Crystal structure of Escherichia coli methionyl-tRNA synthetase at 2.5 Å resolution

Native methionyl-tRNA synthetase from Escherichia coli (a dimer of molecular weight 172,000) can be converted by mild proteolysis into a well-defined monomeric fragment of molecular weight 64,000. This fragment retains full specificity towards methionine and tRNA^Met, and has unimpaired activity in both the activation and aminoacylation reactions.This paper describes the structure of the active fragment, as determined by an X-ray crystallographic study at 2.5 Å resolution using five heavy-atom derivatives. The elongated molecule (90 Å × 52 Å × 44 Å) contains several α-helices, which account for 43% of the residues. Three domains can be distinguished in the structure: (1) a central core beginning at the N-terminus, consisting of a five-stranded parallel pleated sheet with α-helices connecting the β-strands; (2) a second domain with less-ordered structure, inserted between the third and fourth strand of the central sheet; (3) a C-terminal domain, beginning after the fifth parallel strand, very rich in α-helices.These three domains are organized in a biglobular structure; one globule contains the first and the second domain (N-terminal globule), the other the third domain. The two globules, linked together by a single chain, are separated by a large cleft.The most salient feature of the structure is the presence, in the N-terminal domain, of a “nucleotide binding fold” similar to that first observed in dehydrogenases. This makes methionyl-tRNA synthetase, and possibly all aminoacyl-tRNA synthetases, a new member of this family of nucleotide binding proteins possessing the characteristic “Rossmann fold”.     

Crystal structure of ferric Aplysia limacina myoglobin at 2 X 0 A resolution

The three-dimensional structure of ferric myoglobin from the mollusc Aplysia limacina has been refined at 2 X 0 A resolution. The crystallographic R factor, calculated at this stage, is 0 X 194. Despite its high content of apolar residues (both aromatic and aliphatic), Aplysia limacina myoglobin, which contains only one histidine residue (at the proximal position), has a structure that conforms to the common eight-helices globin fold observed in other phyla.     

Conservation and DNA sequence arrangement of the DNA polymerase I gene region from Klebsiella aerogenes, Klebsiella pneumoniae and Escherichia coli

Linked multiple mutation is observed after treatment of Escherichia coli with methyl methanesulfonate, N-methyl-N′-nitro-N-nitrosoguanidine, ethyl methanesulfonate, and N-ethyl-N-nitro-N-nitrosoguanidine but not ultraviolet light. Induction of linked multiple mutations requires the uvrE⁺ gene product indicating the involvement of the mismatch repair system. The observation of linked multiple mutations is not due to mutagenesis occurring in a subpopulation of cells. Growing point mutagenesis also occurs after treatment with these mutagens but not with ultraviolet light. It is likely that the excess of mutations observed with these mutagens at growing points is at least partly a relative effect, rather than one due to an absolute increase of reactivity at the DNA growing point region. This relative effect may result from the operation of an inducible repair mechanism which removes O⁶-alkylguanine residues from the DNA distal to the bacterial growing point. The adaptive response, first described by Robins &; Cairns (1979) prefers O⁶-methylguanine over O⁶-ethylguanine.     

Non-random layout of the amino acid loci on the genome of Escherichia coli

A strong correlation exists between the relative frequencies of occurrence of the amino acids in bulk Escherichia coli protein and their genetic map positions when the latter are indexed against the position of the origin of DNA synthesis. The greater the production of the amino acid, the closer its operon is to the origin.     

The secondary attachment site for bacteriophage lambda in the proA/B gene of Escherichia coli

We have determined the nucleotide sequence of a secondary λ attachment site in $\text{pro}\text{A}\text{B}$, a site that accounts for 3% of lysogens isolated from Escherichia coli strains deleted for the primary site. Direct sequence analysis of the transducing bacteriophages carrying the left and right att junctions, as well as the recombinant pro⁺ phage reveals that the $\text{pro}\text{A}\text{B}$ site shares an 11-nucleotide interrupted homology with the core sequence of the primary site. We have compared the $\text{pro}\text{A}\text{B}$att site with other secondary attachment sites to gain insights into the structural features important for λ integration.     

