Search

This paper reports the biochemical characterization of the flavoprotein L-aspartate oxidase from Escherichia coli. Modification of a previously published procedure allowed overexpression of the holoenzyme in an unproteolysed form. L-Aspartate oxidase is a monomer of 60 kDa containing 1 mol of non-covalently bound FAD/mol protein. A polarographic and two spectrophotometric coupled assays have been set up to monitor the enzymatic activity continuously. L-Aspartate oxidase was subjected to product inhibition since iminoaspartate, which results from the oxidation of L-aspartate, binds to the enzyme with a dissociation constant (Kd) equal to 1.4 μM. The enzyme binds FAD by a simple second-order process with Kd 0.67 μM. Site-directed mutagenesis of the residues E43, G44, S45, F47 and Y48 located in the putative binding site of the isoallossazinic portion of FAD reduces the affinity for the coenzyme. [ABSTRACT FROM AUTHOR]

Three different phenylalanyl-tRNA synthetases have been purified to near homogeneity, one from a wild-type strain of Escherichia coli and the others from two independently isolated p-fluorophenylalanine-resistant strains. The mutant enzymes were not able to use p-fluorophenylalanine as a substrate for activation and attachment to tRNA. They proved to be indistinguishable from the wild-type enzyme by several electrophoretic and immunological criteria. The α and β subunits of all three enzymes have been prepared by a method described in this paper. The isolated subunits per se did not reveal any significant enzyme activity, but combined they were able to form active phenylalanyl-tRNA synthetase after a defined reconstitution process. Mixed reconstitution experiments between wild-type and mutant subunits indicate that the mutant a subunit is responsible for p-fluorophenylalanine resistance and therefore seems to carry the phenylalanine-binding site or to participate in its formation. [ABSTRACT FROM AUTHOR]

Asp19 and His20 of Escherichia coli aspartate transcarbamoylase (EC 2.1.3.2) function in the binding of the triphosphate and ribose moieties of ATP and CTP and thereby may mediate important heterotropic regulation. The roles of these residues were investigated by individually mutating each of them to alanine and determining both the kinetic parameters and the structures of the mutant enzymes. The structures were determined by X-ray crystallography at 2.15 and 2.75 Å resolution for His20Ar and Asp19Ar, respectively. Analysis was carried out on the unliganded T-state form. The structures of the mutants did not show gross structural divergence from the canonical T-state, but showed small and systematic differences that were analyzed by global conformational analysis. Structural analysis and comparison with other regulatory-chain mutants confirmed that the Asp19Ar mutant represents the stabilized T-state, while structural analysis of the His20Ar form indicated that it represents an equilibrium shifted towards the R-state. Global analysis of the Asp19Ar and His20Ar enzymes suggested a possible role as molecular modulators of the heterotropic effects caused by the binding of nucleotides at the regulatory site. These studies highlighted the structural determinants of T- or R-state stabilization. Additionally, application of the `consensus modeling' methodology combined with high-resolution data allowed the determination of unclear structural features contributing to nucleotide specificity and the role of the N-termini of the regulatory chains. [ABSTRACT FROM AUTHOR]

Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 Å resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from the coordinates of the Hg atom (one site per subunit of the trimeric enzyme) using the program ARP/wARP. After refinement with anisotropic temperature factors a highly accurate model of the bacterial dUTPase was obtained. Data to 1.45 Å from a native crystal were also collected and the 100 K structures were compared. inspection of the refined models reveals that a large part of the dUTPase remains rather mobile upon freezing, with 14% of the main chain being totally disordered and with numerous side chains containing disordered atoms in multiple discrete conformations. A large number of those residues surround the active-site cavity. Two glycerol molecules (the cryosolvent) occupy the deoxyribose-binding site. Comparison between the native enzyme and the mercury complex shows that the active site is not adversely affected by the binding of mercury. An unexpected effect seems to be a stabilization of the crystal lattice by means of long-range interactions, making derivatization a potentially useful tool for further studies of inhibitor- substrate-analogue complexes of this protein at very high resolution. [ABSTRACT FROM AUTHOR]

A ribonucleoprotein prepared by strong ribonuclease digestion of a complex of 16-S ribosomal RNA and proteins S4 and S20 from Escherichia coli has been characterized; its nucleotide sequence, the positions of enzyme cuts and the sequence excisions have been placed in the completed sequence of 16-S RNA. The positions and yields of enzyme cuts, and excisions of sequence, are compared with those of various ribonucleoproteins prepared with S4 or S20 alone, and with the ribonuclease-resistant S4 RNA prepared from renatured 16-S RNA in the absence of ribosomal protein. These data yield important information on the topography and organization of the 5′ third of the 16-S RNA which is selectively maintained in its native conformation by the bound proteins; they also provide criteria for testing secondary structural models of this region of 16-S RNA. [ABSTRACT FROM AUTHOR]

Two physically and genetically distinct forms of ribosephosphate isomerase have been identified in Escherichia coli K12. The constitutive ribosephosphate isomerase A has a Km for ribose 5-phosphate (4.4 ± 0.5 mM) six times greater than that of the inducible ribosephosphate isomerase B (0.83 ± 0.13 mM). Treatment of the enzymes with 1.25 mM iodoacetate resulted in 100% loss of activity for ribosephosphate isomerase B, whereas ribosephosphate isomerase A was unaffected. Various cellular metabolites were tested and found to be without significant effect on either enzyme. The two enzymes could be separated by filtration on Sephadex G75 superfine and their apparent molecular weights were 45000 for ribosephosphate isomerase A and 32000–34000 for ribosephosphate isomerase B. Under certain conditions the two enzymes showed different patterns of heat inactivation but the results with ribosephosphate isomerase A varied in an unusual way with the protein concentration. Ribosephosphate isomerase B was formed inducibly in a mutant lacking ribosephosphate isomerase A but there was no evidence for the production of ribosephosphate isomerase B in wild-type cells. The formation of ribosephosphate isomerase B was not a consequence of the ribosephosphate isomerase A mutation, since strains could be constructed which formed both enzymes constitutively in the anticipated amounts. The ribosephosphate isomerase formed by a secondary mutant obtained from a ribosephosphate-isomerase-A-negative strain was identified as ribosephosphate isomerase B on the basis of its Km, elution profile from Sephadex G75, inhibition by iodoacetate, and heat inactivation. The ribosephosphate isomerases of another Escherichia coli K12 strain, X289, were investigated, since their properties were reported to be different from many of these described here for ribosephosphate isomerases A and B. In our hands strain X289 contained two ribosephosphate isomerases apparently identical to ribosephosphate isomerases A and B. The evidence to date suggests that ribosephosphate isomerase A catalyses the formation of ribose 5-phosphate from ribulose 5-phosphate and also participates in the reverse reaction during ribose and adenosine catabolism. The normal physiological role of the inducible ribosephosphate isomerase B is still uncertain. [ABSTRACT FROM AUTHOR]

