Localization of the zinc binding site of aspartate transcarbamoylase in the regulatory subunit

A 70-amino acid zinc-binding polypeptide from the regulatory chain of aspartate transcarbamoylase forms a stable complex with the catalytic subunit leading to markedly altered enzyme activity

In an effort to clarify effects of specific protein-protein interactions on the properties of the dodecameric enzyme aspartate transcarbamoylase (carbamoyl-phosphate:L-aspartate carbamoyltransferase, EC 2.1.3.2), we initiated studies of a simpler complex containing an intact catalytic trimer and three copies of a fragment from the regulatory chain. The partial regulatory chain was expressed as a soluble 9-kDa zinc-binding polypeptide comprising 11 amino acids encoded by the polylinker of pUC18 fused to the amino terminus of residues 84-153 of the regulatory chain; this polypeptide includes the zinc domain detected in crystallographic studies of the holoenzyme. In contrast to intact regulatory chains, the zinc-binding polypeptide is monomeric in solution because it lacks the second domain responsible for dimer formation and assembly of the dodecameric holoenzyme. The isolated 9-kDa protein forms a tight, zinc-dependent complex with catalytic trimer, as shown by the large shift in electrophoretic mobility of the trimer in nondenaturing polyacrylamide gels. Enzyme assays of the complex showed a hyperbolic dependence of initial velocity on aspartate concentration with Vmax and Km for aspartate approximately 50% lower than the values for free catalytic subunit. A mutant catalytic subunit containing the Lys-164----Glu substitution exhibited a striking increase in enzyme activity at low aspartate concentrations upon interaction with the zinc domain because of a large reduction in Km upon complex formation. These changes in functional properties indicate that the complex of the zinc domain and catalytic trimer is an analog of the high-affinity R ("relaxed") state of aspartate transcarbamoylase, as proposed previously for a transiently formed assembly intermediate composed of one catalytic and three regulatory subunits. Conformational changes at the active sites, resulting from binding the zinc-containing polypeptide chains, were detected by difference spectroscopy with trinitrophenylated catalytic trimers. Isolation of the zinc domain of aspartate transcarbamoylase provides a model protein for study of oligomer assembly, communication between dissimilar polypeptides, and metal-binding motifs in proteins.

Properties of a 19-kDa Zn2+-binding protein and sequence of the Zn2+-binding domains

A novel 19-kDa protein has been described recently [Brand, I.A. and Söling, H.-D. (1986) J. Biol. Chem. 261, 5895-5900] which is able to inactivate 6-phosphofructo-1-kinase reversibly in a Zn2+-dependent manner. We present now additional biochemical and physicochemical data concerning this protein. It is extremely acidic with 40% glutamic and 15% aspartic acid residues. It contains no sulfur, aromatic amino acids, histidine or isoleucine. The protein has four binding sites for Zn2+ with an apparent Kd of about 6 microM. Two of these binding sites are called unspecific as Zn2+ is displaced from these binding sites at physiological concentrations of free Mg2+ (0.75 mM) and at high salt concentrations (100 mM NaCl). Whereas Mg2+-binding to the two other so-called specific Zn2+-binding sites occurs only at Mg2+ concentrations at about 5 mM. The four Zn2+-binding sites were detected on a tryptic peptide (T8) of 43 amino acid residues, which still possessed biological activity. This peptide has been sequenced and is characterized by four clusters of acidic amino acids separated by only a few neutral amino acids. The two specific Zn2+-binding sites could be detected in the C-terminal portion of T8, the two unspecific Zn2+-binding sites must therefore be located at the N-terminal portion. The Zn2+-binding domains of the 19-kDa Zn2+-binding protein described here are completely different from those of the 'zinc finger' discovered in several DNA-binding proteins.

Differential scanning calorimetric study of the thermal denaturation of aspartate transcarbamoylase of Escherichia coli