EcoA and EcoE: alternatives to the EcoK family of type I restriction and modification systems of Escherichia coli

The genes (hsd A) encoding EcoA, a restriction and modification system first identified in Escherichia coli 15T-, behave in genetic crosses as alleles of the genes (hsd K) encoding the archetypal type I restriction and modification system of E. coli K12. Nevertheless, molecular experiments have failed to detect relatedness between the A and K systems. We have cloned the hsd A genes and have identified, on the basis of DNA homology, related genes (hsd E) conferring a new specificity to a natural isolate of E. coli. We show that the overall organization of the genes encoding EcoA and EcoE closely parallels that for EcoK. Each enzyme is encoded by three genes, of which only one, hsdS, confers the specificity of DNA interaction. The three genes are in the same order as those encoding EcoK, i.e. hsdR, hsdM and hsdS and, similarly, they include a promoter between hsdR and hsdM from which the M and S genes can be transcribed. The evidence indicates that EcoA and EcoE are type I restriction and modification enzymes, but they appear to identify an alternative family to EcoK. For both families, the hsdR polypeptide is by far the largest, but the sizes of the other two polypeptides are reversed, with the smallest polypeptide of EcoK being the product of hsd S, and the smallest for the EcoA family being the product of hsdM. Physiologically, the A restriction and modification system differs from that of K and its relatives, in that A-specific methylation of unmodified DNA is particularly effective.     

Essential interaction between lambdoid phage 21 terminase and the Escherichia coli integrative host factor

Lambdoid phage 21 requires the Escherichia coli integrative host factor (IHF) for growth. lambda-21 hybrids that have 21 DNA packaging specificity also require IHF. IHF-independent (her) mutants have been isolated. her mutations map in the amino-terminal half of the 21 1 gene. The 1 gene encodes the small subunit of the 21 terminase, and the amino-terminal half of the 1 polypeptide is a functional domain for specifically binding 21 DNA. Hence changes in the DNA-binding domain of terminase, her mutations, render 21 terminase able to function in the absence of IHF. Three of four her mutations studied are trans-dominant. An in vitro system was used to show that packaging of 21 DNA is IHF-dependent. IHF is directly required during the early, terminase-dependent steps of assembly. It is concluded that IHF is a host factor required for function of the 21 terminase. It is proposed, in analogy to the role of IHF in lambda integration, that IHF facilitates proper binding of 21 terminase to phage DNA. Consistent with this proposal, possible IHF-binding sites are present in the 21 cohesive end site.     

Nucleotide sequence of the genes involved in phosphate transport and regulation of the phosphate regulon in Escherichia coli

The pstA(=phoT), pstB and phoU genes are situated at 84 minutes on the Escherichia coli genetic map. All of them are involved in the negative regulation of the phosphate regulon, and all of them except for phoU are required for the binding-protein-mediated, highly specific phosphate transport. We have determined the DNA sequence of about 4 X 10(3) bases of chromosomal segment containing these genes. Four translational reading frames (TRFs) were detected in the region. We attempted to assign the TRFs to the mutant alleles. Plasmids were constructed so that each contained only one of the TRFs, downstream from the lac promoter, to be used for the complementation tests. By this test, TRF-2, TRF-3 and TRF-4 were identified with the pstA(=phoT), pstB and phoU genes, respectively. Alkaline phosphatase-constitutive mutations of the two strains in our collection were complemented by the plasmid with the TRF-1 region. Therefore, we propose to designate the allele phoW. The order of the genes in this region has been established to be phoS-phoW-pstA(=phoT)-pstB-phoU counterclockwise on the E. coli genetic map.     

Catalytic conformation of carboxypeptidase A. The structure of a true reaction intermediate stabilized at subzero temperatures

