives rearrangement of the protein structure.

Redox protein electron-transfer mechanisms: electrostatic interactions as a determinant of reaction site in c-type cytochromes

The effect of ionic strength on the rate constant for electron transfer has been used to determine the magnitude and charge sign of the net electrostatic potential which exists in close proximity to the sites of electron transfer on various c-type cytochromes. The negatively charged ferricyanide ion preferentially reacts at the positively charged exposed heme edge region on the front side of horse cytochrome c and Paracoccus cytochrome c2. In contrast, at low ionic strength, the positively charged cobalt phenanthroline ion interacts with the negatively charged back side of cytochrome c2, and at high ionic strength at a positively charged site on the front side of the cytochrome. With horse cytochrome c, over the ionic strength range studied, cobalt phenanthroline reacts only at a positively charged site which is probably not at the heme edge. These inorganic oxidants do not react at the relatively uncharged exposed heme edge sites on Azotobacter cytochrome c5 and Pseudomonas cytochrome c-551, but rather at a negatively charged site which is away from the heme edge. The results demonstrate that at least two electron-transferring sites on a single cytochrome can be functional, depending on the redox reactant used and the ionic strength. Electrostatic interactions between charge distributions on the cytochrome surface and the other reactant, or interactions involving uncharged regions on the protein(s), are critical in determining the preferred sites of electron transfer and reaction rate constants. When unfavorable electrostatic effects occur at a site near the redox center, less optimal sites at a greater distance can become kinetically important.

Structure of activated aconitase: formation of the [4Fe-4S] cluster in the crystal

The structure of activated pig heart aconitase [citrate(isocitrate) hydro-lyase, EC 4.2.1.3] containing a [4Fe-4S] cluster has been refined at 2.5-A resolution to a crystallographic residual of 18.2%. Comparison of this structure to the recently determined 2.1-A resolution structure of the inactive enzyme containing a [3Fe-4S] cluster, by difference Fourier analysis, shows that upon activation iron is inserted into the structure isomorphously. The common atoms of the [3Fe-4S] and [4Fe-4S] cores agree within 0.1 A; the three common cysteinyl S gamma ligand atoms agree within 0.25 A. The fourth ligand of the Fe inserted into the [3Fe-4S] cluster is a water or hydroxyl from solvent, consistent with the absence of a free cysteine ligand in the enzyme active site cleft and the isomorphism of the two structures. A water molecule occupies a similar site in the crystal structure of the inactive enzyme.

Refinement of the 7 Fe ferredoxin from Azotobacter vinelandii at 1.9 A resolution

The recently redetermined structure of the 7 Fe ferredoxin from Azotobacter vinelandii has been refined against a new 1.9 A data set. The crystallographic R-factor is 0.215 for all 9586 observed reflections 8.0 to 1.9 A. The model contains 106 amino acid residues, two Fe-S clusters and 21 water molecules. The root-mean-square deviations from ideality of bonds and angles are 0.014 A and 3.3 degrees, respectively. The refinement confirms the presence of two free cysteines: the thiol of C11 is in association with the side-chain of K100; the thiol of C24 is 3.35 A from inorganic sulfur of the [4 Fe-4 S] cluster. The refinement confirms a [3 Fe-4 S] model for the 3 Fe cluster. The two Fe-S clusters have similar bond distances and angles. The structure of the protein for residues 1 to 57 superposes within 0.85 A on residues 1 to 53 of the 8 Fe ferredoxin structure for main-chain N, CA and C atoms, if residues 9, 10, 29 and 30 of 7 Fe ferredoxin are omitted. These residues are part of two loops in contact with residues of the extended C-terminal chain of 7 Fe ferredoxin.

The structure of aconitase

The crystal structure of the 80,000 Da Fe-S enzyme aconitase has been solved and refined at 2.1 A resolution. The protein contains four domains; the first three from the N-terminus are closely associated around the [3Fe-4S] cluster with all three cysteine ligands to the cluster being provided by the third domain. Association of the larger C-terminal domain with the first three domains creates an extensive cleft leading to the Fe-S cluster. Residues from all four domains contribute to the active site region, which is defined by the Fe-S cluster and a bound SO4(2-) ion. This region of the structure contains 4 Arg, 3 His, 3 Ser, 2 Asp, 1 Glu, 3 Asn, and 1 Gln residues, as well as several bound water molecules. Three of these side chains reside on a three-turn 3(10) helix in the first domain. The SO4(2-) ion is bound 9.3 A from the center of the [3Fe-4S] cluster by the side chains of 2 Arg and 1 Gln residues. Each of 3 His side chains in the putative active site is paired with Asp or Glu side chains.