We have studied the ribonucleosidediphosphate reductase of a deoxyuridine-requiring mutant LD195 of Escherichia coli K. This enzyme was purified 50 fold from the mutant and a control strain. In all steps of the purification the mutant strain yielded normal activity of the Bi subunit of the enzyme but approximately 10 % of the wild-type activity of the B2 subunit The activity is similarly reduced for all three substrates tested CDP, UDP, and GDP. The mutation appears to affect the physical structure of the B2 subunit, since addition of high concentrations of sodium acetate can restore enzymatic activity to the partially purified B2 subunit from the mutant strain. In contrast, the same concentrations strongly inhibit the wild- type B2 subunit. Although the mutant has a requirement of deoxyuridine at 42 °C but not at 30 °C (as shown in an accompanying paper), mutant protein B2 is not more thermo-labile than wild-type protein B2 This requirement therefore probably reflects an increased demand of deoxyribonucleotides at higher temperatures. Hydroxyurea inhibits mutant and wild-type ribonucleosidediphosphate reductase to the same extent in vitro. In spite of this, hydroxyurea inhibits growth of the mutant strain at a 20 fold lower concentration than that required for comparable inhibition of growth of the parent. This is explained by the greatly decreased protein B2 activity of the mutant. [ABSTRACT FROM AUTHOR]

Through the use of the analytical active-enzyme-centrifugation method we have been able to measure the sedimentation coefficients of enzymes which have not yet been obtained in highly purified preparations: aspartate-semialdehyde dehydrogenase from Escherichia coli and from yeast and lactate dehydrogenase from rabbit muscle. We have also been able to determine unambiguously the polymerization state of the fully active unit, of β-galactosidase from E. coli, alcohol dehydrogenase from yeast as well as the polymerization state of the fully active unit of two enzymes which undergo an association-dissociation concentration-dependent reaction, glucose-6-phosphate dehydrogenase from yeast and glutamate dehydrogenase from beef liver (for this last enzyme the active-enzyme-centrifugation method has been applied with NAD, NADH, NADP and NADPH as coenzymes and also for its alanine dehydrogenase activity). [ABSTRACT FROM AUTHOR]

A haemoglobin-degrading enzyme from pathogenic Escherichia coli has been cloned, expressed and purified to homogeneity. The pure protein proteolyses haemoglobin and binds haem. In vivo, its role is to remove haem from haemoglobin and pass it to the bacteria, allowing them to overcome the limiting concentration of iron available in the body. The protein has been crystallized using polyethylene glycol to give crystals in a hexagonal space group with unit-cell parameters a = b = 114.6, c = 434.3 Å. X-ray data have been collected to 2.5 Å resolution. This is the first member of the SPATE (serine protease autotransporters of Enterobacteriaceae) family of autotransporter proteins to be crystallized. [ABSTRACT FROM AUTHOR]

Escherichia coli uses the DsbA/DsbB system for introducing disulphide bonds into proteins in the cell envelope. Deleting either dsbA or dsbB or both reduces disulphide bond formation but does not entirely eliminate it. Whether such background disulphide bond forming activity is enzyme-catalysed is not known. To identify possible cellular factors that might contribute to the background activity, we studied the effects of overexpressing endogenous proteins on disulphide bond formation in the periplasm. We find that overexpressing PspE, a periplasmic rhodanese, partially restores substantial disulphide bond formation to a dsbA strain. This activity depends on DsbC, the bacterial disulphide bond isomerase, but not on DsbB. We show that overexpressed PspE is oxidized to the sulphenic acid form and reacts with substrate proteins to form mixed disulphide adducts. DsbC either prevents the formation of these mixed disulphides or resolves these adducts subsequently. In the process, DsbC itself gets oxidized and proceeds to catalyse disulphide bond formation. Although this PspE/DsbC system is not responsible for the background disulphide bond forming activity, we suggest that it might be utilized in other organisms lacking the DsbA/DsbB system. [ABSTRACT FROM AUTHOR]

The article reports on a study of the effect of signal-peptide truncations on the functional expression of escherichia coli y-glutamyltranspeptidase (EcGGT). It examines the influence of signal-peptide to EcGGT using polymerase chain reaction. It shows that induction of Escherichia coli M15 cells with plasmids resulted through the production of expressed proteins and EcGGT. It demonstrates that three enzymes had no GGT activity under the enzyme assay conditions. It also manifests hat 94% of the functional activity was found in the cytoplasmic fraction of Escherichia coli M15 cells.

This undergraduate laboratory experiment integrates multiple techniques (in vitro synthesis, enzyme assays, Western blotting) to determine the production and detection sensitivity of two common reporter proteins (β-galactosidase and luciferase) within an Escherichia coil S30 transcription/translation extract. Comparison of the data suggests that luciferase is the more suitable reporter for this specific in vitro extract system. Simple modifications in the experimental design allow for flexibility in the use of materials and the time required to perform the study. Furthermore, extension into additional experiments and alternative techniques are also discussed. [ABSTRACT FROM AUTHOR]

Cinnamyl alcohol dehydrogenases (CAD; 1.1.1.195) catalyse the reversible conversion ofp-hydroxycinnamaldehydes to their corresponding alcohols, leading to the biosynthesis of lignin in plants. Outside of plants their role is less defined. The gene for cinnamyl alcohol dehydrogenase fromHelicobacter pylori(HpCAD) was cloned inEscherichia coliand the recombinant enzyme characterized for substrate specificity. The enzyme is a monomer of 42.5 kDa found predominantly in the cytosol of the bacterium. It is specific for NADP(H) as cofactor and has a broad substrate specificity for alcohol and aldehyde substrates. Its substrate specificity is similar to the well-characterized plant enzymes. High substrate inhibition was observed and a mechanism of competitive inhibition proposed. The enzyme was found to be capable of catalysing the dismutation of benzaldehyde to benzyl alcohol and benzoic acid. This dismutation reaction has not been shown previously for this class of alcohol dehydrogenase and provides the bacterium with a means of reducing aldehyde concentration within the cell. [ABSTRACT FROM AUTHOR]

