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ABSTRACT: We have constructed a strain that overproduces ribonuclease I of Escherichia coli and we have purified large quantities of the enzyme. Data from fluorescence, CD, and DSC measurements showed that it was a very stable protein. The conformation energy determined from urea and guanidine hydrochloride denaturation experiments was 11.5 kcal mol(-1) at pH 7.5. Thermal denaturation studies indicated that it had a T(m) of 64 degrees C at pH 4.0. RNase I belongs to the RNase T2/S-RNase group of endoribonucleases, but near the amino terminus it has an unusually long hydrophilic segment. Part of this was removed in the deletion construct, RNase I Delta(26-38). We have obtained crystals of both RNase I and of an enzyme-G2'p5'G complex in the P2(1) space group and oligonucleotide complexes with both wild type and mutant enzymes. The current study lays the groundwork for extensive investigation into the structure, function, and physical properties of this widely distributed group of ribonucleases.
Archives of Biochemistry and Biophysics 07/2001; 390(1):42-50. · 2.93 Impact Factor
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ABSTRACT: Single crystals of ribonuclease I from Escherichia coli have been obtained by the vapor diffusion method. The crystals belong to the tetragonal space group P4(1)2(1)2 or its enantiomer P4(3)2(1)2 and have cell parameters a = b = 119.01 A and c = 34.40 A. There is one 27,000 dalton monomer in the asymmetric unit. The crystals diffract to beyond 3.0 A resolution.
Journal of Molecular Biology 12/1993; 234(2):499-501. · 4.00 Impact Factor
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ABSTRACT: The crystal structure of amicyanin, a cupredoxin isolated from Paracoccus denitrificans, has been determined by molecular replacement. The structure has been refined at 2.0 A resolution using energy-restrained least-squares procedures to a crystallographic residual of 15.7%. The copper-free protein, apoamicyanin, has also been refined to 1.8 A resolution with residual 15.5%. The protein is found to have a beta-sandwich topology with nine beta-strands forming two mixed beta-sheets. The secondary structure is very similar to that observed in the other classes of cupredoxins, such as plastocyanin and azurin. Amicyanin has approximately 20 residues at the N-terminus that have no equivalents in the other proteins; a portion of these residues forms the first beta-strand of the structure. The copper atom is located in a pocket between the beta-sheets and is found to have four coordinating ligands: two histidine nitrogens, one cysteine sulfur, and, at a longer distance, one methionine sulfur. The geometry of the copper coordination is very similar to that in the plant plastocyanins. Three of the four copper ligands are located in the loop between beta-strands eight and nine. This loop is shorter than that in the other cupredoxins, having only two residues each between the cysteine and histidine and the histidine and methionine ligands. The amicyanin and apoamicyanin structures are very similar; in particular, there is little difference in the positions of the coordinating ligands with or without copper. One of the copper ligands, a histidine, lies close to the protein surface and is surrounded on that surface by seven hydrophobic residues. This hydrophobic patch is thought to be important as an electron transfer site.
Protein Science 06/1993; 2(5):739-52. · 2.80 Impact Factor
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ABSTRACT: The amino acid sequence of the iron-sulfur-flavoprotein, trimethylamine dehydrogenase, isolated from the bacterium W3A1 has been deduced from the x-ray diffraction pattern obtained at 2.4-A resolution. This sequence has been compared to portions of the primary sequence derived by gas-phase sequencing of isolated peptides obtained from cyanogen bromide and endoprotease Arg-C and Asp-N digestions of the purified enzyme. A consensus sequence has resulted and is comprised of 729 amino acids with Ala at both NH2- and COOH-terminal positions. The consensus sequence contains 13 cysteine residues. Approximately 80% of the sequence has been confirmed by direct sequencing with approximately 81% agreement with the x-ray deduced sequence. The calculated subunit molecular mass of the apoenzyme is 78,899 Da, in good agreement with published values of approximately 83,000. The anomalous scattering map from the native protein has also been shown to provide accurate information about the positions of most of the weak anomalous scattering centers such as sulfur or phosphorus atoms and to complement x-ray or chemical sequencing methods.
