Proteolytic signal sequences (PEST) in the mammalian aminoacyl-tRNA synthetase complex

Eight aminoacyl-tRNA synthetases together with three unidentified proteins are associated as a multi-enzyme complex in mammalian cells. Partial peptide sequences for lysyl- and aspartyl-tRNA synthetases are determined and no highly hydrophobic peptides are found. The partial amino acid sequences for two of the unidentified proteins in the complex are shown to have substantial homology and each has a number of unique sequences. The results suggest that the two unidentified proteins are fragments of synthetases. The partial sequences revealed the presence of PEST sequences in at least three proteins. Inasmuch as PEST sequences are signals for intracellular degradation, the mammalian synthetase complex may have evolved to protect these synthetases against intracellular proteolysis.

Evidence from cassette mutagenesis for a structure-function motif in a protein of unknown structure

The three-dimensional structure of most enzymes is unknown; however, many enzymes may have structural motifs similar to those in the known structures of functionally related enzymes. Evidence is presented that an enzyme of unknown structure [Ile-transfer RNA (tRNA) synthetase] may share a functionally important structural motif with an enzyme of related function (Tyr-tRNA synthetase). This approach involves (i) identifying segments of Ile-tRNA synthetase that have been unusually conserved during evolution, (ii) predicting the function of one such segment by assuming a structural relation between Ile-tRNA synthetase and Tyr-tRNA synthetase, and (iii) testing the predicted function by mutagenesis and subsequent biochemical analysis. Random mutations were introduced by cassette mutagenesis into a ten-amino-acid segment of Ile-tRNA synthetase that was predicted to be involved in the formation of the binding site for isoleucine. Few amino acid substitutions appear to be tolerated in this region. However, one substitution (independently isolated twice) increased the Michaelis constant Km for isoleucine in the adenylate synthesis reaction by greater than 6000-fold, but had little effect on the Km for adenosine triphosphate, the apparent Km for tRNA, or the rate constant kcat.

Peptides at the tRNA binding site of the crystallizable monomeric form of E. coli methionyl-tRNA synthetase

A protein affinity labeling derivative of E. coli tRNA(fMet) carrying lysine-reactive cross-linking groups has been covalently coupled to monomeric trypsin-modified E. coli methionyl-tRNA synthetase. The cross-linked tRNA-synthetase complex has been isolated by gel filtration, digested with trypsin, and the tRNA-bound peptides separated from the bulk of the free tryptic peptides by anion exchange chromatography. The bound peptides were released from the tRNA by cleavage of the disulfide bond of the cross-linker and purified by reverse-phase high-pressure liquid chromatography, yielding three major peptides. These peptides were found to cochromatograph with three peptides of known sequence previously cross-linked to native methionyl-tRNA synthetase through lysine residues 402, 439 and 465. These results show that identical lysine residues are in close proximity to tRNA(fMet) bound to native dimeric methionyl-tRNA synthetase and to the crystallizable monomeric form of the enzyme, and indicate that cross-linking to the dimeric protein occurs on the occupied subunit of the 1:1 tRNA-synthetase complex.

Preliminary crystallographic study of the phenylalanyl-tRNA synthetase from Thermus thermophilus HB8

Phenylalanyl-tRNA synthetase (EC 6.1.1.20) from the extreme thermophile Thermus thermophilus HB8 has been isolated and crystallized. The enzyme was found to consist of two types of subunits with molecular masses 38 X 10(3) (alpha) and 94 X 10(3) (beta) and is likely to be a tetrameric protein with a molecular mass of about 260 X 10(3) (alpha 2 beta 2). Crystals of phenylalanyl-tRNA synthetase were grown by the hanging-drop technique at 4 degrees C in the presence of ammonium sulfate. Trigonal crystals, space group P3(1)21, with cell dimensions a = b = 176 A and c = 142 A (1 A = 0.1 nm), are suitable for medium-resolution X-ray analysis.

Affinity labelling of E. coli leucyl-tRNA synthetase with 3'-oxidized tRNA(Leu)

The E. coli leucyl-tRNA synthetase (E.C. 6.1.1.4) was specifically labelled with 3'-oxidized tRNA(Leu) (tRNA(oxLeu)). The procedure involves a Schiff's base formation and its subsequent reduction by sodium cyanoborohydride. Stoichiometric inactivation of aminoacylation was achieved with the incorporation of 1 mol of tRNA(oxLeu) per mol LeuRS. On the other hand, the amino acid activation activity of LeuRS-tRNA(ox) complex was partially inhibited. After extensive digestion of the complex by pancreatic ribonuclease, the amino acid activation activity was fully recovered, while the aminoacylation activity was not restored at all.