Although isopentenyl diphosphate–dimethylallyl diphosphate isomerase is thought to be essential for archaea because they use the mevalonate pathway, its corresponding activity has not been detected in any archaea. A novel type of the enzyme, which has no sequence similarity to the known, well-studied type of enzymes, was recently reported in some bacterial strains. In this study, we describe the cloning of a gene of a homologue of the novel bacterial isomerase from a thermoacidophilic archaeon Sulfolobus shibatae. The gene was heterologously expressed in Escherichia coli, and the recombinant enzyme was purified and characterized. The thermostable archaeal enzyme is tetrameric, and requires NAD(P)H and Mg2+ for activity, similar to its bacterial homologues. Using its apoenzyme, we were able to confirm that the archaeal enzyme is strictly dependent on FMN. Moreover, we provide evidence to show that the enzyme also has NADH dehydrogenase activity although it catalyzes the isomerase reaction without consuming any detectable amount of NADH. [ABSTRACT FROM AUTHOR]

The Escherichia coli disulfide bond isomerase DsbC rearranges incorrect disulfide bonds during oxidative protein folding. It is specifically activated by the periplasmic N-terminal domain (DsbDα) of the transmembrane electron transporter DsbD. An intermediate of the electron transport reaction was trapped, yielding a covalent DsbC-DsbDα complex. The 2.3 A crystal structure of the complex shows for the first time the specific interactions between two thiol oxidoreductases. DsbDα is a novel thiol oxidoreductase with the active site cysteines embedded in an immunoglobulin fold. It binds into the central cleft of the V-shaped DsbC dimer, which assumes a closed conformation on complex formation. Comparison of the complex with oxidized DsbDα reveals major conformational changes in a cap structure that regulates the accessibility of the DsbDα active site. Our results explain how DsbC is selectively activated by DsbD using electrons derived from the cytoplasm. [ABSTRACT FROM AUTHOR]

The active-site cysteines of the Escherichia coli periplasmic protein disulfide bond isomerase (DsbC) are kept reduced by the cytoplasmic membrane protein, DsbD. DsbD, in turn, is reduced by cytoplasmic thioredoxin, indicating that DsbD transfers disulfide-reducing potential from the cytoplasm to the periplasm. To understand the mechanism of this unusual mode of electron transfer, we have undertaken a genetic analysis of DsbD. In the process, we discovered that the previously suggested start site for the DsbD protein is incorrect. Our results permit the formulation of a model of DsbD membrane topology. Also, we show that six cysteines of DsbD conserved among DsbD homologs are essential for the reduction of DsbC, DsbG and for a reductive pathway leading to c-type cytochrome assembly in the periplasm. Our findings suggest a testable model for the DsbD-dependent transfer of electrons across the membrane, involving a cascade of disulfide bond reduction steps. [ABSTRACT FROM AUTHOR]

The transport of bacterial outer membrane proteins to their destination might be either a one-step process via the contact zones between the inner and outer membrane or a two-step process, implicating a periplasmic intermediate that inserts into the membrane. Furthermore, folding might precede insertion or vice versa. To address these questions, we have made use of the known 3D-structure of the trimeric porin PhoE of Escherichia coli to engineer intramolecular disulfide bridges into this protein at positions that are not exposed to the periplasm once the protein is correctly assembled. The mutations did not interfere with the biogenesis of the protein, and disulfide bond formation appeared to be dependent on the periplasmic enzyme DsbA, which catalyzes disulfide bond formation in the periplasm. This proves that the protein passes through the periplasm on its way to the outer membrane. Furthermore, since the disulfide bonds create elements of tertiary structure within the mutant proteins, it appears that these proteins are at least partially folded before they insert into the outer membrane. [ABSTRACT FROM AUTHOR]

The genes coding for the mature part of the lipases from Staphylococcus aureus NCTC8530 and Staphylococcus hyicus have been cloned and overexpressed in Escherichia coli as fusion proteins with an N-terminal hexa-histidine tag The enzymes accumulated in the cytoplasm and were purified using sequential precipitation with protamine sulphate and ammonium sulphate, followed by metal-affinity and hydroxyapatite chromatography. The yield of pure lipase was 4.5 mg/g wet cells for S. aureus lipase and 13 mg/g for S hyicus lipase. The purified enzymes need calcium for activity, albeit with different affinities, and a low residual activity was found in the absentee of calcium. In contrast to S. hyicuss lipase, not only strontium but also barium can replace calcium with full retention of activity of S, aureus lipase. Whereas S. hyicus lipase is optimally active at pH 8.5, the optimum pH for enzymatic activity for S. aureus lipase was found to be pH 6.5. The S. aureus lipase has a narrow substrate specificity: short-chain triacylglycerols and acyl esters of both p-nitrophenol and umbelliferone are readily degraded, whereas medium- and long-chain lipids, as well as phospholipids, are poor substrates. In contrast, S. hyicus lipase prefers phospholipids as substrate and hydrolyses neutral lipids irrespective of their chain length. The results are discussed in view of the large sequence similarity between both lipases. [ABSTRACT FROM AUTHOR]

