Structural consequences of a one atom mutation on aspartate transcarbamylase from E. coli

Tyr-240 of the catalytic chain of aspartate transcarbamylase from E. coli has been substituted by Phe using site-directed mutagenesis. The regulatory mechanisms of the mutant enzyme have been shown to be slightly less effective than the wild-type enzyme. A study of the structural consequences of the mutation using solution X-ray scattering and computer simulations is reported here. No significant change from the wild-type enzyme is detectable in the quaternary structure. Simulations suggest that the only effect of the mutation is an increased mobility of the mutated side chain.

Kinetic consequences of site-specific mutation of Glu-239----Gln in E. coli aspartate transcarbamylase: comparison with catalytic subunits and Phe-240 mutant enzyme

The kinetic characteristics of E. coli aspartate transcarbamylase, altered by site-specific mutagenesis of Glu-239----Gln, have been determined by equilibrium isotope-exchange kinetics and compared to the wild-type system. In wild-type enzyme, residue Glu-239 helps to stabilize the T-state structure by multiple bonding interactions with Tyr-165 and Lys-164 across the c1-c4 subunit interface; upon conversion to the R-state, these bonds are re-formed within c-chains. Catalysis of both the [14C]Asp in equilibrium C-Asp and [32P]ATP in equilibrium Pi exchanges by mutant enzyme occurs at rates comparable to those for wild-type enzyme. Saturation with different reactant/product pairs produced kinetic patterns consistent with strongly preferred order binding of carbamyl-P prior to Asp and carbamyl-Asp release before Pi. The kinetics for the Gln-239 mutant enzyme resemble those observed for catalytic subunits (c3), namely a R-state enzyme (Hill coefficient nH = 1.0) and Km (Asp) approximately equal to 6 mM. The Glu-239----Gln mutation appears to destablize both the T- and R-states, whereas the Tyr-240----Phe mutation destablizes only the T-state.

Structure of a single amino acid mutant of aspartate carbamoyltransferase at 2.5-A resolution: implications for the cooperative mechanism

One of the many interactions important for stabilizing the T state of aspartate carbamoyltransferase occurs between residues Tyr240 and Asp271 within one catalytic chain. The functional importance of this polar interaction was documented by site-directed mutagenesis in which the tyrosine was replaced by a phenylalanine [Middleton, S. A., & Kantrowitz, E. R. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 5866-5870]. In the Tyr240----Phe mutant, the aspartate concentration required to achieve half-maximum velocity is reduced to 4.7 from 11.9 mM for the native enzyme. Here, we report an X-ray crystallographic study of the Tyr240----Phe enzyme at 2.5-A resolution. While employing crystallization conditions identical with those used to grow cytidine triphosphate ligated T-state crystals of the native enzyme, we obtain crystals of the mutant enzyme that are isomorphous to those of the native enzyme. Refinement of the mutant structure to an R factor of 0.219 (only eight solvent molecules included) and subsequent comparison to the native T-state structure indicate that the quaternary, tertiary, and secondary structures of the mutant are similar to those for the native T-state enzyme. However, the conformation of Phe240 in one of the two crystallographically independent catalytic chains contained in the asymmetric unit is significantly different from the conformation of Tyr240 in the native T-state enzyme and similar to the conformation of Tyr240 as determined from the R-state structure [Ke, H.-M., Lipscomb, W. N., Cho, Y. J., & Honzatko, R. B. (1988) J. Mol. Biol. (in press)], thereby indicating that the mutant has made a conformational change toward the R state, localized at the site of the mutation in one of the catalytic chains.

