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

A comparative assessment of the zinc–protein coordination in 2Zn–insulin as determined by X-ray absorption fine structure (EXAFS) and X-ray crystallography

Accurate ( ca .0.1Å) knowledge of the metal environment in metalloproteins is essential to understanding their function. Single crystal X-ray analysis has provided detailed descriptions of metal environments in a number of crystallizable proteins but their accuracy has often been limited by their restricted diffraction patterns. The technique of X-ray absorption fine structure (EXAFS) is not limited to crystals and can provide very accurate radial distances between metal ions and their ligands. It has therefore great potential for the study of biochemical metal-containing systems in solution. The method depends on the analysis of the oscillations in the absorption or fluorescence spectrum extending over several hundreds of electron volts above the metal absorption edge. The very intense synchrotron X-ray sources make EXAFS applicable to biological systems where the metal ion concentration is low, typically in the millimolar range. We have determined EXAFS spectra for 2Zn–insulin and a variety of Zn–ligand model compounds of known crystal structures in both the absorption and the fluorescence modes. The X-ray crystallographic refinement of 2Zn-insulin with 1.5 Å data provides estimated standard deviations for well defined atoms ranging from 0.03 to 0.06 Å which thus determine the zinc-ligand distances sufficiently accurately for comparison with those derived from EXAFS. The experimental procedures for obtaining the spectra with the use of the storage ring doris at the Deutsche Elektrononen Synchrotron (DESY) are described. The shapes of the exafs spectra of 2Zn-insulin and the zinc complexes are remarkably similar. These results emphasize one of the major weaknesses of the technique: the difficulty in distinguishing between atoms of similar atomic mass such as oxygen and nitrogen in the present instance. The small but real effect of solvent on the spectrum of one complex has important implications; it reveals the ability of EXAFS to provide evidence for structural changes in the metal coordination and that other structures possibly more relevant to function may exist. For the detailed analysis we used ab initio calculations on the model compounds. The method used is outlined and the programs are cited; the theoretical basis for these calculations is to be found in Lee & Pendry ( Phys . Rev . B 11, 2795-2811 (1975)). Its application to the 2Zn-insulin EXAFS spectrum showed that there is good agreement in both the exafs and the X-ray crystallographic methods for the CE1 and NE2 to Zn radial distance; significant discrepancies, however, exist for the other atoms in the coordinating structure. This failure stems essentially from the smaller contribution of outer atoms to the EXAFS spectrum. To resolve these correctly the amplitudes in the EXAFS spectrum need to be more accurate, and there needs to be a more adequate theory to deal with multiple scattering effects. Until these have been achieved it is probably more profitable to make use of our exact knowledge of the bonding behaviour and geometry of such coordinating groups as imidazole rings.

Crystal structures of aspartate carbamoyltransferase ligated with phosphonoacetamide, malonate, and CTP or ATP at 2.8-A resolution and neutral pH

The R-state structures of the ATP and CTP complexes of aspartate carbamoyltransferase ligated with phosphonoacetamide and malonate have been determined at 2.8-A resolution and neutral pH. These structures were solved by the method of molecular replacement and were refined to crystallographic residuals between 0.167 and 0.182. The triphosphate, the ribose, and the purine and pyrimidine moieties of ATP and CTP interact with similar regions of the allosteric domain of the regulatory dimer. ATP and CTP relatively increase and decrease the size of the allosteric site in the vicinity of the base, respectively. For both CTP and ATP at pH 7, the gamma-phosphates are bound to His20 and are also near Lys94, while the alpha-phosphates interact exclusively with Lys94. The 2'-hydroxyls of both CTP and ATP are near the amino group of Lys60. The pyrimidine ring of CTP makes specific hydrogen bonds at the allosteric site: the NH2 group donates hydrogen bonds to the main-chain carbonyls of Ile12 and Tyr89 and the pyrimidine ring carbonyl oxygen accepts a hydrogen bond from the amino group of Lys60; the nitrogen at position 3 in the pyrimidine ring is hydrogen bonded to a main-chain NH group of Ile12. The purine ring of ATP also makes numerous interactions with residues at the allosteric site: the purine NH2 (analogous to the amino group of CTP) donates a hydrogen bond to the main-chain carbonyl oxygen of Ile12, the N3 nitrogen interacts with the amino group of Lys60, and the N1 nitrogen hydrogen bonds to the NH group of Ile12. The binding of CTP and ATP to the allosteric site in the presence of phosphonoacetamide and malonate does not dramatically alter the structure of the allosteric binding site or of the allosteric domain. Nonetheless, in the CTP-ligated structure, the average separation between the catalytic trimers decreases by approximately 0.5 A, indicating a small shift of the quaternary structure toward the T state. In the CTP- and ATP-ligated R-state structures, the binding and occupancy of phosphonoacetamide and malonate are similar and the structures of the active sites are similar at the current resolution of 2.8 A.