The enzyme myristoyl-CoA:protein N-myristoyltransferase is responsible for the attachment of a myristoyl group to the N-terminal glycine of a number of cell, viral and fungal proteins. In order to overcome the difficulties of purification of this enzyme from tissue sources, we have produced an N-terminally polyhistidine-tagged version of the enzyme and expressed this in Escherichia coli. The resulting enzyme has a molecular mass of 53 kDa arid is fully active showing the expected specificity for myristic acid and causing the N-terminal inyristoylation of both synthetic peptide and protein substrates in vitro. The enzyme exhibits a broad pH optimum peaking at a pH of 8.0 and has a Km for myristoyl-CoA of 7.6 μM. The two synthetic peptide substrates based on the N-terminal sequence of the catalytic subunit of protein kinase A (GNAAAARR) and of p60src (GSS- KSKPKDPSQRRRY) have different kinetic parameters with Km, values of 115.2 μM and 44.2 μM and Vmax values of 95 and 120 nmol - min-1 - mg-2, respectively. The expressed enzyme is partially inhibited (50%) by iodoacetamide at 5 mM and fully inhibited by diethylpyrocarbonate at 10mM. This latter inhibition can be prevented by including histidine in the incubation of the enzyme and inhibitor. Antisera raised to synthetic peptides based on sequences derived from the N- and C- terminus of the human enzyme reacted with the expressed protein on Western blots, but only the N-terminal sequence reacted with the native protein suggesting that the C-terminus may he riot he accessible. The enzyme can catalyse the removal of a myristoyl group from myristoylated peptides but does so only in the presence of added coenzyme A. [ABSTRACT FROM AUTHOR]

Ribonuclease H (Escherichia coli) contains one strong magnesium-binding site, as determined by metal-titration experiments monitored by high field ¹H-NMR and also by direct titration calorimetry. Kinetic and thermodynamic parameters were evaluated by 25Mg-NMR and were as follows; dissociation constant Kd, ∼60±10 μM; activation free energy ΔG*, ∼49.8±0.9 kJ; on/off-rate for magnesium binding kon, ∼ 1.8X1 8 M ¹ s ¹, koff, ∼ 1.1X14 s 1; quadrupole coupling constant Xa, 1.2±0.2 MHz. The dissociation constant was independently determined by standard analysis of ¹H chemical shifts in magnesium-titration experiments and by microcalorimetry (Kd∼20±20 μM). Cobalt hexamine, which also activates Rnase H [Jou, R. & Cowan, J. A. (1991) J. Am. Chem. Soc. 113, 6685–6686], appears to bind at the same location as M 2+ (aqueous). Assignments of C2H and C4H protons to specific histidine residues have been made by two-dimensional correlated spectroscopy experiments. Direct 25Mg-NMR pH titrations show that an ionizable residue (pKa∼5.8), most likely one of the carboxylates in the active site, influences magnesium binding. On the basis of the magnesium coordination chemistry elucidated herein, recent proposals on active-site chemistry are critically assessed and general physicochemical aspects of magnesium-binding sites on proteins and enzymes are discussed. [ABSTRACT FROM AUTHOR]

We previously found a trypsin-like proteinase which momentarily appears immediately before DNA synthesis in the cell cycle of Escherichia coli synchronized by phosphate starvation and which is closely related to the initiation of DNA replication (Kato, M., Irisawa, T., Morimoto, Y. and Muramatu, M., unpublished results). The proteinase was named proteinase In. It was purified approximately 2880-fold with a recovery of 15%. The isolated enzyme appeared homogeneous by gel filtration and electrophoresis. Its molecular mass was estimated by analytical gel filtration and SDS/PAGE as approximately 66 kDa. The isoelectric point of proteinase In is 4.9 and its optimal pH is approximately 9. Although protein In hydrolyzes fluorogenic substrate for trypsin, its hydrolytic activity seems markedly affected by amino-acid sequence lying towards the N-terminal from the P1 (lysine, arginine) residue. The proteinase does not hydrolyze N2-benzoyl-D,L-arginine-4-nitronanilide and fluorogenic substrates for chymotrypsin and elastase. The proteinase activity is inhibited by leupeptin, antipain and 4-nitrophenyl 4-guanidinobenzoate, but the effects of tosyl-L-lysine chloromethane, diisopropylfluorophosphate, benzamidine and pentamidine isethionate on the proteinase activity are weak or not inhibitory. Its activity is strongly affected in the presence of NaCl and KCl, and at a concentration of 1.5 M, these increase the activity 14-fold and 13-fold, respectively, above that without salt. Proteinase In was strongly inhibited by various esters of trans-4-guanidinome-thylcyclohexanecarboxylic acid, and their inhibitory effects were roughly correlated with those on growth of E. coli. Proteinase activity was found in the cytoplasmic fraction. [ABSTRACT FROM AUTHOR]

L2, L3, L4, L16 and L20 are proteins of the 50S ribosomal subunit of Escherichia coli which are essential for the assembly and activity of the peptidyl transferase centre. These proteins have been modified with the histidinespecific reagent, diethylpyrocarbonate, while L17 and LI8 were treated as controls. Each modified protein tested was able to participate in the reconstitution of a 50S particle when replacing its normal counterpart, although the particles assembled with modified L2 were heterogeneous. However, although they could support assembly, modified L16 and L20 were not themselves reconstituted stably, and modified L2 and L3 were found in less than stoichiometric amounts. Particles assembled in the presence of modified L16 retained significant peptidyl transferase activity (60-70% at 10 mM diethylpyrocarbonate) whereas those reconstituted with modified L2, L3, L4 or L20 had low activity (10-30% at 10 mM diethylpyrocarbonate). The particles assembled with the modified control portein, L17, retained 80% of their peptidyl transferase activity under the same conditions. The histidine residues within the essential proteins therefore contribute to ribosome structure and function in three significant ways; in the correct assembly of the ribosomal subunit (L2), for the stable assembly of the proteins within the ribosomal particle (L20 and L16 in particular), and directly or indirectly for the subsequent activity of the peptidyl transferase centre (L2, L3, L4 and L20). The essential nature of the unmodified histidines for assembly events precludes the use of the chemical-modification strategy to test the proposal that a histidine on one of the proteins might participate in the catalytic activity of the centre. [ABSTRACT FROM AUTHOR]

1. Diacyiglycerol kinase apoprotein was purified from membranes of Escherichia coli K 12 by a six-step procedure that included HPLC. The proposed assignment of the enzyme to the dgkA gene [Lightner et a!. (1983) J. Blot Chem. 258, 10856-10861] could be supported by molecular mass determination (≈ 14 kDa), N-terminal sequencing (Met-Ala-Aso), cyanogen bromide fragmentation and amino acid analysis. As predicted, proline was absent. 2. The membrane-associated as well as the butan-1-ol-dissolved enzyme survived heating to 100°C. 3. Alkylglycoside detergents were found to constitute an additional class of lipid activators. 4. The enzyme apoprotein in a non-activating substrate/detergent solution was capable of autocatalytic self-activation which was attributed to a novel feedback activation mechanism involving phosphatidic acid (diacylglycerol 3-phosphate). [ABSTRACT FROM AUTHOR]

