Catalytic Role Of Metal Ion Research Articles

Elucidating the role of metal ions in carbonic anhydrase catalysis

Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn2+, tetrahedral to octahedral conversion for Co2+, octahedral for Ni2+, and trigonal bipyramidal for Cu2+) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 Å) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.

The catalytic role of the M2 metal ion in PP2Cα.

PP2C family phosphatases (the type 2C family of protein phosphatases; or metal-dependent phosphatase, PPM) constitute an important class of signaling enzymes that regulate many fundamental life activities. All PP2C family members have a conserved binuclear metal ion active center that is essential for their catalysis. However, the catalytic role of each metal ion during catalysis remains elusive. In this study, we discovered that mutations in the structurally buried D38 residue of PP2Cα (PPM1A) redefined the water-mediated hydrogen network in the active site and selectively disrupted M2 metal ion binding. Using the D38A and D38K mutations of PP2Cα as specific tools in combination with enzymology analysis, our results demonstrated that the M2 metal ion determines the rate-limiting step of substrate hydrolysis, participates in dianion substrate binding and stabilizes the leaving group after P-O bond cleavage. The newly characterized catalytic role of the M2 metal ion in this family not only provides insight into how the binuclear metal centers of the PP2C phosphatases are organized for efficient catalysis but also helps increase our understanding of the function and substrate specificity of PP2C family members.

Catalytic role of metal ion in the selection of competing reaction paths: a first principles molecular dynamics study of the enzymatic reaction in ribozyme.

By using finite temperature first principles molecular dynamics, the mechanism of the enzymatic reaction of ribozyme was investigated for both the anionic and the radical charge states of the modeled RNA fragment. In the case of the anionic system, a pseudorotation and the subsequent 3' --> 2' migration occur in a vacuum, rather than the self-cleavage of the phosphodiester. On the other hand, when either a divalent metal ion (Mg(2+)) catalyst or the continuous hydrogen bond network of the solvent is present, the reaction path of the anionic species changes dramatically, going toward the transesterification channel. In a radical system, the transesterification can occur without a metal catalyst, as a consequence of the displacement of a hole (empty electronic state) along the reaction path. Thus, the present analysis suggests that a metal ion might be essential not only in lowering the activation barrier but also in selecting the reaction path among those corresponding to possible different charge states of the intermediate structure in vivo. Furthermore, simulation of the anionic species in solution shows that, in the absence of a metal catalyst, water molecules cooperate with the proton transfer via a proton wire mechanism and the hydrogen bond network plays a crucial role in preventing pseudorotations. On the other hand, when a metal cation is present in the vicinity of the site where the nucleophilic attack occurs, the hydrogen bond network is interrupted and detachment of the proton, enhanced by the catalyst, does not give rise to any proton-transfer process.

Fixation of atmospheric carbon dioxide by a series of hydroxo complexes of divalent metal ions and the implication for the catalytic role of metal ion in carbonic anhydrase. Synthesis, characterization, and molecular structure of [LM(OH)]n (n = 1 or 2) and LM(.mu.-CO3)ML (M(II) = Mn, Fe, Co, Ni, Cu, Zn; L = HB(3,5-iso-Pr2pz)3)

By using the hindered tris(pyrazoly)borate ligand HB(3,5-iPr[sub 2]pz)[sub 3], (hydrotris(3,5-diisopropyl-1-pyrazolyl)-borate), a series of hydroxo complexes of first-row divalent metal ions (Mn (1), Fe (2), Co (3), Ni (4), Cu (5), Zn (6)) was synthesized. X-ray crystallography was applied to 1-5, establishing that all these hydroxo complexes have a dinuclear structure solely bridged with a bis(hydroxo) unit. The structure of 6 was characterized by spectroscopy, which indicates that 6 is monomeric. All these hydroxo complexes were found to react with CO[sub 2], even atmospheric CO[sub 2], to afford [mu]-carbonato dinuclear complexes of Mn (7), Fe (8), Co (9), Ni (10), Cu (11), and Zn (12). The molecular structures of the complexes 8-12 were determined. A variety of coordination modes of the carbonate group was seen. In 10 and 11, the carbonate group is bound to both metal centers bidentately in a symmetric fashion, while in 8 and 9, the carbonate coordination modes are described as an unsymmetric bidentate. The carbonate group in 12 is coordinated to one zinc ion bidentately, but it is bound to the other zinc ion unidentately. From IR data, the coordination mode of the carbonate group in 7 was suggested to be similar to those found inmore » 8 and 9. Thus, the order of the coordination distortions of the carbonate groups in this series of [mu]-carbonato dinuclear complexes is determined. 40 refs., 8 figs., 4 tabs.« less

Micellar and Metal Ion Catalysis in the Pyridoxal-Promoted α,β-Elimination of S-Phenylcysteine

Abstract The effects of metal ions and detergents on the pyridoxal-catalyzed α,β-elimination reaction of S-phenylcysteine have been investigated in 0.01 M borate buffer at 50 °C (the copper ion catalysis at 40 °C in the presence of CTAB micelles). Both copper(II) and nickel(II) ions markedly accelerated the elimination reaction of S-phenylcysteine. Since the catalytic efficiency of nickel(II) seems to be obtained due to the poor coordination ability of the leaving group in the present reaction, the previous working hypothesis which was provided for the elucidation of catalytic roles of metal ions in the α,β-elimination of O-phosphothreonine has now been approved. Among cationic, anionic, and non-ionic detergents employed in this work as apoenzyme models, only CTAB of cationic nature showed a considerable rate acceleration even in the absence of metal ions. The micellar binding constant was evaluated from the saturation-type correlation between reaction rate and CTAB concentration. The surfactant micelles demonstrated some enzyme-like features of catalysis in the pyridoxal-promoted α,β-elimination reaction, where the reaction is controlled by the entropy term. The CTAB catalysis was greatly inhibited by organic and inorganic anions due to the electrostatic nature of the micellar surface. The catalytic mechanisms for the micellar reactions and their significance as an enzyme model system are discussed.