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Aminoacyl-tRNA synthetases catalyse a key reaction in protein biosynthesis. They match the 20 amino acids to the genetic code by specifically attaching them to their adaptors, transfer ribonucleic acid (tRNA) molecules. The reaction proceeds in two steps: the amino acid is first activated by adenosine triphosphate (ATP) to form aminoacyl adenylate, and then the aminoacyl group is transferred to the terminal ribose of tRNA. This family of enzymes is divided into two classes, based on the similarities in primary structure and architecture of the active site domains; the two architectures are characterized by two modes of binding of ATP, the intermediate aminoacyl adenylate and the acceptor end of tRNA, which result in two regioselectivities of amino acid attachment to the terminal ribose of the tRNA. Aminoacyl-tRNA synthetases are modular enzymes; to the central active site module are attached various domains with diverse functions such as tRNA-binding and amino acid editing. The primary subject of this article are structural and functional aspects of these enzymes. Key Concepts Aminoacylation is a key reaction in protein biosynthesis, as it matches the standard 20 amino acids to the genetic code. Aminoacylation is generally catalysed by aminoacyl-tRNA synthetases, a family of 20 enzymes, one for each standard amino acid and a set of corresponding (cognate isoacceptor) tRNAs. Aminoacylation proceeds in two steps, where the amino acid is first activated by ATP to form aminoacyl adenylate, a mixed anhydride, and then transferred to form an ester bond with the terminal ribose of tRNA. Aminoacyl-tRNA synthetases are divided into two classes, based on the similarities in primary structure (sequence) and architecture of their active site domains. Aminoacyl-tRNA synthetases are modular enzymes; to the central active site module are attached various domains with diverse functions such as tRNA-binding and amino acid editing. Aminoacyl-tRNA synthetases are highly specific enzymes, attaching the correct amino acids to the corresponding tRNAs with high fidelity. Aminoacyl-tRNA synthetases of the two classes generally bind the acceptor arm of tRNA in two ways that constitute mirror images of each other, resulting in two different regioselectivities of amino acid attachment to the tRNA. Keywords: structure and function; aminoacylation; translation; protein synthesis; transfer ribonucleic acid (tRNA)

The crystal structures of histidyl- (HisRS) and threonyl-tRNA synthetase (ThrRS) from E. coli and glycyl-tRNA synthetase (GlyRS) from T. thermophilus, all homodimeric class IIa enzymes, were determined in enzyme-substrate and enzyme-product states corresponding to the two steps of aminoacylation. HisRS was complexed with the histidine analog histidinol plus ATP and with histidyl-adenylate, while GlyRS was complexed with ATP and with glycyl-adenylate; these complexes represent the enzyme-substrate and enzyme-product states of the first step of aminoacylation, i.e. the amino acid activation. In both enzymes the ligands occupy the substrate-binding pocket of the N-terminal active site domain, which contains the classical class II aminoacyl-tRNA synthetase fold. HisRS interacts in the same fashion with the histidine, adenosine and α-phosphate moieties of the substrates and intermediate, and GlyRS interacts in the same way with the adenosine and α-phosphate moieties in both states. In addition to the amino acid recognition, there is one key mechanistic difference between the two enzymes: HisRS uses an arginine whereas GlyRS employs a magnesium ion to catalyze the activation of the amino acid. ThrRS was complexed with its cognate tRNA and ATP, which represents the enzyme-substrate state of the second step of aminoacylation, i.e. the transfer of the amino acid to the 3'-terminal ribose of the tRNA. All three enzymes utilize class II conserved residues to interact with the adenosine-phosphate. ThrRS binds tRNA(Thr) so that the acceptor stem enters the active site pocket above the adenylate, with the 3'-terminal OH positioned to pick up the amino acid, and the anticodon loop interacts with the C-terminal domain whose fold is shared by all three enzymes. We can thus extend the principles of tRNA binding to the other two enzymes.