Evidence for dispensable sequences inserted into a nucleotide fold

Previous experimental results along with the structural modeling presented indicate that a nucleotide fold starts in the amino-terminal part of Escherichia coli isoleucyl-transfer RNA synthetase, a single chain polypeptide of 939 amino acids. Internal deletions were created in the region of the nucleotide fold. A set of deletions that collectively span 145 contiguous amino acids yielded active enzymes. Further extensions of the deletions yielded inactive or unstable proteins. The three-dimensional structure of an evidently homologous protein suggests that the active deletions lack portions of a segment that connects two parts of the nucleotide fold. Therefore, the results imply that removal of major sections of the polypeptide that connects these two parts of the fold does not result in major perturbation of the nucleotide binding site.

Characterization by tandem mass spectrometry of structural modifications in proteins

Tandem mass spectrometry can be used to solve a number of protein structural problems that are not amenable to conventional methods for amino acid sequencing. Typical problems that use this approach involve characterization of peptides with blocked amino termini or peptides that have been otherwise posttranslationally processed, such as, by phosphorylation or sulfation. The structure and homogeneity of synthetic peptides can also be evaluated. Since peptides can be selectively characterized in the presence of other peptides or contaminants, the need for extensive purification is reduced or eliminated.

Improved detection of anti-Jo-1 antibody, a marker for myositis, using purified histidyl-tRNA synthetase

The increased detection of anti-Jo-1 antibody afforded by the use of the purified antigen, histidyl-tRNA synthetase, in counterimmunoelectrophoresis is demonstrated. Using purified antigen, anti-Jo-1 antibody was detected in the sera of 16/33 (48.5%) patients with confirmed myositis and in 20/45 (44.5%) patients with confirmed or possible myositis. This rate is approximately double that obtained with commercial thymus extracts both in this study and seven others reported in the literature. The presence of antibody shows marked correlation with the activity of myositis at the time of serum sampling and with the presence of interstitial lung disease. Detection rates are similar in patients with polymyositis and dermatomyositis both with and without additional connective tissue diseases.

Crystals of seryl-tRNA synthetase from Escherichia coli. Preliminary crystallographic data

Crystals of seryl-tRNA synthetase from Escherichia coli can be grown from ammonium sulphate/octyl glucoside solutions in two days. The crystals appear to be very suitable for X-ray analysis, diffracting to at least 2.8 A resolution and being resistant to radiation damage. The crystals are monoclinic (space group C2) with cell parameters a = 148.2 A, b = 90.6 A, c = 69.5 A and beta = 119.0 degrees. Depending on whether the asymmetric unit is the enzyme monomer (Mr 48,414) or dimer the Vm value would be either 4.12 or 2.10 A3/dalton. Although the former would indicate a rather high solvent content, other proteins crystallized in the presence of octyl glucoside have Vm values similar to this.

Phenylalanyl-tRNA synthetases as an example for comparative and evolutionary aspects of aminoacyl-tRNA synthetases

Aminoacyl-tRNA synthetases are indispensable components of protein synthesis in all three lines of evolutionary descent, eubacteria, archaebacteria and eukaryotes. Furthermore they are also present in the translational apparatus of the semi-autonomous organelles, mitochondria and chloroplasts, of the eukaryotic cell. Therefore aminoacyl-tRNA synthetases are appropriate objects for comparative molecular biology in order to obtain a comprehensive picture of the evolution of the translational process. The analysis of the phenylalanyl-tRNA synthetase in a large variety of organisms and organelles in this respect is the most advanced. In addition to comparison of quaternary structure, analysis includes functional aspects of accuracy mechanisms (proofreading) and comparison of structural features by means of substrate analogs. Evolutionary relationships are furthermore elucidated using the immunological approach and heterologous aminoacylation.

Parasite-specific interaction of N-[4-(4'nitroanilino)-phenyl]-S-(beta-carboxyethyl)-dithiocar bamic acid-ester with arginyl-tRNA-synthetase from Dirofilaria immitis

A potent inhibition of arginyl-tRNA-synthetase from Dirofilaria immitis by N-[4-(4'nitroanilino)-phenyl]-S-(beta-carboxylethyl)-dith iocarbamic acid-ester (CGP 8065) is demonstrated, which indicates the charging of amino acids to tRNA as a possible target for the chemotherapeutic attack by this filaricidal compound. CGP 8065 competes with ATP; the inhibition constant was determined to be 13 micrograms ml-1 (34 microM). The Michaelis constants for arginine and ATP were found to be 5 microM and 0.4 mM, respectively. The inhibition of arginyl-tRNA-synthetase by CGP 8065 was shown to be specific for D. immitis; the isofunctional enzymes from Ascaris suum and rat liver were not affected.