The structure of the mixed anhydride, acyl-enzyme intermediate of the esterolytic reaction of carboxypeptidase A is characterized by application of cryoenzymologic, magnetic resonance, and molecular graphics methods with use of the Co²⁺-substituted enzyme and the specific spin-label ester substrate O-3-(2,2,5,5-tetra-methylpyrrolinyl-1-oxyl)-propen-2-oyl-l-β-phenyllactate. A radial separation of 7·7 Å between the active site Co²⁺ and the nitroxide group in the low temperature-stabilized acyl-enzyme intermediate is determined on the basis of their spin-spin (dipole-dipole) interactions. Application of molecular graphics techniques shows that the only configuration of the substrate that is sterically accommodated by the active site yields a calculated metal ion-to-nitroxide distance of 7·8 Å. Steric accommodation of the spin-label in the active site requires severe torsional distortion around the aliphatic double bond of the propenoyl side-chain. Examination of the structure of the enzyme: spin-label intermediate reveals that the distortion arises from steric interactions of the pyrrolinyl group with the protein at a position that corresponds to the site occupied by the penultimate amide residue of an oligopeptide substrate from the site of cleavage. Together with kinetic data showing that hydrolysis of the spin-label is governed by rate-limiting deacylation, the results indicate that geometric distortion of substrates by secondary interactions with the enzyme, in general, is an obligatory part of the catalytic action of carboxypeptidase A. When viewed with respect to requirements for stereoelectronic control of bond cleavage in tetrahedral adducts of esters and amides (Deslongchamps, 1975) the results suggest that torsional distortion during catalysis results in rotation around the scissile bond of the substrate, and that this rotation is required to form the mixed anhydride reaction intermediate. These findings further support the interpretation that the hydrolysis of esters and amides catalyzed by carboxypeptidase A proceeds according to similar mechanisms except that formation of the mixed anhydride is rate-determining in peptide hydrolysis while deacylation of the mixed anhydride is rate-limiting in ester hydrolysis.Additionally, in this study application of the extension of the theory of the Solomon-Bloembergen-Morgan equations derived by Lindner (1965) for paramagnetic metal ions with S ≥ 1 demonstrates that the zero-field splitting of the high-spin Co²⁺ in the metal-substituted enzyme has no significant influence in determination of the relaxation enhancement of solvent protons by the active site metal ion.     

Immunochemical analysis of molecular forms of protein synthesis initiation factors in crude cell lysates of Escherichia coli

Three initiation factors (IF1, IF2, and IF3) have been highly purified from Escherichia coli and extensively characterized, but little is known about the molecular forms of these proteins as they occur in vivo. We have analyzed molecular-weight and charge forms in crude cell lysates by polyacrylamide gel electrophoresis followed by immunoblotting with antibodies specific for the initiation factors. Freshly grown bacterial cells were lysed by sonication in buffer containing sodium dodecyl sulfate, and the lysate was fractionated by gel electrophoresis. Proteins from the gel were electrotransferred to a nitrocellulose sheet which was treated with a specific rabbit antiserum followed by radiolabeled Staphylococcus aureus protein A. Autoradiography showed only one major band each for IF1 and IF3, exactly corresponding to the isolated factors. For IF2, two molecular-weight forms were detected which were identical with purified IF2a and IF2b. No evidence for precursor forms was found. Two-dimensional gel analysis showed no charge heterogeneity for IF1, IF2a, and IF3, but multiple forms were seen for IF2b. Analysis of phosphoproteins from cells grown in radioactive phosphate medium ruled out the possibility that phosphorylation occurs on the initiation factors, elongation factors, or ribosomal proteins.     

Further sequence analysis of the phage lambda receptor site. Possible implications for the organization of the lamB protein in Escherichia coli K12

We present the DNA sequence alterations due to seven lamB missense mutations yielding resistance to phages lambda and K10. They reveal five different amino acid positions in the LamB protein. Three positions (245, 247 and 249) define a new region required for phage adsorption. The two other positions (148 and 152) belong to a region where mutations to phage resistance has already been detected. These two regions are hydrophilic and could belong to turns of the protein located at the surface of the cell. All the missense mutational alterations to phage resistance sequenced in the LamB protein correspond to 10 sites located in four different segments of the polypeptide chain. We discuss their location in terms of the notion of phage receptor site and of a working model for the organization of this protein in the outer membrane of Escherichia coli.     