A loop involving catalytic chain residues 230-245 is essential for the stabilization of both allosteric forms of Escherichia coli aspartate transcarbamylase

The allosteric transition of Escherichia coli aspartate transcarbamylase involves significant alterations in structure at both the quaternary and tertiary levels. On the tertiary level, the 240s loop (residues 230-245 of the catalytic chain) repositions, influencing the conformation of Arg-229, a residue near the aspartate binding site. In the T state, Arg-229 is bent out of the active site and may be stabilized in this position by an interaction with Glu-272. In the R state, the conformation of Arg-229 changes, allowing it to interact with the beta-carboxylate of aspartate, and is stabilized in this position by a specific interaction with Glu-233. In order to ascertain the function of Arg-229, Glu-233, and Glu-272 in the catalytic and cooperative interactions of the enzyme, three mutant enzymes were created by site-specific mutagenesis. Arg-229 was replaced by Ala, while both Glu-233 and Glu-272 were replaced by Ser. The Arg-229----Ala and Glu-233----Ser enzymes exhibit 10,000-fold and 80-fold decreases in maximal activity, respectively, and they both exhibit a 2-fold increase in the aspartate concentration at half the maximal observed velocity, [S]0.5. The Arg-229----Ala enzyme still exhibits substantial homotropic cooperativity, but all cooperativity is lost in the Glu-233----Ser enzyme. The Glu-233----Ser enzyme also shows a 4-fold decrease in the carbamyl phosphate [S]0.5, while the Arg-229----Ala enzyme shows no change in the carbamyl phosphate [S]0.5 compared to the wild-type enzyme. The Glu-272 to Ser mutation results in a slight reduction in maximal activity, an increase in [S]0.5 for both aspartate and carbamyl phosphate, and reduced cooperativity. Analysis of the isolated catalytic subunits from these three mutant enzymes reveals that in each case the changes in the kinetic properties of the isolated catalytic subunit are similar to the changes caused by the mutation in the holoenzyme. PALA was able to activate the Glu-233----Ser enzyme, at low aspartate concentrations, even though the mutant holoenzyme did not exhibit any cooperativity, indicating that cooperative interactions still exist between the active sites in this enzyme. It is proposed that Glu-233 of the 240s loop helps create the high-activity-high-affinity R state by positioning the side chain of Arg-229 for aspartate binding while Glu-272 helps stabilize the low-activity-low-affinity T state by positioning the side chain of Arg-229 so that it cannot interact with aspartate.(ABSTRACT TRUNCATED AT 400 WORDS)

Function of arginine-234 and aspartic acid-271 in domain closure, cooperativity, and catalysis in Escherichia coli aspartate transcarbamylase

Two mutant versions of Escherichia coli aspartate transcarbamylase were created by site-specific mutagenesis. Arg-234 of the 240s loop was replaced by serine in order to help deduce the function of the interactions that normally occur between Arg-234 and both Glu-50 and Gln-231 in the R state of the enzyme. The other mutation involved the replacement of Asp-271 by asparagine to further test the functional importance of the Tyr-240-Asp-271 link that has previously been proposed to stabilize the T state of the enzyme [Middleton, S. A., & Kantrowitz, E. R. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 5866-5870]. The Arg-234----Ser holoenzyme exhibits no cooperativity, a 24-fold reduction in maximal velocity, normal affinity for carbamyl phosphate, and substantially reduced affinity for aspartate and N-(phosphonoacetyl)-L-aspartate (PALA). Unlike the wild-type enzyme, the heterotropic effectors ATP and CTP are able to influence the activity of the Arg-234----Ser enzyme at saturating aspartate concentrations. The Arg-234----Ser catalytic subunit exhibits a 33-fold reduction in maximal activity, an aspartate Km of 261 mM, compared to 5.7 mM for the wild-type catalytic subunit, and only a small alteration in the Km for carbamyl phosphate. Together these results provide additional evidence that the interdomain bridging interactions between Glu-50 of the carbamyl phosphate domain and both Arg-167 and Arg-234 of the aspartate domain are necessary for the stabilization of the high-activity-high-affinity configuration of the active site of the enzyme. Furthermore, without the interdomain bridging interactions, the holoenzyme no longer exhibits homotropic cooperativity.(ABSTRACT TRUNCATED AT 250 WORDS)

Function of arginine-166 in the active site of Escherichia coli alkaline phosphatase