The thermal denaturation of Escherichia coli aspartate transcarbamoylase (c6r6) in the absence and presence of various ligands has been studied by means of high-sensitivity differential scanning calorimetry (DSC). As previously reported [Vickers, K.P., Donovan, J.W., & Schachman, H.K. (1978) J. Biol. Chem. 253, 8493-8498], the denaturational endotherm consists of two peaks, the lower of which is due to denaturation of the three regulatory, r2, subunits while the upper involves the two catalytic, c3, subunits. The temperature of maximal excess apparent specific heat, tm, of the lower peak is raised from the value of 51.4 degrees C for the isolated subunit to 66.8 degrees C as a result of subunit interactions, whereas tm for the c3 peak is essentially the same in the isolated subunit and in the holoenzyme, indicating that the denatured r2 subunits do not interact with the c3 subunits. The total specific denaturational enthalpy for c6r6, 4.83 +/- 0.16 cal g-1, is significantly larger than the weighted mean, 4.08 cal g-1, of the enthalpies for c3 and r2. The fact that no endotherm is observed when previously scanned protein is rescanned indicates that the denaturation is irreversible, as is also the case with the r2 and c3 subunits. Empirical justification for analyzing the data in terms of equilibrium thermodynamics is cited. The observed DSC curves can be expressed within experimental uncertainty as the sum of five sequential two-state steps. The value of t 1/2, the temperature of half-completion, for each step increases with increasing protein concentration, indicating that some dissociation of the protein takes place during denaturation.(ABSTRACT TRUNCATED AT 250 WORDS)

The yeast ARGRII regulatory protein has homology with various RNases and DNA binding proteins

Three regulatory proteins are involved in the post-transcriptional control of arginine metabolism in Saccharomyces cerevisiae: ARGRI, ARGRII and ARGRIII. The 880 amino acid ARGRII protein, like some DNA binding proteins, possesses in its N-terminal sequence a cysteine-rich region that presents homology to the zinc binding region of Escherichia coli aspartate transcarbamylase. ARGRII also has a region of 90 amino acids that is 30% homologous to the E. coli ARGR repressor. Moreover a 87 amino acid long sequence of ARGRII contains three stretches with significant homology to some viral, bacterial and pancreatic RNases. We propose a model in which the RNase-like sequence could regulate the expression of arginine anabolic messenger RNAs.

In vivo formation of hybrid aspartate transcarbamoylases from native subunits of divergent members of the family Enterobacteriaceae

The genes encoding the catalytic (pyrB) and regulatory (pyrI) polypeptides of aspartate transcarbamoylase (ATCase, EC 2.1.3.2) from several members of the family Enterobacteriaceae appear to be organized as bicistronic operons. The pyrBI gene regions from several enteric sources were cloned into selected plasmid vectors and expressed in Escherichia coli. Subsequently, the catalytic cistrons were subcloned and expressed independently from the regulatory cistrons from several of these sources. The regulatory cistron of E. coli was cloned separately and expressed from lac promoter-operator vectors. By utilizing plasmids from different incompatibility groups, it was possible to express catalytic and regulatory cistrons from different bacterial sources in the same cell. In all cases examined, the regulatory and catalytic polypeptides spontaneously assembled to form stable functional hybrid holoenzymes. This hybrid enzyme formation indicates that the r:c domains of interaction, as well as the dodecameric architecture, are conserved within the Enterobacteriaceae. The catalytic subunits of the hybrid ATCases originated from native enzymes possessing varied responses to allosteric effectors (CTP inhibition, CTP activation, or very slight responses; and ATP activation or no ATP response). However, each of the hybrid ATCases formed with regulatory subunits from E. coli demonstrated ATP activation and CTP inhibition, which suggests that the allosteric control characteristics are determined by the regulatory subunits.

Zinc-sulfur bonds of aspartate transcarbamylase studied by x-ray absorption spectroscopy

X-ray absorption spectra have been recorded for aspartate transcarbamylase [unligated and ligated with the transition-state analogue N-(phosphonoacetyl)-L-aspartate] and for the model compound zinc dimethyldithiocarbamate. The spectra confirm that, in the enzyme, the zinc atom is ligated to four sulfur atoms, with a mean distance of 2.34 +/- 0.03 A. A spread in bond lengths of 0.1 +/- 0.03 A is possible, due to thermal and/or static disorder. No significant difference was found between the spectra of the ligated and unligated enzymes.