The crystal structures of glycyl-tRNA synthetase (GlyRS) from Thermus thermophilus, a homodimeric class II enzyme, were determined in the enzyme-substrate and enzyme-product states corresponding to the first step of aminoacylation. GlyRS was cocrystallized with glycine and ATP, which were transformed by the enzyme into glycyl-adenylate and thus gave the enzyme-product complex. To trap the enzyme-substrate complex, the enzyme was combined with the glycine analog ethanolamine and ATP. The ligands are bound in fixed orientations in the substrate-binding pocket of the N-terminal active site domain, which contains the classical class II aminoacyl-tRNA synthetase (aaRS) fold. Since glycine does not possess a side-chain, much of the specificity of the enzyme is directed toward excluding any additional atoms beyond the alpha-carbon atom. Several carboxylate residues of GlyRS line the glycine binding pocket; two of them interact directly with the alpha-ammonium group. In addition, the enzyme utilizes the acidic character of the pro-L alpha-hydrogen atom by contacting it via a glutamate carboxylic oxygen atom. A guanidino eta-nitrogen atom of the class II aaRS-conserved motif 2 arginine interacts with the substrate carbonyl oxygen atom. These features serve to attract the small amino acid substrate into the active site and to position it in the correct orientation. GlyRS uses class II-conserved residues to interact with the ATP and the adenosine-phosphate moiety of glycyl-adenylate. On the basis of this similarity, we propose that GlyRS utilizes the same general mechanism as that employed by other class II aminoacyl-tRNA synthetases.

Histidyl-tRNA synthetase (HisRS) differs from other class II aminoacyl-tRNA synthetases (aaRS) in that it harbors an arginine at a position where the others bind a catalytic Mg2+ ion. In computer experiments, four mutants of HisRS from Escherichia coli were engineered by removing the arginine and introducing a Mg2+ ion and residues from seryl-tRNA synthetase (SerRS) that are involved in Mg2+ binding. The mutants recreate an active site carboxylate pair conserved in other class II aaRSs, in two possible orders: Glu-Asp or Asp-Glu, replacing Glu-Thr in native HisRS. The mutants were simulated by molecular dynamics in complex with histidyl-adenylate. As controls, the native HisRS was simulated in complexes with histidine, histidyl-adenylate, and histidinol. The native structures sampled were in good agreement with experimental structures and biochemical data. The two mutants with the Glu-Asp sequence showed significant differences in active site structure and Mg2+ coordination from SerRS. The others were more similar to SerRS, and one of them was analyzed further through simulations in complex with histidine, and His+ATP. The latter complex sampled two Mg2+ positions, depending on the conformation of a loop anchoring the second carboxylate. The lowest energy conformation led to an active site geometry very similar to SerRS, with the principal Mg2+ bridging the α- and β-phosphates, the first carboxylate (Asp) coordinating the ion through a water molecule, and the second (Glu) coordinating it directly. This mutant is expected to be catalytically active and suggests a basis for the previously unexplained conservation of the active site Asp-Glu pair in class II aaRSs other than HisRS. Proteins 32:362–380, 1998. © 1998 Wiley-Liss, Inc.

Three previously described mutant Escherichia coli glutaminyl-tRNA synthetase (GlnRS) proteins that incorrectly aminoacylate the amber suppressor derived from tRNATyr (supF) with glutamine were cocrystallized with wild-type tRNAGln and their structures determined. In two of the mutant enzymes studied, Asp235, which contacts base pair G3-C70 in the acceptor stem, has been changed to asparagine in GlnRS7 and to glycine in GlnRS10. These mutations result in changed interactions between Asn235 of GlnRS7 and G3-C70 of the tRNA and an altered water structure between Gly235 of GlnRS10 and base pair G3-C70. These structures suggest how the mutant enzymes can show only small changes in their ability to aminoacylate wild-type cognate tRNA on the one hand and yet show a lack of discrimination against a noncognate U3-A70 base pair on the other. In contrast, the change of Ile129 to Thr in GlnRS15 causes virtually no change in the structure of the complex, and the explanation for its ability to misacylate supF is unclear.

The crystal structure at 2.6 A of the histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate has been determined. The enzyme is a homodimer with a molecular weight of 94 kDa and belongs to the class II of aminoacyl-tRNA synthetases (aaRS). The asymmetric unit is composed of two homodimers. Each monomer consists of two domains. The N-terminal catalytic core domain contains a six-stranded antiparallel beta-sheet sitting on two alpha-helices, which can be superposed with the catalytic domains of yeast AspRS, and GlyRS and SerRS from Thermus thermophilus with a root-mean-square difference on the C alpha atoms of 1.7-1.9 A. The active sites of all four monomers are occupied by histidyl-adenylate, which apparently forms during crystallization. The 100 residue C-terminal alpha/beta domain resembles half of a beta-barrel, and provides an independent domain oriented to contact the anticodon stem and part of the anticodon loop of tRNA(His). The modular domain organization of histidyl-tRNA synthetase reiterates a repeated theme in aaRS, and its structure should provide insight into the ability of certain aaRS to aminoacylate minihelices and other non-tRNA molecules.