The function of arginine residue 166 in the active site of Escherichia coli alkaline phosphatase was investigated by site-directed mutagenesis. Two mutant versions of alkaline phosphatase, with either serine or alanine in the place of arginine at position 166, were generated by using a specially constructed M13 phage carrying the wild-type phoA gene. The mutant enzymes with serine and alanine at position 166 have very similar kinetic properties. Under conditions of no external phosphate acceptor, the kcat for the mutant enzymes decreases by approximately 30-fold while the Km increases by less than 2-fold. When kinetic measurements are carried out in the presence of a phosphate acceptor, 1.0 M Tris, the kcat for the mutant enzymes is reduced by less than 3-fold, while the Km increases by more than 50-fold. For both mutant enzymes, in either the absence or the presence of a phosphate acceptor, the catalytic efficiency as measured by the kcat/Km ratio decreases by approximately 50-fold as compared to the wild type. Measurements of the Ki for inorganic phosphate show an increase of approximately 50-fold for both mutants. Phenylglyoxal, which inactivates the wild-type enzyme, does not inactivate the Arg-166----Ala enzyme. This result indicates that Arg-166 is the same arginine residue that when chemically modified causes loss of activity [Daemen, F.J.M., & Riordan, J.F. (1974) Biochemistry 13, 2865-2871]. The data reported here suggest that although Arg-166 is important for activity is not essential. The analysis of the kinetic data also suggests that the loss of arginine-166 at the active site of alkaline phosphatase has two different effects on the enzyme. First, the binding of the substrate, and phosphate as a competitive inhibitor, is reduced; second, the rate of hydrolysis of the covalent phosphoenzyme may be diminished.

Propagation of allosteric changes through the catalytic-regulatory interface of Escherichia coli aspartate transcarbamylase

Each of two previously isolated strains of Escherichia coli containing a single nonsense codon within the pyrB gene was suppressed with four different nonsense suppressors. The kinetic analysis using crude extracts of these nonsense-suppressed strains indicated that the mutant aspartate transcarbamylases had altered cooperativity and affinity for aspartate as judged by the substrate concentration at half of the maximal velocity. Both pyrB genes were cloned and then sequenced. In both cases, a single base change was identified which converted a glutamine GAC codon into a TAC nonsense codon. Both mutations occurred in the catalytic chain of aspartate transcarbamylase and were identified at positions 108 and 246. The glutamine at position 108 in the wild-type structure is located at the interface between the catalytic and regulatory chains and is involved in a number of interactions with backbone and side chains of the regulatory chain. The glutamine at position 246 in the wild-type structure is located in the 240s loop of the enzyme. Two additional mutant versions of aspartate transcarbamylase were created by site-directed mutagenesis to further investigate the 108-position in the structure, a glutamine to tyrosine substitution at position 108 of the catalytic chain, and an asparagine to glycine change at position 113 of the regulatory chain, a residue which interacts directly with glutamine-108 in the wild-type structure. Both mutant enzymes have reduced affinity for aspartate. However, the Tyr-108 mutant enzyme exhibits a reduced Hill coefficient while the Gly-113 enzyme exhibits an increased Hill coefficient. The response to the allosteric effectors ATP and CTP is also changed for both the mutant enzymes.(ABSTRACT TRUNCATED AT 250 WORDS)

Relationship between domain closure and binding, catalysis, and regulation in Escherichia coli aspartate transcarbamylase