Zinc(II), cadmium(II), and mercury(II) thiolate transitions in metallothionein

The metal-specific absorption envelopes of zinc-, cadmium-, and mercury-metallothioneins and of complexes of these metal ions with 2-mercaptoethanol have been analyzed in terms of Jørgensen's electronegativity theory for charge-transfer excitations by using the spectra of zinc(II), cadmium(II), and mercury(II) tetrahalides as references. By Gaussian analysis the difference absorption spectra of the various forms of metallothionein vs. thionein and of the corresponding 2-mercaptoethanol complexes vs. 2-mercaptoethanol were resolved into three components. For each metal derivative the location of the lowest energy band is in good agreement with the position of the first ligand-metal charge-transfer (LMCT) transition (type t2 leads to a1) predicted from the optical electronegativity difference of the thiolate ligands and of the central metal ion by assuming tetrahedral coordination. There is also a correspondence between the effects of the metal ion on the position of the first LMCT band and the binding energy of the 2p electrons of the sulfur ligands as found by X-ray photoelectron spectroscopic measurements [Sokolowski, G., Pilz, W., & Weser, U. (1974) FEBS Lett. 48, 222]. Due to the lack of exact structural information, the assignment of the two other resolved metal-dependent bands remains conjectural, but it is likely that they include a second LMCT transition (type t2 leads to a1) analogous to that occurring in tetrahalide complexes of group-2B metal ions. The simplicity of the resolved thiolate spectra and their correspondence to those of tetrahedral models support the view that the various metal-binding sites of metallothionein are chemically similar and that the coordination environment of the metal ion has a symmetry related to that of a tetrahedron [Vasák, M. (1980) J. Am. Chem. Soc. 102, 3953].

Propagation of conformational changes in Ni(II)-substituted aspartate transcarbamoylase: effect of active-site ligands on the regulatory chains

Although the importance of ligand-promoted conformational changes in allosteric enzymes has been recognized, it often has been difficult to determine whether the effects of binding are propagated to remote positions in different chains. Efforts were made, therefore, to demonstrate that changes due to ligand binding to the catalytic chains of aspartate transcarbamoylase (carbamoylphosphate:L-aspartate carbamoyltransferase, EC 2.1.3.2) of Escherichia coli are "communicated" to the regulatory chains. For these studies the endogenous zinc in the latter chains was replaced by nickel, which served as a discriminating spectral probe. The Ni(II)-enzyme was constructed by dissociating the native enzyme, separating the catalytic and regulatory subunits, removing Zn(II) from the latter, replacing it with Ni(II), and reconstituting the enzyme from native catalytic and Ni(II)-containing regulatory subunits. Ni(II) derivatives containing either six Ni(II) or five Ni(II) and one Zn(II) possess the allosteric properties of the native enzyme and exhibit absorption bands at 360 and 440 nm due to charge transfer transitions. Smaller bands were also observed at 665 and 720 nm from d-d transitions, which are consistent with tetrahedral geometry in the coordination sphere of nickel. Binding of the bisubstrate ligand N-(phosphonacetyl)-L-aspartate to the catalytic subunit of Ni(II)-aspartate transcarbamoylase perturbed the Ni(II) chromophore, giving rise to two difference spectral bands (at 390 and 465 nm). Spectral titrations showed that the conformational changes at the metal-ion-binding sites were complete even though about one-third of the active sites were unoccupied. This propagation of conformational changes is in accord with other evidence indicating that the allosteric transition in aspartate transcarbamoylase is concerted.

Three-dimensional structures of aspartate carbamoyltransferase from Escherichia coli and of its complex with cytidine triphosphate

X-ray diffraction studies to nominal resolutions of 3.0 A for unliganded aspartate carbamolytransferase (EC 2.1.3.2)(R32 crystal symmetry) and of 2.8 A for the complex of aspartate carbamoyltransferase with cytidine triphosphate (P321 crystal symmetry) have yielded traces of the polypeptide chains of the catalytic (C) and regulatory (R) chains in the hexameric C6R6 molecules. The independent molecular structures of the liganded and unliganded forms of the enzyme are very nearly identical. In the regulatory chain there is a CTP-binding domain that interacts with an adjacent regulatory subunit and a zinc-binding domain that interacts with the catalytic subunit. In the catalytic chain a polar domain shows interactions between adjacent pairs of C chains to form each trimer C3 while an equatorial domain shows intramolecular C3--C3 interactions. The active site is at or near the interface between adjacent C chains within the trimers. Probably each active center involves amino acid residues from adjacent C chains.

A kinetic model of cooperativity in aspartate transcarbamylase

A relatively simple kinetic model is proposed to account simultaneously for data on the binding of carbamyl phosphate and succinate to aspartate trans carbamylase (ATCase), and for the relaxation spectrum associated with this binding. The model also accounts for measurements of the initial velocity of the reaction of ATCase with respect to aspartate and carbamyl phosphate. The principal assumption made is that ATCase consists of three identical noninteracting cooperative dimers. Ordered binding and both sequential and concerted conformational changes in the dimers are needed to account for the properties of ATCase. The values of the parameters of this model can be determined by fitting to existing experimental evidence. Various new quantitative predictions are made that can serve as additional tests of the proposed theory.