tRNA(2Gln) made in vitro by transcription with T7 RNA polymerase does not contain the pseudouridines at positions 38, 39, and 55, the 4-thiouridine at position 8, or any of the methylated bases found in the tRNA(2Gln) made in vivo. Cocrystals of unmodified tRNA(2Gln) complexed with glutaminyl-tRNA synthetase from Escherichia coli are isomorphous with those of the complex with modified tRNA(2Gln). A difference electron density map between the complexes with modified and unmodified tRNAs calculated at 2.5-A resolution shows no differences in the protein or tRNA structures, except for some very small shifts in atoms contacting the thiol at the 4 position of uridine 8 that are required to accommodate the smaller oxygen in the unmodified tRNA. Perhaps the most functionally significant change in the unmodified tRNA is the absence of the specifically bound water molecules that are observed to cross-link the N5 of the pseudo-uridines to their 5' phosphate. This suggests a possible role for pseudouridinylation in stabilization of the tRNA through water-mediated linking of these modified bases to the backbone, which is consistent with the lower thermal stability of the unmodified tRNA. An identical water-bridging structure is possible at four of the five other psuedo-uridines in known tRNA structures.

The molecular replacement method has been applied to the heavy-atom problem in a case for which a heavy-atom model existed for one crystal form, and both native and derivative data were available for another crystal form of the same molecule; the absolute values of difference amplitudes for the second form were used in the calculation. The key requirement for obtaining a solution is that the contents of the asymmetric unit are the same and the same heavy-atom compound is used in both cases.

Efficient crystal handling at cryotemperatures requires flexible tools. A standard goniometer head has been modified such that it retains eucentricity and allows any position between the coaxial and vertical orientations relative to a horizontal spindle axis, corresponding to the positions of data collection and crystal transfer, respectively. This is accomplished by a large arc on which slides the upper portion of the goniometer head containing all three translational and one rotational degree of freedom. The arc can be removed when the head is coaxial with the spindle. The head is designed to accept commercially available cryotools. In addition, a heat-shield assembly can be installed to prevent the formation of ice.

Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) variants with the K65R or L74V substitution display resistance to several nucleoside analogs. An in vitro dNTP exclusion assay revealed an increased fidelity for K65R RT compared with wild-type RT, but little change for L74V RT. When the forward mutation rates were measured via a gap-filling assay, the K65R variant displayed an 8-fold decrease in the overall mutation rate (1.0 x 10(-3) versus 8.6 x 10(-3) for wild-type HIV-1 RT), whereas the rate for the L74V variant was closer to that for wild-type RT (5.0 x 10(-3)). The increase in overall fidelity observed for K65R RT is the largest reported for any drug-resistant HIV-1 RT variant. Nucleotide sequence analysis of lacZalpha mutants generated by variant RTs indicated that K65R RT displays uniform reduction in most types of errors, whereas L74V RT does not. Modeling the substitutions into the x-ray structure of the ternary complex revealed that the major influence of Leu(74) in stabilizing the templating base is unaffected by Val substitution, whereas the K65R substitution appears to increase the stringency of dNTP binding. It is speculated that the increased fidelity of K65R RT is due to an altered interaction with the dNTP substrate.

The crystal structure of an enzyme–substrate complex with histidyl-tRNA synthetase from Escherichia coli , ATP, and the amino acid analog histidinol is described and compared with the previously obtained enzyme–product complex with histidyl-adenylate. An active site arginine, Arg-259, unique to all histidyl-tRNA synthetases, plays the role of the catalytic magnesium ion seen in seryl-tRNA synthetase. When Arg-259 is substituted with histidine, the apparent second order rate constant ( k cat / K m ) for the pyrophosphate exchange reaction and the aminoacylation reaction decreases 1,000-fold and 500-fold, respectively. Crystals soaked with MnCl 2 reveal the existence of two metal binding sites between β- and γ-phosphates; these sites appear to stabilize the conformation of the pyrophosphate. The use of both conserved metal ions and arginine in phosphoryl transfer provides evidence of significant early functional divergence of class II aminoacyl-tRNA synthetases.