Crystallization and preliminary X-ray diffraction studies of a toxic crystal protein from a subspecies of Bacillus thuringiensis

The toxic crystal protein (Mr 64,000) from a subspecies of the bacterium Bacillus thuringiensis has been solubilized and recrystallized yielding diffraction quality crystals. Crystals are obtained by a change in pH and ionic strength using Na2CO3. They can also be obtained by a change in ionic strength only using NaBr as the precipitant. The space group of both forms is C222(1) with a = 133, b = 116, c = 104 A and one molecule/asymmetric unit. Still photographs show reflections to 3.0-A resolution.

7-Iron ferredoxin revisited

The crystal structure of the 7Fe ferredoxin from Azotobacter vinelandii has been redetermined using area detector data to 2.7-A resolution and a new derivative. Tetragonal crystals of the protein were maintained at pH 8.0. The results show that the structure previously reported was in error and confirms a recent independent report of the structure (Stout, G.H., Turley, S., Sieker, L. C., and Jensen, L. H. (1988) Proc. Natl. Acad. Sci. U. S. A. 85, in press). The protein fold is similar to the homologous 8Fe ferredoxin structure for the N-terminal half of the protein; the C-terminal residues wrap around this structure. The structure contains a 3Fe cluster coordinated by cysteines 8, 16, and 49 and a 4Fe cluster coordinated by cysteines 20, 39, 42, and 45. However, there are two free sulfhydryls, cysteines 11 and 24, in the new model. Cysteine 24 is in contact with the [4Fe-4S] cluster. Cysteine 11 is shielded from solvent by residues 86-90.

Electron-transfer reactions between flavodoxin semiquinone and c-type cytochromes: comparisons between various flavodoxins

As an extension of previous work from this laboratory using Clostridium pasteurianum flavodoxin [Tollin, G., Cheddar, G., Watkins, J. A., Meyer, T. E., & Cusanovich, M. A. (1984) Biochemistry 23, 6345-6349], we have measured the rate constants as a function of ionic strength for electron transfer from the semiquinones of Clostridium MP, Anacystis nidulans, and Azotobacter vinelandii flavodoxins to the following oxidants: cytochrome c from tuna and horse, Paracoccus denitrificans cytochrome c2, Pseudomonas aeruginosa cytochrome c-551, and ferricyanide. The rate constants extrapolated to infinite ionic strength (k infinity) for the C. MP flavodoxin are all slightly smaller than for the C. pasteurianum flavodoxin, as would be predicted on the basis of the higher redox potential of the C. MP protein. This indicates that there is a close similarity between the surface topographies of the two proteins in the vicinity of the coenzyme binding site. Moreover, the electrostatic interactions between the two flavodoxins and the various oxidants are also approximately the same. These studies justify our previous use of the crystallographic structure of the C. MP flavodoxin to interpret kinetic results obtained with the structurally uncharacterized C. pasteurianum flavodoxin. Despite their lower redox potentials, both Anacystis and Azotobacter flavodoxins are appreciably less reactive toward all of these oxidants (as much as 2 orders of magnitude in some cases) than are the Clostridium flavodoxins.(ABSTRACT TRUNCATED AT 250 WORDS)

X-ray absorption studies of the copper-beta domain of rat liver metallothionein

Rat liver metallothionein contains two domains, each of which enfolds a separate metal-thiolate cluster. The binding stoichiometry of these clusters depends on the particular metal ion bound. In the aminoterminal beta domain the cluster can accommodate either three Cd(II) ions or six Cu(I) ions. The Cd ions are known to be coordinated in a tetrahedral geometry. In order to better understand the binding of Cu ions in this domain, the Cu-beta domain fragment of metallothionein was prepared and investigated by x-ray absorption spectroscopy. Quantitative analysis of the EXAFS data indicates copper-sulfur distances of 2.25 +/- 0.03 A. The EXAFS amplitudes and distance results are most consistent with trigonal coordination. A trigonal biprism is proposed for the Cu6Cys9 complex in which Cu occupies each vertex and cysteinyl sulfur bridges at each of the nine edges.