Biochemistry of zinc

The biochemistry of zinc has come under intensive investigation at the molecular level during the past 20 years. More than 70 zinc metalloenzymes are now known, and they span a broad range of biologic activities. Substitution of zinc by cobalt, for example, serves to locate a paramagnetic probe at the active site of the enzyme which can then provide information regarding the coordination properties of the metal and the active site environment.

An intermediate complex in the dissociation of aspartate transcarbamylase

The multisubunit enzyme aspartate transcarbamylase consists of six copies of two types of polypeptide chains, catalytic (C) and regulatory (R). A complex formed by the partial dissociation of this enzyme has been isolated. This species, which has the structure C(6)R(4), is a likely intermediate in the stepwise dissociation of aspartate transcarbamylase induced by mercurials. The formation of the complex is the result of the release of a single regulatory dimer (R(2)) from the parent molecule.The specific activity of the intermediate is essentially the same as that of aspartate transcarbamylase. By contrast, both homotropic and heterotropic interactions are reduced, but not abolished. These observations suggest that the allosteric transitions involved in the control mechanisms do not require the intact structure C(6)R(6).

Effects of metal binding on protein structure

A distinction has been made between ‘metalloproteins’ and ‘metal-protein complexes’. The former exhibit high metal-ligand stability constants (the metal is not removed during the isolation of the protein), while the latter bind metal ions only loosely (Vallee, 1955). Actually, all proteins can be considered as existing as metal-protein complexes. Selectivity, however, among proteins in their tendency to combine with inorganic ions (both with regard to the type of ion as well as number of ions) suggests that particular configurations produce specific reactive sites. In turn, binding of ions to these sites alters the electronic and consequently the steric conformation of the protein. Thus, effects on macromolecular conformation may not only be due to structural changes of the solvent induced by ions, which modifies solvent-macromole interaction, but also to specific ligation of the ions to the protien which alters local molecular arrangement.

Aspartate transcarbamoylase from Escherichia coli: electron density at 5.5 A resolution

The allosteric enzyme, aspartate transcarbamoylase (EC 2.1.3.2), has previously been shown in our x-ray diffraction studies to have D(3)-32 symmetry. There are six catalytic (C) and six regulatory (R) chains in the molecular complex (R(6)C(6)). Our three-dimensional x-ray diffraction study of this enzyme (R32, a = 131 A, c = 200 A) at 5.5 A resolution shows a spatial arrangement of the two catalytic trimers C(3) above and below an equatorial belt of three regulatory dimers R(2). The molecule is about 110 x 110 x 90 A in largest dimensions, and is shown here to contain a large central aqueous cavity about 50 x 50 x 25 A in size. Location of the single sulfhydryl of each catalytic chain, and correlation of its reactivity with enzymatic activity in the molecule, suggests that the nearby active sites are most probably accessible from the central cavity, but probably not directly from the external solution. The most obvious access to the central cavity consists of six channels, each about 15 A in diameter, near the regulatory region. A component of the regulatory mechanism may be modulation of access of substrates through these channels.

The thiol group in the catalytic chains of aspartate transcarbamoylase

The allosteric enzyme aspartate transcarbamoylase (EC 2.1.3.2) was previously shown to consist of two functionally distinct types of polypeptide chains. X-ray diffraction and chemical studies showed that there are six copies of both catalytic (C) and regulatory (R) chains, and that the intact molecular complex (C(6)R(6)) has D(3) symmetry. Organomercurials react preferentially with the four thiol groups on each R chain, dissociating the molecular complex. We show that 2-chloromercuri-4-nitrophenol reacts specifically and rapidly with the single C-chain thiol, which is believed to be near the catalytic site. This reaction inactivates the enzyme in solution and does not dissociate the molecular complex. Spectrophotometric titration and mercury analysis indicates that six molecules of this mercurial are firmly bound to the enzyme (R(6)C(6)), and crystallographic studies establish that only six sites, related by D(3) symmetry, are modified. The known low reactivity of this C-chain thiol with other sulfhydryl reagents, the unusual structural requirements in the reaction with 2-chloromercuri-4-nitrophenol, and the spectral properties of the resulting derivative provide insight into the environment of this thiol. Probably, at least one positively charged group of the enzyme is nearby, and the environment of this thiol is at least partially hydrophobic.