Aminoacyl-tRNA synthetases (aaRS) bind their substrates-ATP, amino acids and tRNA- and stabilize putative transition states in the aminoacylation reaction. Here, we discuss the common and distinguishing structural and functional themes of the 20 known aaRS, which can be divided into two main classes (I and II) and into further subgroups on this basis.

Five distinct acyl-CoA dehydrogenases are currently known. These are short, medium, long and 2-methyl-branched-chain acyl-CoA dehydrogenases, and isovaleryl-CoA dehydrogenase. We tested these five acyl-CoA dehydrogenases for their ability to dehydrogenase valproyl-CoA using pure enzyme preparations isolated from rat liver mitochondria. The activities of the pure human short-chain, medium-chain, and isovaleryl enzymes purified from post-mortem livers, and a long-chain acyl-CoA dehydrogenase preparation partialy purified from placental mitochondria, were also tested. Valproyl-CoA was dehydrogenated at a significant rate (0.167 μmol/min per mg protein) only by rat 2-methyl-branched-chain acyl-CoA dehydrogenase. Human 2-methyl-branched-chain acyl-CoA dehydrogenase has not been purified; therefore, it could not be tested. Since four other human acyl-CoA dehydrogenases did not dehydrogenate isobutyryl-CoA, 2-methylbutyryl-CoA (obligatory intermediates from valine and isoleucine, respectively) nor valproyl-CoA, it is reasonable to assume that valproyl-CoA is dehydrogenated by 2-methyl-branch-chain acyl-CoA dehydrogenase in man as well. We identified 2-propyl-2-pentenoyl-CoA as the reaction product from valproyl-CoA by mass spectral analysis of the acyl moiety. Valproyl-CoA, at 0.3 mM, moderately inhibited human acyl-CoA dehydrogenases with the exception of the long-chain enzyme. 5 mM free valproic acid inhibited the activities of various acyl-CoA dehydrogenases only very weakly.

Publisher Summary This chapter describes a methodology for isolation of the RNase P holoenzyme from E. coli, preparation of the individual RNA and protein subunits, reconstitution of the holoenzyme from purified subunits, and detection of the enzymatic activity of RNase. The preparation of RNase P obtained by chromatography on Sepharose 4B is resuspended in buffer C and dialyzed against the same buffer. To improve the purification of C5 protein preparative polyacrylamide gel electrophoresis has been used with some success. This procedure involves electroelution of C5 protein from the gels followed by precipitation with acetone in order to remove traces of sodium dodecyl sulfate (SDS) from the preparation. The cell pellet is placed in a prechilled mortar, on ice, and mixed with twice its weight of cold alumina. The cells are ground by hand with a chilled pestle. When a homogeneous paste is obtained, 10 ml of buffer A is added and mixed with the paste. The supernatant is centrifuged again for 30 min at 15,500 rpm (30,000 g). About 90% of the overproduced C5 protein is in the supernatant (S30).

VP is an eight carbon branched chain fatty acid. It is widely used as an anti-convulsant. Serious toxic side effects have occasionally been observed. VP is considered to be mainly metabolized via β-oxidation and glucuronide formation, and has been shown to inhibit fatty acid oxidation. However, the enzymatic mechanisms are currently unknown. We studied the VP-CoA oxidation by acyl-CoA dehydrogenases (ADs) and its inhibitory action on these enzymes using purified enzyme preparations. ADs catalyze the first reaction of the β-oxidation. Five of them are known. They are short (SCAD), medium (MCAD), long chain acyl-CoA dehydrogenases (LCAD), isovaleryl-CoA dehydrogenase (IVD) and 2-meBCAD. We purified all five of them to homogeneity from rat liver. We also purified SCAD, MCAD and IVD to homogeneity from human liver. Human LCAD was partially purified from placenta mitochondria. AD activities were assayed spectrophotometrically using phenazine methosulfate and dichloroindophenol (DCIP) as electron acceptors. Only 2-meBCAD dehydrogenated VP-CoA. The specific activity was 167 nmol of DCIP reduced/min/mg protein. This value was 7.6 percent of that for S-2-methylbutyryl-CoA, the best substrate for this enzyme. 2-Propyl-2-pentenoyl-CoA was identified as the reaction product by using GC/MS. No other ADs dehydrogenated VP-CoA to any significant degree. Inhibitory effects were tested using human Ads. 0.1 mM VP-CoA slightly inhibited MCAD alone. At 0.3 mM, it moderately inhibited SCAD, MCAD and IVD: the inhibition ranged from 18% for IVD to 25% for MCAD.