An in vitro transcription-translation system was developed using cell-free extracts from the symbiotic nitrogen-fixing bacterium Rhizobium meliloti strain 41. Conditions for preparation of the 30 000 x g supernatant extract and for measurement of protein-synthesizing activity were determined and compared to the activity of an Eschericha coli cell-free system. Genes expressed in the free-living or in the symbiotic state were studied. The product of a recA-like gene (41-kDA protein) was synthesized both in R. meliloti and E. coli extracts, although less efficiently in the heterologous system. In agreement with earlier results obtained in E. coli minicells, three proteins (44, 28.5 and 23 kDa) were synthesized from a cloned 3.3 x 10⊃-base DNA region carrying genes for nodulation (nod). However, differences in the transcription-translation of nod and host specificity (hsn) genes were observed when protein expression was compared in R. meliloti and E. coli cell-free extracts, and the possible explanations of these findings are discussed. [ABSTRACT FROM AUTHOR]

Recombinant, normal human medium-chain acyl-CoA dehydrogenase (MCADH) and the common, human disease-causing K304E mutant ([Glu304]MCADH) protein were expressed in Escherichia coli using an optimized system, and the enzymes were purified to apparent homogeneity. The crucial factor leading to the production of active [Glu304]MCADH protein is the expression in E. coli cells at reduced temperature (28°C). Expression in the same system at 37°C results in very low amounts of active mutant protein. Several catalytic and physicochemical parameters of these two proteins have been determined and were compared to those of purified pig kidney MCADH. Although [Glu304]MCADH has approximately the same rate of substrate reduction with dodecanoyl-CoA and the same Vmax as human MCADH with the best substrate for the latter, octanoyl-CoA, the Km in the mutant MCADH is fourfold higher, which generates a correspondingly lower catalytic efficiency. Importantly, Vmax obtained using the natural acceptor, electron transfer flavoprotein, is only a third that for human MCADH. The Vmax/Km versus chain-length profile of the mutant shows a maximum with dodecanoyl-CoA which differs markedly from that of human MCADH, which has maximal efficiency with octanoyl-CoA. The substrate specificity of the mutant is broader with a less pronounced activity peak resembling long-chain acyl-CoA dehydrogenase. The purified mutant enzyme exhibits a reduced, thermal stability compared to human wild-type MCADH. The major difference between the two proteins expressed in E. coli is the more pronounced lability of the K304E mutant in crude extracts, which suggests a higher susceptibility to attack by endogenous proteases. Differences between tetrameric [Glu304]MCADH which survives the first step(s) of purifiction and corresponding MCADH are minor. The overall differences in properties of [Glu304]MCADH together with its impaired folding and tetramer assembly may contribute to the generation of the abnormalities observed in patients homozygous for the K304E mutation. [ABSTRACT FROM AUTHOR]

Upon the cessation of exponential growth, Bacillus subtilis enters a transition phase leading to either sporulation or a non-sporulating stationary phase. During this transition period, cells secrete degradative enzymes, become competent for DNA transformation, are motile and acquire resistance to oxidative killing. We now report that mrgA, originally identified as a gene repressed by metal ions, encodes a member of the Dps/PexB family of general stress proteins. Like Escherichia coli (PexB), MrgA forms highly stable, multimeric protein-DNA complexes which accumulate in stationary-phase cells and protect against oxidative kiiling. MrgA is part of an inducible oxidative stress response in B. subtilis: mrgA is induced by hydrogen peroxide, and a strain lacking MrgA displays increased sensitivity to oxidative killing. In addition, a hydrogen peroxide-resistant mutant, which constitutively overproduces catalase and alkyl hydroperoxide reductase, also overproduces MrgA. These results indicate a complex interplay between metal ions and the expression of the B. subtilis oxidative stress response. [ABSTRACT FROM AUTHOR]

The substrates of ion- and lipid-stimulated protein kinase activity in extracts of Escherichia coli were purified by chromatography. Subsequent N-terminal sequencing suggests that these substrates include the following: a novel 80 kDa protein co-purifying with RNA polymerase but partially homologous to elongation factor G; a protein with an apparent molecular weight of 65 kDa identified as the ribosomal protein S1; and a 32 kDa protein identified as succinyl CoA synthetase, a key enzyme in the tricarboxylic acid cycle. The phosphorylation of these three proteins was markedly stimulated by the addition of manganese, and occurred on threonine, serine or tyrosine residues as indicated by the stability of the phosphoresidues during acid treatment. In addition, a calcium-stimulated protein of 70kDa was identified as the heat-shook protein DnaK, and a 17kDa lipid-stimulated phosphoprotein as nucleotide diphosphate kinase. [ABSTRACT FROM AUTHOR]

Threonine dehydratase is the key enzyme in L-isoleucine synthesis, since it is allosterically feedback-inhibited by L-isoleucine. With the aim of obtaining regulatorily altered mutants of the threonine dehydratase of Corynebacterium glutamicum, amino acids were specifically exchanged and a new biological system of mutant selection was developed, based on the intoxication of Escherichia coli by ketobutyrate, which is the dehydratase reaction product. A collection of 19 mutant enzymes was generated and genetically and biochemically characterized comprising a whole range of regulatorily and catalytically altered enzymes. Of particular interest is the mutant Val-323-Ala, which is characterized by the fact that the L-isoleucine inhibition is entirely abolished so that the enzyme is always present in a relaxed, high-activity state. Correspondingly, the Hill coefficient is 1.4, in contrast to the value of 3.4 characteristic of the wild-type enzyme. Another peculiar mutant generated is the double mutant His-278-Arg-Leu-351-Ser. Here, again, L-isoleucine no longer inhibits catalytic activity, but the effector still promotes major structural changes of the protein, as ascertained from the L-isoleucine-dependent loss of pyridoxal-5'-phosphate from this mutant enzyme. Further enzymes obtained are reduced in L-isoleucine inhibition to a varying degree. Detailed studies on the structure of the enzyme revealed a partially very high similarity of the secondary structure to the mechanistically identical β-subunit of the tryptophan synthase. This provides further indications concerning the localization of the regulatory and catalytic domain of threonine dehydratase. [ABSTRACT FROM AUTHOR]