Crystal structure of Cd,Zn metallothionein

The anomalous scattering data from five Cd in the native protein were used to determine the crystal structure of cadmium, zinc (Cd,Zn) metallothionein isoform II from rat liver. The structure of a 4-Cd cluster was solved by direct methods. A 2.3 A resolution electron density map was calculated by iterative single-wavelength anomalous scattering. The structure is folded into two domains. The amino terminal domain (beta) of residues 1 to 29 enfolds a three-metal cluster of one Cd and two Zn atoms coordinated by six terminal cysteine thiolate ligands and three bridging cysteine thiolates. The carboxyl terminal domain (alpha) of residues 30 to 61 enfolds a 4-Cd cluster coordinated by six terminal and five bridging cysteine thiolates. All seven metal sites have tetrahedral coordination geometry. The domains are roughly spherical, and the diameter is 15 to 20 A; there is limited contact between domains. The folding of alpha and beta is topologically similar but with opposite chirality. Redundant, short cysteine-containing sequences have similar roles in cluster formation in both alpha and beta.

Crystal structure of Azotobacter cytochrome c5 at 2.5 A resolution

The crystal structure of cytochrome c5 from Azotobacter vinelandii has been solved and refined to an R value of 0.29 at 2.5 A resolution. The structure of the oxidized protein was solved using a monoclinic crystal form. The structure was solved by multiple isomorphous replacements, re-fit to a solvent-leveled multiple isomorphous replacement map, and refined by restrained least squares. The structure reveals monomers associated about the crystallographic 2-fold axis by hydrophobic contacts at the "exposed heme edge". The overall conformation for the monomer is similar to that of Pseudomonas aeruginosa cytochrome c551. However, relative to a common heme conformation, c5 and c551 differ by an average of 6.8 A over 82 alpha-carbon positions and the propionates of c5 are much more exposed to solvent. The shortest heme--heme contact at the "dimer" interface is 6.3 A (Fe to Fe 16.4 A). Alignment of c5 and c551 shows that the two cytochromes, in spite of sequence differences, have remarkably similar charge distributions. A disulfide stacks on a tyrosine between the N- and C-terminal helices.

Selective oxidative destruction of iron-sulfur clusters. Ferricyanide oxidation of Azotobacter vinelandii ferredoxin I

The destructive oxidation of aerobically isolated 7Fe Azotobacter vinelandii ferredoxin I [(7Fe)FdI] by Fe(CN)3-6 is examined using low-temperature magnetic circular dichroism (MCD) and EPR. The results demonstrate that oxidation of the [3Fe-3S] cluster occurs only after essentially complete destruction of the [4Fe-4S] cluster. It is therefore feasible by controlled Fe(CN)3-6 oxidation to obtain a partially metallated form of FdI, (3Fe)FdI, containing only a [3Fe-3S] cluster. The MCD and EPR data demonstrate that the [3Fe-3S] cluster in (3Fe)FdI is essentially identical in structure to that in the native protein.

Iron-sulfur cluster in aconitase. Crystallographic evidence for a three-iron center

Native x-ray diffraction data from single crystals of inactive aconitase from pig heart (Mr 80,000) have been collected on oscillation films to 2.7 A. Analysis shows that significant measurements of the anomalous scattering signal from the Fe-S cluster in the enzyme are available in the film data. The 5.0-A resolution anomalous difference Patterson function contains vectors for one Fe-S cluster (one aconitase molecule) per asymmetric unit in space group P2(1)2(1)2 with a = 173.6, b = 72.0, and c = 72.7 A. At 2.7-A resolution, the vector map is best interpreted by three Fe sites separated from each other by less than 3 A. The single-crystal diffraction data thus confirm the presence of a 3Fe center in the inactive form of aconitase. Furthermore, the data provide crystallographic evidence that 3Fe clusters exhibit structural heterogeneity. The Fe-Fe vectors cannot be interpreted in terms of 4-A distances as observed for the [3Fe-3S] cluster in Azotobacter ferrodoxin (Ghosh, D., O'Donnell, S., Furey, W., Robbins, A. H., and Stout, C. D. (1982) J. Mol. Biol. 158, 73-109). The results are therefore in agreement with a [3Fe-4S] cluster having 2.7-A Fe-Fe distances (Beinert, H., Emptage, M. H., Dreyer, J.-L., Scott, R. A., Hahn, J. E., Hodgson, K. O., and Thomson, A. J. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 393-396). However, the data do not unambiguously discriminate between this model and other 3Fe clusters having short Fe-Fe distances.

The amino acid sequence of the dihaem cytochrome c4 from the bacterium Azotobacter vinelandii

An amino acid sequence is proposed for the cytochrome c4 from the bacterium Azotobacter vinelandii strain OP. It is a single polypeptide chain of 190 residues, with two sets of haem-attachment cysteine residues at positions 14/17 and 119/122. Proteins with similar sequences are also present in denitrifying pseudomonads. There is similarity in sequence between the two halves of the cytochrome c4 molecule, and each half also shows similarity to the sequences of certain monohaem cytochromes c isolated from organisms that are not obviously closely related to A. vinelandii. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50125 (17 pages) at the British Library Lending Division, Boston Spa, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment.