Sequence information within the lamB genes in required for proper routing of the bacteriophage lambda receptor protein to the outer membrane of Escherichia coli K-12

The structure of Satellite tobacco necrosis virus (STNV) has been determined to 3.0 Å resolution by X-ray crystallography. Electron density maps were obtained with phases based on one heavy-atom derivative and several cycles of phase refinement using the 60-fold non-crystallographic symmetry in the particle. A model for one protein subunit was built using a computer graphics display. The subunit is constructed mainly of a β-roll structure forming two β-sheets, each of four antiparallel strands. The N-termini of the subunits form bundles of three α-helices extending into the RNA region of the virus at the 3-fold axis. The topology of the polypeptide chain is the same as, and the conformation clearly similar to, that of the shell domains of the Tomato bushy stunt virus (TBSV) and Southern bean mosaic virus (SBMV) protein subunits. The subunit packing in the T = 1 STNV structure is, however, significantly different from the packing of these T = 3 viruses: parts of some of the structural elements facing the RNA in TBSV and SBMV are utilized for subunit-subunit contacts in STNV. No RNA structure is obvious in the present icosahedrally averaged electron density maps. The protein surface facing the RNA contains mainly hydrophilic residues, especially lysine and arginine.     

Escherichia coli mutants defective in the gamma subunit of proton-translocating ATPase: intracistronic mapping of the defective site and the biochemical properties of the mutants

Various hybrid plasmids carrying a portion of the gene for the gamma subunit of the H+-ATPase of Escherichia coli complemented five mutants defective in the enzyme in a genetic test, indicating that the mutants are defective in the gamma subunit. Since the nucleotide sequence of genomic DNA carried on the plasmids is known, the defective site(s) of the mutants could be located within the gene for the gamma subunit as follows: KF10 and NR70, KF1, and KF12 and KF13 have a mutation causing a defect(s) in amino acid residues 1 to 82, 83 to 167, and 168 to 287, respectively, of the gamma subunit. The biochemical properties of all these mutants except NR70 were analyzed in terms of proton permeability of the membranes and assembly of F1. Results suggested that KF1 and KF10 have defective F1 without at least the alpha and beta subunits on their membranes, whereas KF12 and KF13 have F1's of rather similar structure to that of the wild type. Attempts were made to purify F1 oF KF12 as a single complex. Although the F1 complex dissociated during purification, active alpha and beta subunits of KF12 were partially purified. On the basis of these biochemical and genetic results, it is suggested that structural alterations in the primary sequence of the gamma subunit corresponding to residues 1 to 167 cause more extensive defects in the assembly of F1 than alteration in the sequence of residues 168 to 287.     

Temperature dependence of the rate constants of the Escherichia coli RNA polymerase-lambda PR promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening

The kinetics of formation and of dissociation of open complexes (RPo) between Escherichia coli RNA polymerase (R) and the lambda PR promoter (P) have been studied as a function of temperature in the physiological range using the nitrocellulose filter binding assay. The kinetic data provide further evidence for the mechanism R + P in equilibrium I1 in equilibrium I2 in equilibrium RPo, where I1 and I2 are kinetically distinguishable intermediate complexes at this promoter which do not accumulate under the reaction conditions investigated. The overall second-order association rate constant (ka) increases dramatically with increasing temperature, yielding a temperature-dependent activation energy in the range 20 kcal (near 37 degrees C) to 40 kcal (near 13 degrees C) (1 kcal = 4.184 kJ). Both isomerization steps (I1----I2 and I2----RPo) appear to be highly temperature dependent. Except at low temperatures (less than 13 degrees C) the step I1----I2, which we attribute to a conformational change in the polymerase with a large negative delta Cp degrees value, is rate-limiting at the reactant concentrations investigated and hence makes the dominant contribution to the apparent activation energy of the pseudo first-order association reaction. The subsequent step I2----RPo, which we attribute to DNA melting, has a higher activation energy (in excess of 100 kcal) but only becomes rate-limiting at low temperature (less than 13 degrees C). The initial binding step R + P in equilibrium I1 appears to be in equilibrium on the time-scale of the isomerization reactions under all conditions investigated; the equilibrium constant for this step is not a strong function of temperature and is approximately 10(7) M-1 under the standard ionic conditions of the assay (40 mM-Tris . HCl (pH 8.0), 10 mM-MgCl2, 0.12 M-KC1). The activation energy of the dissociation reaction becomes increasingly negative at low temperatures, ranging from approximately -9 kcal near 37 degrees C to -30 kcal near 13 degrees C. Thermodynamic (van't Hoff) enthalpies delta H degrees of open complex formation consequently are large and temperature-dependent, increasing from approximately 29 to 70 kcal as the temperature is reduced from 37 to 13 degrees C. The corresponding delta Cp degrees value is approximately -2.4 kcal/deg. We propose that this large negative delta Cp degrees value arises primarily from the burial of hydrophobic surface in the conformational change (I1 in equilibrium I2) in RNA polymerase in the key second step of the mechanism.(ABSTRACT TRUNCATED AT 400 WORDS)     