The c. 110kDa haemolysin toxin secreted by Escherichia coli and other pathogenic Gram-negative bacteria is synthesized as the non-toxic precursor, prohaemolysin (proHlyA), which is unable to target mammalian cell membranes until activated intracellularly by an unknown mechanism dependent upon the coexpressed c. 20kDa protein, HlyC. We have established in vitro post-translational activation of proHlyA in membrane-depleted cell extract fractions from E. coli recombinant strains containing (separately) the proHlyA and HlyC proteins. In vitro activation was calcium-independent and effective over a pH range of 6 to 9 and at temperatures from 42°C to 4°C. HlyC cell extract was also able to activate proHlyA which had been secreted out of ceils containing the export proteins HlyB and HlyD. Fractionation of HlyC cell extracts by sucrose gradient centrifugation and molecular weight chromatography revealed activating fractions as having a molecular mass of 40kDa, suggesting that the HlyC activator is present physiologically in a multimeric form. Cell extracts containing activation-competent HlyC and proHlyA were inactive following dialysis, but activity was restored by complementation with a cell extract lacking both proteins. HlyC and proHlyA proteins which were overproduced separately from recombinant expression plasmids were inactive following purification, but activity could again be restored with a Hly-negative cell extract. These experiments demonstrated that HlyC is not sufficient for activation; an additional cellular factor is required. The cellular factor was found in enterobacteria but not other bacteria or eukaryotic cells. It was cytosolic, protease-sensitive, and behaved as a c. 10kDa polypeptide in a number of assays including dialysis, sucrose gradient centrifugation, and gel filtration chromatography. Thus activation was possible in a defined in vitro reaction containing only purified proHlyA, HlyC, and the... [ABSTRACT FROM AUTHOR]

Hydrogenase activity and other hydrogenase-related functions can be restored to hydC mutants by the specific addition of nickel salts to the growth medium. These mutants are defective in all three hydrogenase isoenzymes and the restoration is dependent upon protein synthesis. The cellular nickel content of the mutant when grown in LB medium is less than 1% of that of the parental strain. Partial suppression of the hydrogenase phenotype of hydC mutants occurs when growth takes place in a different medium. This correlates with an increased cellular nickel content. The phenotype of the mutant is also fully suppressed by growth in media of very low magnesium content. Such media facilitate nickel uptake via the magnesium transport system, which leads to the acquisition of a normal cellular nickel content. Mutations in the fnr gene, which encodes a transcriptional regulator for several anaerobically expressed enzymes, abolishes hydC expression and gives rise to a defective hydrogenase phenotype. The hydrogenase phenotype of fnr is closely similar to that of hydC in all respects examined. The hydrogenase activity of fnr strains can be restored by the presence of a functional hydC gene on a multicopy plasmid. The hydrogenase phenotype of fnr strains therefore arises indirectly via suppression of hydC, which leads to a low cellular nickel content. Nickel has no influence on fumarate reductase or nitrate reductase activities in fnr strains. The hydrogen-metabolism phenotype of fnr strains is, therefore, dependent upon their ability to acquire nickel from growth media. It is likely that hydC encodes a specific transport system for nickel. [ABSTRACT FROM AUTHOR]

Escherichia coli strains have been isolated in which 3, 39 or 805 5′-end codons of lacZ, the gene for the cytoplasmic enzyme β-galactosidase are fused to codon 9 of lacY, the gene for lactose permease. Lactose-permease-deficient cells, carrying the lacZ-Y fusions on F′ lac pro episomes, are phenotypically positive on eosin/methylene blue/lactose or on melibiose plates, demonstrating that the β-D-galactosidase-lactose-permease chimaeras transport lactose and melibiose in vivo. The apparent affinity for β-D-galactopypanosyl 1-thio-β-D-galactopyranoside (GalSGal) in cells is similar to that of the wild-type gene product. The maximum velocity of active GalSGal transport is reduced in all three fusion strains. Both lactose and p-nitrophenyl α-galactopyranoside inhibit GalSGal uptake. As demonstrated by immunoblot experiments the chimaeras cross-react with polyclonal antibodies directed against native lactose permease and they are present in the cell envelope fraction of homogenates. Their apparent molecular weights upon electrophoresis in NaDodSO4/polyacrylamide gels correspond to those expected from t heir respective primary sequences, taking into account the migration properties of wild-type lactose permease. It is proposed that substitution of eight N-terminal lactose permease residues by N-terminal β-galactosidase residues neither prevents membrane incorporation of permease nor completely impairs the ability In transport ,galactosides actively. Alternative interpretations of the experimental results are discussed. [ABSTRACT FROM AUTHOR]

Various experiments were carried out in an attempt to determine the possible physiological function of the N-acetylmuramoyl-L-alanine amidase purified from Escherichia coli K12 on the basis of its activity on N-acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-diaminopimelic acid [MurNAc-LAla-DGlu(msA2pm)]. A Km value of 0.04 mM was determined with this substrate. Specificity studies revealed that compounds with a MurNAc-LAla linkage are the most probable substrates of this enzyme in vivo. Purified amidase had no effect on purified peptidoglycan and only low levels (1-2.5%) of cleaved MurNAc-LAla linkages were detected in peptidoglycan isolated from normally growing cells. However, the action of the amidase in vivo on peptidoglycan was clearly detectable during autolysis. The amidase activity of cells treated by osmotic shock, ether or toluene, as well as that of mutants with altered outer membrane composition was investigated. Attempts to reveal a transfer reaction catalysed by amidase were unsuccessful. Furthermore, by its location and specificity, amidase was clearly not involved in the formation of UDP-MurNAc. The possibility that it might be functioning in vivo as a hydrolase degrading exogeneous peptidoglycan fragments in the periplasma was substantiated by the fact that MurNAc itself and MurNAc-peptides could sustain growth of E. coli as sole carbon and nitrogen sources. Finally, out of 200 thermosensitive mutants examined for altered amidase activity, only two strains had less than 50% of the normal level of activity, whereas ten strains were found to possess more than 50%. In fact, two of the overproducers encountered presented a 4--5-fold increase in activity. [ABSTRACT FROM AUTHOR]