Spectroscopic studies of ferricyanide oxidation of Azotobacter vinelandii ferredoxin I

The Fe(CN)3-(6) oxidation of the crystallographically characterized [[3Fe-3S], [4Fe-4S]] ferredoxin I of Azotobacter vinelandii has been studied using absorption, circular dichroism, magnetic circular dichroism, and EPR spectroscopies. A paramagnetic intermediate is observed en route to Fe-S cluster-free apoprotein, possessing an anisotropic g approximately equal to 2 EPR signal, surviving to temperatures greater than 77 K. This species is shown to result from 3-electron oxidation of the [4Fe-4S] cluster, without modification of the [3Fe-3S] cluster. However, it does not give rise to observable paramagnetic magnetic circular dichroism in the visible-near UV spectral region and is therefore neither an oxidized HIPIP [4Fe-4S] cluster nor an oxidized [3Fe-3S] cluster. We identify the paramagnetic species as a cysteinyldisulfide radical formed on dissociation of an oxidized cysteinate and an oxidized sulfide ion from the [4Fe-4S] cluster. This conclusion is consistent with the observed reaction stoichiometry, the spectroscopic results obtained, known EPR spectra of disulfide radicals, and the reconstitution of the native [4Fe-4S] cluster by dithiothreitol alone. This reaction, earlier interpreted as a HIPIP-type oxidation, is a previously uncharacterized oxidation reaction of [4Fe-4S] clusters.

Crystals of cadmium, zinc metallothionein

Single crystals have been grown of Cd,Zn metallothionein isoform II from rat liver. The space group is P41212(P43212) with unit cell dimensions a = b = 31.0 A and c = 120.0 A, and one molecule in the crystallographic asymmetric unit. The crystals are square bipyramids elongated on the tetragonal c-axis and are grown by repetitive seeding. The crystals are suitable for high resolution structure analysis. Assays of dissolved crystals show that the crystals have the same Cd and Zn content and amino acid composition as the native, as-isolated protein.

Single crystals of cadmium, zinc metallothionein

Single crystals have been grown of Cd,Zn metallothionein isoform II from rat liver. The space group is P4(1)2(1)2 (P4(3)2(1)2) with unit cell dimensions a = b = 31.0 A and c = 120.0 A, and one molecule in the crystallographic asymmetric unit. The crystals are square bipyramids elongated on the tetragonal c-axis and are grown by repetitive seeding. The crystals are suitable for high resolution structure analysis. Assays of dissolved crystals show that the crystals have the same Cd and Zn content and amino acid composition as the native, as-isolated protein.

Structure of Azotobacter vinelandii 7Fe ferredoxin. Amino acid sequence and electron density maps of residues

The complete amino acid sequence of the 7Fe ferredoxin from Azotobacter vinelandii (Av Fd) was determined by repetitive Edman degradation of the whole protein and of peptides derived from CNBr cleavage or chymotrypsin digestion. The sequence was confirmed by the 2A electron density maps for the residues calculated with difference Fourier coefficients. The density maps for all residues are included in the paper. Av Fd has several important differences with the clostridial-type ferredoxins: (i) Av Fd is 106 residues (versus 55-60 for other bacterial ferredoxins); (ii) Av Fd has 9 cysteines, one of which (residue 24) is not homologous with the bacterial ferredoxins; (iii) Av Fd has 2 extra residues between 2 cysteines (residues 11 and 16) homologous to cysteines in the bacterial ferredoxins; and (iv) Av Fd has the unique sequence -Cys-Val-Glu-Val-Cys- (residues 16-20) which are two of the ligands of the 3Fe:3S center. These sequence features are compared to the sequences of various ferredoxin groups. Structure predictions for other suspected 7Fe ferredoxins are discussed.