Journal of Biological Chemistry 05/1992; 267(10):6611-9. · 4.77 Impact Factor
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W C Stallings,
S S Abdel-Meguid, L W Lim,
H S Shieh,
H E Dayringer,
N K Leimgruber,
R A Stegeman,
K S Anderson,
J A Sikorski,
S R Padgette,
G M Kishore
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ABSTRACT: 5-enol-Pyruvylshikimate-3-phosphate synthase (EPSP synthase; phosphoenolpyruvate:3-phosphoshikimate 1-carboxyvinyltransferase, EC 2.5.1.19) is an enzyme on the pathway toward the synthesis of aromatic amino acids in plants, fungi, and bacteria and is the target of the broad-spectrum herbicide glyphosate. The three-dimensional structure of the enzyme from Escherichia coli has been determined by crystallographic techniques. The polypeptide backbone chain was traced by examination of an electron density map calculated at 3-A resolution. The two-domain structure has a distinctive fold and appears to be formed by 6-fold replication of a protein folding unit comprising two parallel helices and a four-stranded sheet. Each domain is formed from three of these units, which are related by an approximate threefold symmetry axis; in each domain three of the helices are completely buried by a surface formed from the three beta-sheets and solvent-accessible faces of the other three helices. The domains are related by an approximate dyad, but in the present crystals the molecule does not display pseudo-symmetry related to the symmetry of point group 32 because its approximate threefold axes are almost normal. A possible relation between the three-dimensional structure of the protein and the linear sequence of its gene will be described. The topological threefold symmetry and orientation of each of the two observed globular domains may direct the binding of substrates and inhibitors by a helix macrodipole effect and implies that the active site is located near the interdomain crossover segments. The structure also suggests a rationale for the glyphosate tolerance conferred by sequence alterations.
Proceedings of the National Academy of Sciences 07/1991; 88(11):5046-50. · 9.68 Impact Factor
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ABSTRACT: Single crystals of glycosylated recombinant human renin have been obtained using the hanging-drop vapor diffusion method with polyethylene glycol and sodium chloride as coprecipitants. The crystals belong to the cubic space group P2(1)3 with a = 143.0 A and contain two molecules of renin in the asymmetric unit. A self-rotation function study using 5.5 A data shows the orientation of a non-crystallographic 2-fold axis relating these two monomers.
Journal of Molecular Biology 12/1989; 210(1):239-40. · 4.00 Impact Factor
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ABSTRACT: Crystals of trimethylamine dehydrogenase have been examined by difference Fourier methods at 6.0-A resolution after partial reduction by substrate and by dithionite in the presence of inhibitor. Similar studies of the inhibited oxidized enzyme and of the enzyme reduced fully by dithionite alone were also carried out. In all cases ligand binding at the active site occurred. In addition, there were small structural changes, possibly side chain movements, in the inhibited oxidized enzyme and somewhat larger changes in the partially reduced crystals. The largest changes occurred with the fully reduced enzyme. However, in no cases were subunit or domain movements observed nor were changes observed in the position of the FMN or [4Fe-4S] cofactors. Parallel studies of crystalline trimethylamine dehydrogenase were carried out by EPR spectroscopy. The results show that the electronic states of the crystalline enzyme under the conditions of the difference Fourier studies are comparable to those which occur in solution under similar conditions.
Journal of Biological Chemistry 08/1989; 264(20):11887-92. · 4.77 Impact Factor
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Journal of Molecular Biology 11/1988; 203(4):1137-8. · 4.00 Impact Factor
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ABSTRACT: Analysis of the 2.4-A resolution electron density map of trimethylamine dehydrogenase has revealed the unexpected presence of one molecule of ADP/subunit. This binding has been confirmed chemically. The binding site is located at the analogous position of the ADP moiety of FAD in glutathione reductase, the FAD and NADPH binding domains of which resemble two of the domains of trimethylamine dehydrogenase. Comparison of the environments of the ADP moieties in the two proteins indicates that 32 residues in 6 peptides are in equivalent positions with a root mean square deviation for C alpha positions of 1.11 A. Twelve of these amino acids are identical, based on the electron density-derived "x-ray" sequence of trimethylamine dehydrogenase. Detailed analysis of the environment of the ADP moiety indicates that most of the conserved residues are not in direct contact with the cofactor. Some of them probably represent the "fingerprint" of the beta alpha beta binding fold found in dinucleotide binding proteins, but the remaining conserved residues may indicate a closer evolutionary relationship between these two proteins.