tRNA (adenine-l-)-methyltransferase was isolated from the extreme thermophile Thermus flavus, strain 71. It was purified about 2000-fold by ammonium sulfate fractionation and affinity chromatography on tRNA bound to aminohydroxybutylcellulose via its oxidized 3′ end. The purified protein preparation is free of nuclease and aminoacyl-tRNA synthetase activity and contains no more than 4% of tRNA (guanine-7-)-methyltransferase activity. The only activity of the enzyme is to methylate A58 in the Tψ loop of tRNA. Out of the eight purified tRNAs examined, only yeast tRNATrp was not utilized as a substrate. The enzyme is highly thermostable. It is most active at 75°C. tRNA (adenine-1-)-methyltransferase has a Km of 0.4–0.5 μM for tRNAGln2 from Eseherichia coli and a Km of 6 μM for S-adenosyl-L-methionine. [ABSTRACT FROM AUTHOR]

From an Escherichia coli purine auxotroph a mutant defective in phosphoribosylpyrophosphate (PRib-PP) synthetase has been isolated and partially characterized. In contrast to the parental strain, the mutant was able to grow on nucleosides as purine source, whereas growth on purine bases was reduced. Kinetic analysis of the mutant PRib-PP synthetase revealed an apparent Km for ATP and ribose 5-phosphate of 1.0 mM and 240 µ;M respectively, compared to 60 µ;M and 45 µM respectively for the wild-type enzyme, ADP, which inhibits the wild-type enzyme at a concentration of 0.5 mM ribose 5-phosphate, stimulated the mutant enzyme. The activity of PRib-PP synthetase in crude extract was higher in the mutant than in the parent. When starved for purines an accumulation of PRib-PP was observed in the parent strain, while the pool decreased in the mutant. During pyrimidine starvation derepression of PRib-PP synthetase activity was observed in both strains, although to a lesser extent in the mutant. Our data suggest that the mutant harbors a mutation in the structural gene for PRib-PP synthetase. The mutation responsible for the altered PRib-PP synthetase was located in the purBhemA region at 26 min on the recalibrated linkage map. [ABSTRACT FROM AUTHOR]

Phosphofructokinase has been purified from Escherichia coli strain K-12 grown in a glucose-limited chemostat, both aerobically and anaerobically. The enzymes migrated together in polyacrylamide gel electrophoresis, had the same subunit size in denaturing (dodecylsulfate) gels Mr approx. 34000) and the same kinetic characteristics as described earlier for E. coli phosphofructokinase [e.g. Blangy et al. (1968) J. Mol. Biol. 31, 13–35]: a sigmoid curve of velocity vs. fructose 6-phosphate concentration, activation by ADP, and inhibition by phosphoenolpyruvate. Findings [e.g. Doelle (1975) Eur. J. Biochem. 50, 335–342] of quite different enzymes in aerobic and anaerobic cells were not confirmed. [ABSTRACT FROM AUTHOR]

The binding of 10 isomeric α-amino-heptanoic acids, of two isomeric α-amino-octanoic acids, of isoleucinol and valinol, and of various α-hydroxy acids to isoleucyl-tRNA synthetase from Escherichia coli MRE 600 has been investigated by an ultracentrifuge method. It was found that the enzyme requires a primary amino group together with a not-too-small side chain as prerequisites for ligand recognition. Though the enzyme is absolutely specific for the L isomers, it is fairly tolerant against replacement of the carboxyl group of the natural substrate by more or less hydrophobic substituents. These findings can be explained in terms of Ogston's three-point-attachment model, if it is additionally assumed that there is no further space available in the binding region normally occupied by the α-hydrogen atom to accept other substituents which are as bulky as the carboxyl moiety. Similarly, the architecture of the binding region of the aliphatic side chain is discussed. Our measurements show that the free energy of binding strongly depends on the size and the structure of the remainder of the molecule. None of the isoleucine analogues employed is bound as tightly as the natural substrate itself, but there is a clear preference for side chains branched at the/3-carbon atom. The functioning of the side-chain recognition site is best understood by imagining a two-finger glove, of which one finger is tailored to a methyl and the other to an ethyl group. Both these fingers, together with the binding region for the glycine moiety and a steric barrier against a fourth substituent bulkier than hydrogen, are responsible for a high steric specificity towards the one side chain over its Cβ epimer. [ABSTRACT FROM AUTHOR]

Ribonucleotide reductase from Escherichia coli consists of two nonidentical subunits, proteins B1 and B2. The activity of the enzyme in crude extracts prepared from mechanically disrupted bacteria is very low. Enzyme activity is stimulated 5 to 10-fold by addition of an excess of either subunit. Concentrated extracts from cells lysed gently on Cellophane discs (Schaller et al.) contained 10 to 20-fold higher activity than extracts from mechanically disrupted cells. This activity was not further stimulated by either B1 or B2. The system is suitable for complementation tests for the analysis of temperature-sensitive mutants affecting the ribonucleotide reductase system. Concentrated high-speed supernatants from E. coli treated with lysozyme (Wickner et al.) also contained a high ribonucleotide reductase activity, which was stimulated slightly or not at all by addition of B1 and B2. This active form of the enzyme was unstable and could not be purified. The results suggest that the intracellular form of the enzyme consists of a tight complex of proteins B1 and B2, possibly stabilized by other intracellular structures. [ABSTRACT FROM AUTHOR]

2-Amino-4-oxo-5-chloropentanoic acid inactivates specifically the homoserine dehydrogenase activity of the bifunctional enzyme, aspartokinase I - homoserine dehydrogenase I. The asparto-kinase activity remains essentially untouched and retains its threonine sensitivity. The inactivation of the dehydrogenase requires the covalent binding of one equivalent of the analogue per subunit. Alkylation does not affect the tetrameric state of the protein. The alkylating agent, a substrate analogue, meets the qualitative and quantitative requirements of an affinity label. [ABSTRACT FROM AUTHOR]

