Internal thermodynamics of position 51 mutants and natural variants of tyrosyl-tRNA synthetase

Natural variation and evolution impose structural changes on an enzyme that can affect the energetics of catalysis. The energy profile of reaction could, in theory, be altered in three distinct ways: uniform binding changes, differential binding changes, and catalysis of elementary steps. Residue threonine-51 of tyrosyl-tRNA synthetase from Bacillus stearothermophilus is subject to natural variation, being replaced by alanine and proline in the enzymes from Bacillus caldotenax and Escherichia coli, respectively. The consequences of this variation on the energetics of formation of tyrosyl adenylate have been investigated by constructing free energy profiles for wild-type and mutant enzymes constructed by introducing these amino acids into the B. stearothermophilus enzyme. Mutation of Thr-51 to alanine, proline, and cysteine by site-directed mutagenesis improves the stabilization of the transition state in the formation of tyrosyl adenylate. Most marked is the mutation Thr-51----Pro-51 which stabilizes the transition state by 2.2 kcal/mol and accelerates the forward rate 20-fold to a level near that of the enzyme from E. coli. However, the improved transition-state binding is accompanied by an even greater stabilization of tyrosyl adenylate. This reduces the rate of pyrophosphorolysis of tyrosyl adenylate and/or weakens the binding of pyrophosphate in the reverse reaction, shifting the equilibrium between enzyme-bound reactants greatly in favor of the enzyme-intermediate complex. The more stable mutant enzyme-tyrosyl adenylate complexes have lower rates of aminoacylation, suggesting that mutations which stabilize the intermediate slow down the subsequent transfer of tyrosine from tyrosyl adenylate to tRNA.(ABSTRACT TRUNCATED AT 250 WORDS)

A model of synthetase/transfer RNA interaction as deduced by protein engineering

The recognition of transfer-RNA by their cognate aminoacyl-tRNA synthetases is the crucial step in the translation of the genetic code. In order to construct a structural model of the complex between the tyrosyl-tRNA synthetase (TyrTS) from Bacillus stearothermophilus and tRNATyr, 40 basic residues at the surface of the TyrTS dimer have been mutated by site-directed mutagenesis and heterodimers created in vitro by recombining subunits derived from different mutants. As reported here a cluster of basic residues (Arg 207-Lys 208) in the N-terminal domain of one TyrTS subunit interacts with the acceptor stem of tRNATyr and two separated clusters of basic residues (Arg 368-Arg 371; Arg 407-Arg 408-Lys 410-Lys 411) in the C-terminal domain of the other subunit interact with the anticodon arm. The TyrTS would thus clamp the tRNA in a fixed orientation. The precise alignment of the flexible... ACCA 3' end of the tRNA for attack on the tyrosyl adenylate is made by contacts closer to the catalytic groups of the enzyme, such as with Lys 151.

Reversible dissociation of dimeric tyrosyl-tRNA synthetase by mutagenesis at the subunit interface

Dimeric tyrosyl-tRNA synthetase from Bacillus stearothermophilus exhibits half-of-the-sites reactivity and negative cooperativity in binding of tyrosine. Protein engineering has been applied to the enzyme to determine whether it can be reversibly dissociated into monomers and if the monomers are active. The target for mutation is the residue Phe-164. The side chain of Phe-164 in one subunit interacts with its symmetry-related partner in the other. Mutation of Phe-164----Asp-164 gives a mutant [TyrTS(Asp-164)] that undergoes dissociation at high pH when the aspartate residues are ionized. The monomer is inactive and does not bind tyrosine. Dissociation is enhanced at low concentrations of enzyme by a mass action effect. Kinetic and binding measurements on TyrTS(Asp-164) with tyrosine and tyrosyl adenylate show that the monomer has very weak affinity for these ligands. Accordingly, dimerization is favored by high concentrations of tyrosine and ATP since the dimeric form has a high affinity for the ligands. The presence of tRNA does not encourage dimer formation, and so it must bind to the monomer. TyrTS(Asp-164) is fully active at pH 6 where dimerization is favored but has low activity at pH 7.8 where dissociation is favored. It should now prove possible to engineer heterodimers that may be used to investigate the subunit interactions further.