Methionyl-tRNA synthetase from E. coli: direct evidence for exchange of protomers in the dimeric enzyme by using deuteration and small-angle neutron scattering

Direct demonstration of the reversible dissociation of native dimeric methionyl-tRNA synthetase from E. coli has been obtained using small angle neutron scattering and deuterated enzyme. Structural parameters of the fully deuterated dimer are very similar to the hydrogenated one. Analysis of the variations of the intensity and of the radius of gyration of a stoichiometric mixture of the two types of dimer (hydrogenated and deuterated), as a function of D2O content in the solvent, enabled us to characterize an hybrid dimer, having both hydrogenated and deuterated protomers. By separating the contribution of each protomer to the scattering, the radius of gyration of the protomer in situ and the distance between the centers of mass of each protomer in the dimer are determined.

Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthetase

Few and limited amino acid sequence homologies have been found among eight bacterial aminoacyl transfer RNA (tRNA) synthetases whose primary structures are known. The entire 939-amino acid primary structure of Escherichia coli isoleucyl-tRNA synthetase is now reported. In a sequence of 11 consecutive amino acids matching a sequence in E. coli methionyl-tRNA synthetase, there are ten identical residues and one conservative change. This is the strongest homology recorded between any two aminoacyl tRNA synthetases. This part of the methionine enzyme's three-dimensional structure has been determined, and it occurs in a mononucleotide binding fold; a close three-dimensional structural homology of this part of the enzyme with Bacillus stearothermophilus tyrosyl-tRNA synthetase has also been reported. The three synthetases probably fold identically in this region.

Crystallization of substrate and product analog complexes of tryptophanyl-tRNA synthetase

We have prepared crystals of tryptophanyl-tRNA synthetase from Bacillus stearothermophilus complexed to tryptophan (type II*), and to tryptophanyl-3'(2')-ATP (type IV). The latter compound is a product analog, enzymatically synthesized by acyl transfer of tryptophan from the tryptophanyl-5'-AMP intermediate to a second molecule of ATP. It resembles the 3'-terminal fragment, tryptophanyl-3'(2')-adenosine, of Trp-tRNATrp. Both crystal forms diffract to high resolution. Although both forms are grown from 2 M K2HPO4, they are dramatically different in the shape of the unit cell and in space group symmetry. Type II* crystals are monoclinic (space group P21). However, low-resolution reflections obey the symmetry of space group P321, which indicates both the existence and the location of noncrystallographic symmetry in the monoclinic unit cell. Type IV crystals belong to space group P41212 (or its enantiomorph) and the unit cell is elongated along the fourfold screw axis. Analysis of molecular packing suggests that intermolecular contacts in the two crystal types are very different. Thus, the two structures may exhibit conformational differences related to catalysis by this enzyme. Solution of type II* and type IV crystal structures may provide representations resembling a Michaelis complex and an acyl transfer product complex.

Size polymorphism and the structure of aminoacyl-tRNA synthetases

Although aminoacyl-tRNA synthetases catalyze the same chemical reaction, the individual enzymes have a wide range of sizes. Proteolytic digestion has yielded active catalytic fragments of two synthetases. A set of gene deletions in a large synthetase has been used successfully in the creation of a variety of enzyme fragments that have been studied individually; a fragment with about half of the total polypeptide is sufficient to aminoacylate tRNA in vivo. The results suggest that size polymorphism is caused by fusion, to a core catalytic segment, of variable amounts of additional polypeptide sequences. These sequences may serve to impart additional functions. For example, in one case, a synthetase binds to its own gene promoter and regulates transcription.

Structural organization of high-Mr mammalian aminoacyl-tRNA synthetases. Comparison of multi-enzyme complexes from different sources

Many mammalian aminoacyl-tRNA synthetases have been isolated as high-Mr multi-enzyme complexes. These complexes often contain variable contents of synthetase activities. The complexes may also contain molecules other than synthetases such as tRNA. The observed variations in size, polypeptide composition, and content of enzyme activities of the high-Mr synthetase complexes have been sources of confusion in the understanding of the structural organization of these complexes. A unified scheme of structural organization which encompasses most observations on high-Mr complexes reported in the literature is presented.

[20 years of cooperation in the study of structure and function of tRNA and aminoacyl-tRNA-synthetases]

The article reviews the results of joint projects initiated 20 years ago in the field of tRNA and aminoacyl-tRNA synthetases. Laboratories located at Novosibirsk, Moscow, Kiev and other places remoted geographically effectively cooperated with each other. More than 30 common publications emerged and the data obtained were communicated at several international meetings. The effectiveness of cooperation was achieved by two important factors: (i) mutual scientific and methodological complementarity of the cooperating units, and (ii) absence of administrative pressure. The cooperation was strongly supported by the Scientific Council of Molecular Biology and 10 workshops were sponsored by the Council to facilitate personal contacts and to create an atmosphere of intensive and informal exchange of data and ideas. It is stressed that the experience worked out in this particular field is applicable to other fields of molecular biology.