1. The free energy, enthalpy, and entropy of activation of the enzymatically catalyzed mutarotation of glucose have been determined: ΔG* 11.9 kcal/mol, ΔH* 12.8 kcal/mol, ΔS* 3.1 cal × mol-1 × K-1. 2. The pH-dependence of the enzymatic activity has been investigated. The active center of the mutarotase from Escherichia coli contains one functional group (pK 5.5) which in the dissociated form has only a catalytic function, and a second one (pK 7.6) which is responsible for the binding of the substrate. 3. The binding group of the substrate has been determined. By comparing the Michaelis and inhibitor constants of a variety of substrates and inhibitors it is concluded that the substrate is bound to the enzyme over an equatorial hydroxyl group at C-2 of the carbohydrate ring. 4. The products of the enzymatically catalyzed mutarotation have been analyzed by gas chromatography. These experiments show that the mutarotase catalyzes not only the anomerisation but also the ring isomerisation. The result is interpreted as evidence of an acyclic intermediate of the mutarotation of the aldoses. 5. The results are summarized in a reaction mechanism of the enzymatically catalyzed mutarotation. Its characteristic feature is that it describes the action of the mutarotase from E. coli as a base catalysis. [ABSTRACT FROM AUTHOR]

Phosphodeoxyribomutase has been purified 67-fold from a thymine starved dra- thy- mutant of Escherichia coli K12. The ratio of activities towards Rib-1-P and dRib-1-P did not change during the purification procedure, indicating that the same protein catalyzes the reaction with both substrates. The activity was dependent on the addition of Mn++, Co++ or Ni++ ions. Activity was simulated 10-fold by addition of ribo- or deoxyribose-1,5-diphosphate; the addition of glucose-1,6-diphosphate enhanced the activity 3-fold. A molecular weight of 3200 ± 3000 was estimated by gel-filtration. [ABSTRACT FROM AUTHOR]

A ribosome fraction enriched in "native" subunits by differential centrifugation yields, upon washing in a buffer containing ammonium chloride and magnesium ions, a protein mixture which can dissociate cytoplasmic ribosomes from Saccharomyces cerevisiae into 40 S and 60 S subunits. This heat dependent reaction cannot be related to any marked ribonuclease activity in the protein mixture. Furthermore, the mixture is unable to dissociate Escherichia coli or rabbit reticulocyte ribosomes; this property is unique, since proteolytic enzymes readily dissociate reticulocyte ribosomes as well as yeast ribosomes. Within 30 min of incubation, the factor-dependent dissociation reaches a plateau, due either to the stoichiometric mode of action of the factor, or to the inability of ribosomes to support complete dissociation under the ionic conditions of the experiments. These two points are discussed. [ABSTRACT FROM AUTHOR]

The effect of the sulfhydryl reagent o-mercuriphenyl β-D-galactoside chloride (synthesis given) on β-galactosidase from Escherichia coli K 12 was investigated in view of the suggestion by Wallenfels and Malhotra in 1960 that cysteine participates in the catalytic mechanism of the enzyme. This reagent inactivated β-galactosidase in amounts smaller than 8 sulhydryl equivalents, corresponding to one tenth of the total amount of protein SH groups. No change in the ratio of hydrolase and transferase activities was found in the partially inactivated enzyme. Competitive inhibitors were partially protective and inactivation could be reversed with 2-mercaptoethanol. It was established that o-mercuriphenyl β-D-galactoside chloride could not be regarded as an active site directed reagent for β-galactosidase. The compound is enzymatically hydroiyzed and its reaction product o-mercnriphenyt chloride is a more effective inhibitor than the galactoside itself. The sedimentation behaviour of the inactivated enzyme was comparable to the native enzyme. Yet upon standing, the modified protein tended to dissociate into the monomer of molecular weight 130000 and to aggregate. The modified and inactivated enzyme still exhibited a strong binding capacity: 4 independent binding sites and a dissociation constant equal to 21 μM for the competitive inhibitor 3-nitro4-aminophenyl β-D-thiogalactoside were found by ultracentrifugation studies with absorption optics. Although some SH groups seem to be indirectly involved irt enzyme function, it is evident that their modification, resulting in inactivation, does not significantly reduce substrate binding in the tetramer and that no SH group is involved in the catalytic mechanism itself. [ABSTRACT FROM AUTHOR]

Fingerprints of tryptic digests of phenylalanyl-tRNA synthetase of Escherichia coli NP 3 suggest that the smallest identical subunit is one fourth of the size of the native protein (mol. wt 181000). Determination of the subunit size by gel electrophoresis reveals a molecular weight of 43000 = 2000. By the criteria employed the enzyme therefore seems to be composed of four identical subunits. Phenylalanyl-tRNA synthetase which has been denatured by treatment with 8M urea is able to reform active enzyme indistinguishable by its size from the native protein. Again, a size of about 45000 was determined for the subunits active in the association reaction. [ABSTRACT FROM AUTHOR]

Adenosylcobalamin (coenzyme B12) dependent diol dehydratase (EC 4.2.1.28) catalyzes the conversion of 1,2-diols and glycerol to the corresponding aldehydes. It undergoes mechanism-based inactivation by glycerol. The diol dehydratase-reactivating factor (DDR) reactivates the inactivated holoenzymes in the presence of adenosylcobalamin, ATP and Mg2+ by mediating the release of a damaged cofactor. This molecular chaperone-like factor was overexpressed in Escherichia coli, purified and crystallized in the ADP-bound and nucleotidefree forms by the sandwich-drop vapour-diffusion method. The crystals of the ADP-bound form belong to the orthorhombic system, with space group P212121 and unit-cell parameters a = 83.26, b = 84.60, c = 280.09 Å , and diffract to 2.0 Å. In the absence of nucleotide, DDR crystals were orthorhombic, with space group P212121 and unit-cell parameters a = 81.92, b = 85.37, c = 296.99Å and diffract to 3.0 Å. Crystals of both forms were suitable for structural analysis. [ABSTRACT FROM AUTHOR]

A complex of the ∊-subunit and the central domain of the y-subunit from the ATP synthase of Escherichia coli has been purified and crystallized and preliminary X-ray analysis has been carried out. The crystals belong to space group C2221 with unit-cell parameters a = 76.7, b = 176.1, c = 67.1 Å (at 100 K). Determination of the structure of this protein complex promises to greatly improve the understanding of energy coupling between the F0 and F1 sectors within the enzyme complex. [ABSTRACT FROM AUTHOR]