Fine structure-activity analysis of mutations at position 51 of tyrosyl-tRNA synthetase

Residue Thr-51 at the active site of tyrosyl-tRNA synthetase (Bacillus stearothermophilus) has been replaced with all the smaller amino acids by protein engineering to investigate direct and indirect effects of mutation on substrate binding and catalysis. The gamma-hydroxyl group of Thr-51 was thought to be 0.5 A too far from the ribose ring oxygen of ATP to form a hydrogen bond. Consistent with this, it is found that mutation of Thr-51----Cys-51, which should place the gamma-thiol group within its correct distance for hydrogen bonding, increases the affinity of the enzyme for ATP. Other mutations (Ser-51, Ala-51, and Gly-51) show the contributions to binding of the other atoms in the side chain of Thr-51. A family of enzymes has been produced, TyrTS(Thr-51) (wild type), TyrTS(Ala-51), TyrTS(Cys-51), and TyrTS(Pro-51), in which the value of kcat/KM for ATP in aminoacylation increases along the series. This is achieved by the value of KM decreasing significantly (2.5, 1.25, 0.29, and 0.019 mM, respectively) while there are smaller decreases in kcat (4.7, 4.0, 2.9, and 1.8 s-1, respectively). These variations cause each one of the enzymes to be more active than the others at particular concentrations of ATP. For example, at concentrations of ATP greater than 5.9 mM, TyrTS(Thr-51) is the most active, while TyrTS(Ala-51), TyrTS(Cys-51), and TyrTS(Pro-51) are the most active at 5.9-2.2, 2.2-0.42, and less than 0.42 mM ATP, respectively. Interestingly, position 51 shows variation in tyrosyl-tRNA synthetases isolated from different organisms.

Probing histidine-substrate interactions in tyrosyl-tRNA synthetase using asparagine and glutamine replacements

We have analyzed the interactions of a histidine residue with a substrate using site-directed mutagenesis. Previous studies on tyrosyl-tRNA synthetase from Bacillus stearothermophilus have shown that a histidine residue (His-48) makes an interaction with ATP, which is improved on mutating Thr-51----Pro-51. We find on replacing His-48 in wild-type enzyme with either asparagine or glutamine that Asn-48 is equally as good as His-48 but His-48----Gln-48 leads to a far lower activity. The side chain of an asparagine residue may be superimposed on that of a histidine so that the amide-NH2 group of asparagine occupies the same position as the pi-N of histidine, whereas the equivalent -NH2 group of glutamine may be superimposed upon the tau-N. This suggests that it is the pi-N of histidine that hydrogen bonds with ATP and that there is no significant electrostatic interaction between the histidine and ATP. Incorporating the Pro-51 mutation into each of the Asn-48 and Gln-48 mutants gives an improvement in the affinity of the enzyme for ATP, but this improvement is less than that seen with the wild-type enzyme.

Engineering of tyrosyl tRNA synthetase

The gene encoding the enzyme tyrosyl tRNA synthetase from Bacillus stearothermophilus has been systematically altered using synthetic oligonucleotides as mutagens. The construction of mutations has been facilitated by using strains of bacteria defective in mismatch repair and also by utilising a genetic marker in the M13 strain (such as an amber mutation, or an EcoK or EcoB site) which allows selection for the progeny of M13 replication derived from the minus (mutagenized) strand. Several mutations have been constructed in the ATP binding site to elucidate the roles of individual residues in catalysis and substrate binding and it has even been possible to construct mutants which have improved affinity for ATP. Mutations in various surface lysine and arginine residues have allowed us to identify potential contacts with the tRNA, and indicate that a cluster of basic residues close to the C-terminus of the enzyme probably makes important interactions with the tRNA.

The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus)

In a previous study, a mutant of tyrosyl-tRNA synthetase in which a threonine residue (Thr51) was converted to proline dramatically improved the affinity of the enzyme for its ATP substrate. How does Pro51 improve the enzyme's affinity for ATP? A priori, Pro51 might interact directly with the ATP, or it might distort the polypeptide backbone and thereby force new or improved contacts elsewhere from the enzyme to ATP. By making mutants of the Pro51 enzyme at two residues that make hydrogen bonds to the ATP substrate, we show that Pro51 greatly improves the strength of one of these contacts. Thus the propagation of a structural change in an enzyme induced by mutation may be detected by the introduction of further mutations.

A large increase in enzyme-substrate affinity by protein engineering

A single point mutation has been engineered in the tyrosyl-tRNA synthetase that improves its affinity (KM) for its substrate ATP by a factor of 100. In the crystal structure of the tyrosyl tRNA synthetase (of Bacillus stearothermophilus), the side-chain hydroxyl of Thr 51 appears to make a weak hydrogen bond with the AMP moiety of the substrate intermediate, tyrosyl adenylate. In the absence of substrate, however, the hydroxyl group should make a strong hydrogen bond with water which would favour dissociation of the enzyme-substrate complex. We have used oligodeoxynucleotide-directed mutagenesis to construct two point mutants at this site: one to remove the hydroxyl group (Thr 51 leads to Ala 51) and the other, in addition, to distort the local polypeptide backbone (Thr 51 leads to Pro 51). We report here that both mutants have increased activity (kcat/KM for ATP) but one mutant (Pro 51) shows a massive 25-fold increase due mainly to a lowered KM for ATP. This demonstrates dramatically the potential of in vitro mutagenesis for improving the affinity of an enzyme for its substrate.