Journal of Biological Chemistry 04/1988; 263(7):3075-8. · 4.77 Impact Factor
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ABSTRACT: The structure of flavocytochrome b2 from baker's yeast was solved at 3.0-A resolution by the multiple isomorphous replacement method combined with solvent leveling procedures, using data collected from an area detector. The tetramer of Mr 230,000 has 4-fold symmetry. Each subunit contains a cytochrome domain consisting of the first 100 residues, a flavin-binding domain containing the next 386 residues, and an extended C-terminal tail of 25 residues. The cytochrome domain closely resembles microsomal cytochrome b5, whereas the flavin-binding domain contains a parallel beta 8/alpha 8 barrel motif similar to glycolate oxidase and trimethylamine dehydrogenase. Two of the four cytochrome domains are disordered in the crystals. The flavin ring and heme group are separated by about 16 A between their centers, and their planes are inclined by about 17 degrees to each other.
Proceedings of the National Academy of Sciences 06/1987; 84(9):2629-33. · 9.68 Impact Factor
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ABSTRACT: The three-dimensional structure of trimethylamine dehydrogenase from the methylotrophic bacterium W3A1 has been determined to 2.4-A resolution. The enzyme is composed of two identical 83,000-dalton subunits, each of which is folded into three structural domains. The largest domain, at the NH2 terminus of the molecule, is folded as an eight-stranded parallel alpha/beta barrel. It contains the [4Fe-4S] and covalently bound FMN cofactors separated by about 4 A. The folding topology of the large domain and orientation of the FMN cofactor are very similar to those found in glycolate oxidase. The other two domains contain alpha/beta parallel beta sheet topologies with similar folding patterns. The topologies and spatial arrangements of these two domains are remarkably similar to the FAD- and NADPH-binding domains of glutathione reductase.
Journal of Biological Chemistry 12/1986; 261(32):15140-6. · 4.77 Impact Factor
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ABSTRACT: Single crystals of methanol dehydrogenase from Methylophilus methylotrophus have been prepared by the macroseeding method. The crystals belong to the monoclinic space group C2, and have unit cell parameters a = 125.62 A, b = 63.83 A, c = 83.99 A, and beta = 93.24 degrees. There is one 62,000 Mr monomer in the asymmetric unit. The crystals diffract to beyond 2.0 A resolution.
Journal of Molecular Biology 10/1986; 191(1):141-2. · 4.00 Impact Factor
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ABSTRACT: The structure of p-cresol methylhydroxylase [4-cresol:(acceptor) oxidoreductase (methyl-hydroxylating), EC 1.17.99.1], a flavocytochrome c, has been determined at 6.0-A resolution. The structure analysis is based on two heavy-atom derivatives with anomalous scattering and 2-fold averaging about a noncrystallographic axis. The molecule is an alpha 2 beta 2 tetramer with a cytochrome subunit of Mr approximately 8500 and a flavoprotein subunit of Mr approximately 49,000. The flavoprotein subunits are tightly packed about the molecular 2-fold axis, whereas the cytochrome subunits are located on the outside of the molecule, each in a depression on the surface of a flavoprotein subunit. The results of this study have led to the following conclusions. The alpha 2 beta 2 quaternary structure of the enzyme is different from alpha beta as originally thought. The orientation of the cytochrome subunit and the surface complementarity of the cytochrome and flavoprotein subunits are clearly defined. The cytochrome subunit is similar in size to other small bacterial cytochromes but probably forms a distinct subclass. The titration (by substrate) behavior of the enzyme and other kinetic properties are rationalized by its quaternary structure.