Structural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6-A resolution

The crystal structure of Escherichia coli aspartate carbamoyltransferase complexed with adenosine 5'-triphosphate (ATP) has been solved by molecular replacement and has been refined to a crystallographic residual of 0.17 at 2.6-A resolution by using the computer program X-PLOR. The unit cell dimensions of this crystal form are a = b = 122.2 A and c = 143.3 A and the space group is P321. Although the c-axis unit cell dimension is approximately 1 A longer than the corresponding dimension of the CTP-ligated P321 crystal form (c = 142.2 A), the ATP-ligated enzyme adopts a T-like quaternary structure. The base moiety of ATP interacts with residues Glu10, Ile12, and Lys60 while the ribose is near Asp19 and Lys60; the triphosphate entity is bound to Lys94, although His20 and Arg96 are nearby. We observe a higher occupancy for ATP in the allosteric site of the R1 regulatory chain in comparison to the occupancy of the R6 allosteric site. These crystallographically independent sites are related by a molecular 2-fold axis. There are other violations of the noncrystallographic symmetry that are similar to those observed in the refined CTP-ligated aspartate carbamoyltransferase structure. These infringements on the molecular symmetry might be the result of intermolecular interactions in the crystal. To ensure the most meaningful comparison with the ATP-ligated structure, we refined the previously reported CTP-bound and unligated structures to crystallographic residuals between 0.17 and 0.18 using X-PLOR. These X-PLOR refined structures are not significantly different from the initial structures that had been crystallographically refined by a restrained least-squares method. After making all possible comparisons between the CTP- and ATP-ligated and the unligated T-state structures, we find that the most significant differences are located at the allosteric sites and in small changes in the quaternary structures. At the allosteric site, the binding of CTP and ATP successively enlarges the nucleotide binding cavity, particularly in the vicinity of the base. The changes in the quaternary structure can be characterized by an increase in the separation of the catalytic trimers by approximately 0.5 A as ATP binds to the unligated T structure. On the basis of these structural studies, we discuss the relationships between the conformational differences in the allosteric site and the small changes in the quaternary structure within the T form to the possible mechanisms for CTP inhibition and ATP activation.

EXAFS study of the zinc-binding sites in the protein transcription factor IIIA

The protein transcription factor IIIA (TFIIIA) is involved in the synthesis of 5S RNA in vitro by RNA polymerase III. It can be isolated from Xenopus laevis oocytes as a 7S particle in which the protein is associated with 5S RNA. Recently it has been shown that the native particle contains 7-11 zinc atoms. Analysis of the amino-acid sequence of TFIIIA revealed nine similar domains of approximately 30 amino acids, each containing two invariant pairs of histidines and cysteines, which have been implicated as possible binding sites for the zinc atoms. Other regulatory proteins with sequence homology to the zinc-binding domains of TFIIIA have now been reported. Here, we report the results of an EXAFS (extended X-ray absorption fine structure) study of TFIIIA which shows that the coordination sphere of the zinc sites consists of two cysteine and two histidine residues.