Deletion mutagenesis using an ‘M13 splint’: the N-terminal structural domain of tyrosyl-tRNA synthetase (B. stearothermophilus) catalyses the formation of tyrosyl adenylate

The X-ray crystallographic structure of tyrosyl-tRNA synthetase (TyrTS) comprises only the N-terminal 320 amino acids of the molecule as the C-terminal 99 amino acids are poorly ordered in the crystal. A new technique, employing a single-stranded M13 splint, has been used to direct a deletion in the cloned gene of TyrTS so as to remove the disordered C-terminal region. We find that the truncated enzyme catalyses the formation of tyrosyl adenylate with unchanged Kcat and Km values and the crystallographic model must therefore include all the binding and catalytic residues involved in tyrosine activation. However, the truncated enzyme no longer binds tRNATyr or transfers tyrosine to tRNATyr. This indicates that the structural division of TyrTS is equally a functional one: the N-terminal structural domain catalyses tyrosine activation while the disordered C-terminal domain carries major determinants in tRNA binding.

Site-directed mutagenesis as a probe of enzyme structure and catalysis: tyrosyl-tRNA synthetase cysteine-35 to glycine-35 mutation

Oligodeoxynucleotide-directed mutagenesis has been used on the gene of tyrosyl-tRNA synthetase from Bacillus stearothermophilus to produce mutant enzymes altered at the adenosine 5'-triphosphate (ATP) binding site. Deliberate attempts were made to alter rather than destroy enzymic activity so that kinetic measurements may be made to identify the subtle roles of the enzyme-substrate interactions in catalysis. Cys-35, the -SH group of which is involved in binding the 3'-OH of the ribose ring of ATP, has been mutated to a serine residue [Winter, G., Fersht, A. R., Wilkinson, A. J., Zoller, M., & Smith, M. (1982) Nature (London) 299, 756-758] or glycine residue. The mutant enzymes are less active than the wild type, and the reduction in activity can be attributed to a decrease in the value of kcat and an increase in KM. Thus, the interaction energy of the side chain of Cys-35 with the substrate is not fully realized in the enzyme-substrate complex but is used preferentially to stabilize the transition state. Relative to its absence in the Gly-35 mutant, the side chain of Cys-35 is calculated to stabilize the transition state for pyrophosphate exchange by 1.2 kcal/mol and the transition state for aminoacylation by 1.0 kcal/mol.

The tyrosyl-tRNA synthetase from Escherichia coli. Complete nucleotide sequence of the structural gene

The structural component of the tyrS gene of Escherichia coli, comprising 1269 base pairs, has been fully sequenced by the combined M13/dideoxychain termination approach. The gene has a codon usage pattern which is typical of highly expressed proteins and similar to other Escherichia coli aminoacyl-tRNA synthetase genes. Peptide purification and sequencing has been used to locate the N-terminus and to provide confirmation of 95% of the translated protein sequence. This latter yields on Mr of 47,403 for the Escherichia coli tyrosyl-tRNA synthetase, and reveals considerable homology with the primary structure of the analogous enzyme isolated from Bacillus staerothermophilus.

Cloning and amplified expression of the tyrosyl-tRNA synthetase genes of Bacillus stearothermophilus and Escherichia coli

Two fragments of DNA which carry the genes coding for the tyrosyl-tRNA synthetases of Escherichia coli and Bacillus stearothermophilus have been cloned into the plasmid pBR322 and were selected by complementation of an E. coli temperature-sensitive mutant. Transformation of this strain with either of the recombinant plasmids results in a 100-fold increase in tyrosyl-tRNA synthetase activity measured in vitro and the protein products co-migrate with the corresponding purified enzymes on polyacrylamide gels.

Improved mapping of the tyrS locus in Escherichia coli

A tyrosyl-tRNA synthetase mutant of Escherichia coli was isolated and the tyrS gene assigned a map position between man and pdxH at 36.0 min on the chromosome. The tyrS mutant grew badly on broth as did previously described tyrS mutants. This sensitivity to broth was suppressed by tyrR mutations. F-prime factors were found to complement the tyrS mutation.