Previous evidence, from both crystallographic and biochemical studies, has indicated that profound tertiary and quaternary changes in the structure of Escherichia coli aspartate transcarbamylase occur upon the binding of the bisubstrate analogue N-(phosphonoacetyl)-L-aspartate (PALA). In particular, within a single catalytic polypeptide chain, the aspartate binding domain relocates closer to the carbamyl phosphate binding domain, thereby resulting in a major reorganization of the interface between the two domains. Among the new interactions, salt bridges between Glu-50 and both Arg-167 and Arg-234 are formed. In the present study, site-directed mutagenesis is used to replace Glu-50 by glutamine in the catalytic chain. The Michaelis constant for aspartate of the mutant catalytic subunit is about 10-fold higher and the turnover number 10-fold lower than their respective counterparts in the wild-type catalytic subunit, whereas the dissociation constant for carbamyl phosphate is almost unchanged. For the holoenzyme, this substitution results in an 8-fold decrease in the specific activity, a 20-fold increase in the aspartate concentration that gives half of the maximal velocity, and a loss of cooperativity for both substrates. However, the mutant enzyme is not "frozen" in a low-affinity-low-activity conformation since PALA stimulates the activity severalfold and induces an increase in the sulfhydryl reactivity analogous to that of the wild-type enzyme. Together these results indicate that the stabilization of the aspartate binding domain near the carbamyl phosphate binding domain, through specific interdomain bridging interactions, is necessary for the high-affinity-high-activity configuration of the active site.(ABSTRACT TRUNCATED AT 250 WORDS)

Importance of the loop at residues 230-245 in the allosteric interactions of Escherichia coli aspartate carbamoyltransferase

Site-directed mutagenesis has been used to replace tyrosine-240 with phenylalanine in each of the catalytic chains of aspartate carbamoyltransferase. Tyrosine-240 is part of a loop in the structure of the enzyme, between residues 230 and 245, which undergoes a substantial conformation change as the enzyme becomes ligated [Krause, K. L., Volz, K. W. & Lipscomb, W. N. (1985) Proc. Natl. Acad. Sci. USA 82, 1643-1647]. The mutant enzyme with phenylalanine at position 240 has substantially reduced homotropic interactions and an increased affinity for the substrate aspartate but displays no alteration in maximal observed specific activity. The Hill coefficient decreases from 2.4 for the wild-type enzyme to 1.8 for the mutant, and the aspartate concentration at half the maximal observed velocity decreases from 11.9 mM to 4.7 mM at pH 8.3. Heterotropic interactions of the mutant enzyme are altered to a lesser extent. The catalytic subunit derived from the mutant enzyme exhibits kinetics identical to that of the wild-type catalytic subunit. Reactivity of the mutant enzyme with p-hydroxymercuribenzoate suggests that the unligated enzyme exists in an altered conformation. The properties of the mutant enzyme are explained in terms of the structure of the wild-type enzyme, and a model is proposed to account for the allosteric interactions of the wild-type enzyme in terms of specific interactions involving the 230-245 loop of the enzyme.

Involvement of tryptophan 209 in the allosteric interactions of Escherichia coli aspartate transcarbamylase using single amino acid substitution mutants

Five mutant versions of aspartate transcarbamylase have been isolated, all with single amino acid substitutions in the catalytic chain of the enzyme. A previously isolated pyrB nonsense mutant was suppressed with supB, supC, supD and supG to create enzymes with glutamine, tyrosine, serine or lysine, respectively, inserted at the position of the nonsense codon. Each of these enzymes was purified to homogeneity and kinetically characterized. The approximate location of the substitution was determined by using tryptic fingerprints of the wild-type enzyme and the enzyme obtained with a tyrosine residue inserted at the position of the nonsense codon. By first cloning the pyrBI operon, from the original pyrB nonsense strain, followed by sequencing of the appropriate portion of the gene, the exact location of the mutation was determined to be at position 209 of the catalytic chain. Site-directed mutagenesis was used to generate versions of aspartate transcarbamylase with tyrosine and glutamic acid at this position. The Tyr209 enzyme is identical with that obtained by suppression of the original nonsense mutation with supC. The two enzymes produced by site-directed mutagenesis were purified using a newly created overproducing strain. Kinetic analysis revealed that each mutant has an altered affinity for aspartate, as judged by variations in the substrate concentration at one-half maximal activity. In addition, the mutants exhibit altered Hill coefficients and maximal activities. In the wild-type enzyme, position 209 is a tryptophan residue that is involved in the stabilization of a bend in the molecule near the subunit interface region. The alteration in homotropic cooperativity seems to be due to changes induced in this bend in the molecule, which stabilizes alternate conformational states of the enzyme.