Structure-function relationship in Escherichia coli initiation factors. Environment of the Cys residue and evidence for a hydrophobic region in initiation factor IF3 by fluorescence and ESR spectroscopy

The reactions of rabbit muscle pyruvate kinase with 5′-p-fluorosulfonylbenzoyl adenosine (5′-FSBA) and 5′-p-fluorosulfonylbenzoyl guanosine (5′-FSBG) from pH 7.0 to 8.0 exhibit biphasic inactivation kinetics. These reactions are characterized by three events: a fast reaction yielding partially active enzyme (with 67% of its original activity for the 5′-FSBA reaction and 45% for the 5′-FSBG reaction) which is reactivated by dithiothreitol, and two slower reactions yielding fully inactive enzymes; the product of only one of the two slower reactions is reactivated by dithiothreitol. These reactions are termed fast dithiothreitol-sensitive, slow dithiothreitol-sensitive, and dithiothreitol-insensitive inactivations. The rates of all three phases of the reactions with 5′-FSBA and 5′-FSBG increase as the pH is raised. The 5′-FSBG reaction can be described in terms of initial reaction with a single ionizable group of pK_a 7.80, 8.60, and 7.94 for the fast dithiothreitol-sensitive, slow dithiothreitol-sensitive, and dithiothreitol-insensitive reactions, respectively; pH-independent rate constants of 0.173, 0.133, and 0.0165 min^?1 are calculated for these three phases of the overall reaction. The pH dependence of the dithiothreitol-insensitive inactivation by 5′-FSBA coincides with that for 5′-FSBG, but the data for the dithiothreitol-sensitive reactions with 5′-FSBA indicate that the reaction in each phase occurs at more than one site over the pH range tested. Differential protection by ligands against inactivation by 5′-FSBA and 5′-FSBG at pH 7.4 and 8.0 indicates that, for the fast dithiothreitol-sensitive reactions, the cysteine residues participating in the two reactions are not identical, although in both cases modification has been attributed to formation of a disulfide. For 5′-FSBA, the partial inactivation appears to result from modification of cysteine residues at the noncatalytic nucleotide site, whereas for 5′-FSBG the inactivation is due to modification within the catalytic metal-nucleotide site. Reaction with 5′-FSBG seems to occur at the same locus for both the fast and slow dithiothreitol-sensitive phases, with the rate difference being ascribable to negative cooperativity among subunits. For the slow dithiothreitol-sensitive inactivation by 5′-FSBA, protection by Mg²⁺ and by Mg²⁺ plus ADP suggests that the targets of modification include the active-site cysteine that is modified by 5′-FSBG. The dithiothreitol-insensitive inactivation, shown to be due to reaction of 5′-FSBA with a tyrosine, may result from reaction of both nucleotide analogs with the same residue, although differential protection by the natural ligands suggests that 5′-FSBA and 5′-FSBG bind to two subsites within the active site.     

Three-dimensional structure of a cell wall glycoprotein

Electron microscopy and computer image analysis have been used to determine the three-dimensional structure of the crystalline glycoprotein cell wall layer of the alga Lobomonas piriformis. Images of negatively stained specimens, tilted through a range of angles up to 70 °, were combined to give a map of the molecular envelope to a resolution of 2.0 nm. The cell wall layer consists of crystalline plates the centres and edges of which display distinctly different but isomorphous structures. A comparison of three-dimensional reconstructions of the two areas shows the difference probably to be due to a conformational change of one of the glycoprotein subunits. The structure consists of two sets of dimers composed of rod-shaped subunits which lie with their long axes approximately in the plane of the crystal. The centre-edge transition may have significance in the pathway of accretion of new subunits during cell wall growth.