Proceedings of the National Academy of Sciences 08/1986; 83(13):4626-30. · 9.68 Impact Factor
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ABSTRACT: Single crystals have been prepared of Paracoccus denitrificans amicyanin, a blue copper protein that serves as an electron acceptor for methylamine dehydrogenase. The crystals belong to the monoclinic space group P2(1), and have unit cell parameters a = 20.90 A, b = 56.61 A, c = 27.55 A and beta = 96.41. There is one molecule in the asymmetric unit. The crystals diffract to beyond 1.5 A resolution.
Journal of Molecular Biology 06/1986; 189(1):257-8. · 4.00 Impact Factor
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ABSTRACT: Single crystals of p-cresol methylhydroxylase, a flavocytochrome c from Pseudomonas putida, have been prepared. The crystals are orthorhombic, space group P212121 with unit cell parameters; a = 140.3 A, b = 130.6 A and c = 74.1 A. They contain a single non-symmetric dimer per asymmetric unit and diffract to at least 2.5 A resolution.
Journal of Molecular Biology 07/1985; 183(3):517-8. · 4.00 Impact Factor
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ABSTRACT: An electron density map of trimethylamine dehydrogenase has been calculated at 6.0-A resolution. Protein phases were based on two isomorphous mercury derivatives with similar binding properties, and on anomalous scattering measurements. The map has been averaged about the noncrystallographic 2-fold axis, plotted on transparent sheets and used to construct a wooden model. The elipsoidal dimer has a large inter-subunit interface. Each subunit appears to contain three closely associated domains with the iron-sulfur cluster located between two of them. The map suggests an alpha/beta-structure for two of the domains and a large helix content for the third.
Journal of Biological Chemistry 01/1985; 259(23):14458-62. · 4.77 Impact Factor
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Journal of Molecular Biology 01/1983; 162(4):869-76. · 4.00 Impact Factor
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ABSTRACT: The mechanism of decay of polycistronic trp messenger RNA in Escherichia coli was studied by size analyses of decaying populations. By measuring the sizes of only those molecules that contained the most proximal (E mRNA) of the five messages it was shown directly that cleavages occur, probably at intercistronic junctions, and each one does so independently of cleavages or decay at any other sites, i.e. occurs with random kinetics. The polycistronic fragments of less than full-length size did not arise from premature terminations within the operon. These results agree with earlier conclusions for the lac and gal operons and suggest that the basic mechanisms of decay of polycistronic mRNAs are probably the same with internal cleavages occurring only at the intercistronic junctions.
Journal of Molecular Biology 09/1980; 141(2):227-33. · 4.00 Impact Factor
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ABSTRACT: The size distributions of decaying polycistronic Escherichia coli lac messenger RNA have been followed on polyacrylamide gels. At the same time, equations have been derived that generate the theoretical size distributions of decaying macromolecules for different mechanisms of degradation. Using observed values of lac mRNA metabolism, it was possible to reproduce the in vivo patterns with a model in which cleavage occurs at the start of each of the three messages† and is followed by a net 5′ to 3′ wave of mass loss. Other models of degradation could not generate the observed in vivo patterns. These alternative mechanisms include: (1) the same number of primary cleavage sites (three) but at different positions on the full-length molecule; (2) an exclusive 5′ to 3′ directional degradation from the start of the lac mRNA (no cleavages); or (3) the presence of many internal targets. Further support for primary cleavage at the start of messages came from the observed accumulation of the intact z mRNA released by cleavage at the boundary and from the predictable effects of specific deletions on the resultant size distributions.The significance of these cleavages has been assessed; they could be necessary “processing” events or, conversely, inactivate the message for translation. Full-length molecules as well as cleavage fragments have been fractionated by successive sucrose gradient centrifugation and tested for their capacity to form translation initiation complexes in vitro. Full-length lac RNA could form such complexes at one or more of its three ribosome-loading sites, whereas the y or a message fragments were inactive. These results suggest that a cleavage at or near the start of a message inactivates it.
Journal of Molecular Biology 01/1980; 135(2):369-90. · 4.00 Impact Factor