Structural and functional aspects of domain motions in proteins

Three distinct categories of large-scale flexibility in proteins have been documented by single-crystal X-ray diffraction studies: the relatively free movement of essentially rigid globular domains that are connected by a flexible segment of polypeptide, the reorientation of essentially rigid domains among a few distinct conformations, and the concerted transition of a contiguous region of the surface of a protein from a disordered state to an ordered state. In a number of examples, well-defined functions can be assigned to these large-scale structural changes. The occurrence of such motions in proteins of known structure is reviewed, and the best-studied examples are discussed in detail to allow a critical evaluation of the methods used to identify and study these motions.

Structural homology in the amino-terminal domains of two aminoacyl-tRNA synthetases

The three-dimensional structures of two animoacyl-tRNA synthetases, the methionyl-tRNA synthetase from Escherichia coli (MetRS) and the tyrosyl-tRNA synthetase from Bacillus stearothermophilus (TyrRS), show a remarkable similarity over a span of about 140 amino acids. The region of homologous folding corresponds to a five-stranded parallel beta-sheet, including a mononucleotide-binding fold. One cysteine and two histidine residues that were found to be invariant in the amino acid sequences occupy similar places in the nucleotide-binding fold. In TyrRS, these residues are close to the adenylate binding site, and in MetRS to the Mg2+-ATP binding site.

Yeast tRNAAsp-aspartyl-tRNA synthetase: the crystalline complex

Aspartyl-tRNA synthetase from yeast, a dimer of molecular weight 125,000 and its cognate tRNA (Mr = 24,160) were co-crystallized using ammonium sulfate as precipitant agent. The presence in the crystals of both components in the two-to-one stoichiometric ratio was demonstrated by electrophoresis, biological activity assays and crystallographic data. Crystals belong to the cubic space group I432 with cell parameter of 354 A and one complex particle per asymmetric unit. The solvent content of about 78% is favorable for a low resolution structural investigation. By exchanging H2O for D2O in mother liquors, advantage can be taken from contrast variation techniques with neutron radiations. Diffraction data to 20 A resolution were measured at five different contrasts, two of them being close to the theoretical matching point of RNA and protein in the presence of ammonium sulfate. The experimental extinction of the diffracted signal was observed to be close to 36% D2O, significantly different from the predicted value of 41%. The phenomenon can be explained by the existence of a large interface region between the two tRNAs and the enzyme. These parts of the molecules are hidden from the solvent and their protons are less easily exchangeable. Accessibility studies toward chemicals of tRNAAsp in solution and in the presence of synthetase are in agreement with such a model.

Primary structure of aspartyl-tRNA synthetase from baker's yeast: tryptic and CNBr peptides

The cristallizable aspartyl-tRNA synthetase from Baker's yeast is a dimer made up of identical subunits (Mr 60,000). We report here the results of tryptic digestion and cyanogen bromide cleavage which enabled us to align two lon stretches of sequence of 106 and 111 amino acids, respectively.

A comparative study of essential arginine residues in Gramicidin S synthetase 2 and isoleucyl tRNA synthetase

In gramicidin S synthetase 2 (GS 2) from Bacillus brevis, L-proline, L-valine, L-ornithine, and L-leucine activations to aminoacyl adenylates are progressively inhibited by phenylglyoxal. The inactivation of GS 2 obeys pseudo-first-order kinetics. ATP completely prevents inactivation of GS 2 by phenylglyoxal, whereas amino acids only partially prevent it. In the presence of ATP, four arginine residues per mol of GS 2 are protected from modification by phenylglyoxal as determined by amino acid analysis and the incorporation of [7-14C]phenylgloxal into the enzyme protein, indicating that a single arginine residue is necessary for each amino acid activation. In isoleucyl tRNA synthetase from Escherichia coli, phenylglyoxal inhibits activation of L-isoleucine to isoleucyl adenylate. ATP completely prevents inactivation, although isoleucine only partially prevents it. One arginine residue of isoleucyl tRNA synthetase is protected by ATP from modification by phenylglyoxal, suggesting that a single arginine residue is essential for isoleucine activation. These results support the involvement of arginine residues in ATP binding with GS 2 or isoleucyl tRNA synthetase, and thus indicate that arginine residues of amino acid activating enzymes are essential for the formation of aminoacyl adenylates in both nonribosomal and ribosomal peptide biosynthesis.