Structure of a 7Fe ferredoxin from Azotobacter vinelandii

The structure of the 7Fe ferredoxin from Azotobacter vinelandii has been solved from a 3.0-A multiple isomorphous replacement map. The crystals belong to space group P43212 with a = 55.22, c = 95.20 A, and Z = 1. Heavy-atom derivatives were prepared with K2PtCl4,K2[OsO2(OH)4], and Na3RhCl6. Anomalous scattering data were collected for native (Fe) and Pt derivative crystals. The figure of merit for 3,322 reflections to 3.0 A is 0.74. The structure consists of an NH2-terminal core of residues 1-50 which form the Fe-S cluster sites, and a COOH-terminal chain of residues 51-107 which wraps around this core. The [3Fe-3S] cluster is ligated by cysteines 8, 11, 16, 20, and 49 and a sixth ligand which is either glutamic acid 18 or an exogenous small molecule. The [4Fe-4S] cluster is ligated by cysteines 24, 39, 42, and 45. The coordination of both Fe-S centers has been confirmed by fitting of the cluster atoms and residues 1-50 to unbiased 2Fo-Fc Fourier maps at 2.5-A resolution. The structure of the 3Fe center has also been confirmed with anomalous scattering difference Fourier maps using both isomorphous replacement and refined phases. The partially refined structure at 2.5 A (3,490 reflections, 6.0 sigma(F)) has R = 35%.

Iron-sulfur clusters in Azotobacter ferredoxin at 2.5 A resolution

X-ray crystallographic study of the ferredoxin-like protein (iron-sulfur protein III) from Azotobacter vinelandii has been extended to 2.5-A resolution. A 4.0-A resolution electron density map revealed that the molecule contains two Fe-S clusters of differing size and shape separated by 12 A (Stout, C.D. (1979) Nature 279, 83-84). Recent Mössbauer results by Emptage et al. (Emptage, M.H., Kent, T.A., Huynh, B.H., Rawlings, J., Orme-Johnson, W.H., and Münck, E. (1980) J. Biol. Chem. 255, 1793-1796) have shown that the molecule contains 7 iron atoms as a high potential iron protein-like Fe4 center and a novel 3-Fe center. The 2.5-A electron density map shows two distinctly different Fe-S clusters. The larger cluster consists of a tetranuclear [4Fe-4S] core ligated to the protein at each iron atom. The smaller cluster is distinctly planar and cannot be modeled with [2Fe-2S] or [4Fe-4S] structures. The best model for this cluster is a [3Fe-3S] core. The protein makes six contacts with this cluster.

Two crystal forms of Azotobacter ferredoxin

Two crystal forms of Azotobacter vinelandii (4Fe-4s)2 ferredoxin I (Fd I) have been grown which are suitable for high resolution x-ray diffraction studies. Tetragonal crystals grow as square bipyramids from ammonium sulfate and Tris buffer using a temperature gradient. The space group is P41212 (or P43212) with a = 55.3, c = 95.9 A and 1 molecule/asymmetric unit. Triclinic crystals grow as plates or laths from ammonium sulfate and phosphate buffer at constant temperature. The space group is P1 with a = 46.8, b = 58.7, c = 64.3 A, alpha = = 105 degrees 05 min, beta = 82 degrees 30 min, gamma = 110 degrees 30 min and 4 or 5 molecules/unit cell. Both crystal forms are stable to x-ray irradiation and diffract beyond 3.0 A resolution.

Mechanisms of chain folding in nucleic acids. The (omega, omega) plot and its correlation to the nucleotide geometry in yeast tRNAPhe1

The (omega', omega) polot depicting the internucleotide P-O bond rotation angles in yeast phenylalanyl transfer RNA has established the interdependence of the phosphodiesters and the nucleotide geometries in the folding of the polynucleotide backbone. The plot distinguishes the regions characteristic of secondary helical structures and tertiary structural loops and bends. The folding of the polynucleotide chain is accomplished either solely by rotations around the P-O bonds or in concert with rotations around the nucleotide C4'-C5' bond with or without changes in the sugar ring pucker. In spite of differences in nucleotide sequence and intraloop tertiary interactions in the anticodon and pseudouridine loops, a characteristic repeating structural unit is found for the sugar-phosphate backbone of the tetranucleotide segment around the sharp turns.

Atomic coordinates and molecular conformation of yeast phenylalanyl tRNA. An independent investigation

The atomic coordinates of yeast tRNA(Phe) in the monoclinic crystal form have been determined by an independent analysis from a model built into a 3 A MIR map. The overall molecular structure is found to be in agreement with those reported for the same crystal form by Ladner et al. (1975) and for the orthorhombic form by Quigley et al. (1975) and Kim et al. (1975). However, significant differences between any two of the four models are found in certain local regions of the molecule. The structure is analyzed in terms of the nucleotide stereochemistry and internucleotide phosphodiesters. A striking observation is that the majority of the nucleotide moieties occur in the conformation preferred by the constituent mononucleotides themselves. The internucleotide P-O bonds afford the primary source of flexibility for the folding of the polynucleotide backbone while the sugar pucker and C(4')-C(5') torsions provide the secondary source of flexibility.