Kinetic and spectroscopic characterization of the gamma-carbonic anhydrase from the methanoarchaeon Methanosarcina thermophila.

The zinc and cobalt forms of the prototypic gamma-carbonic anhydrase from Methanosarcina thermophila were characterized by extended X-ray absorption fine structure (EXAFS) and the kinetics were investigated using steady-state spectrophotometric and (18)O exchange equilibrium assays. EXAFS results indicate that cobalt isomorphously replaces zinc and that the metals coordinate three histidines and two or three water molecules. The efficiency of either Zn-Cam or Co-Cam for CO(2) hydration (k(cat)/K(m)) was severalfold greater than HCO(3-) dehydration at physiological pH values, a result consistent with the proposed physiological function for Cam during growth on acetate. For both Zn- and Co-Cam, the steady-state parameter k(cat) for CO(2) hydration was pH-dependent with a pK(a) of 6.5-6.8, whereas k(cat)/K(m) was dependent on two ionizations with pK(a) values of 6.7-6.9 and 8.2-8.4. The (18)O exchange assay also identified two ionizable groups in the pH profile of k(cat)/K(m) with apparent pK(a) values of 6.0 and 8.1. The steady-state parameter k(cat) (CO(2) hydration) is buffer-dependent in a saturable manner at pH 8. 2, and the kinetic analysis suggested a ping-pong mechanism in which buffer is the second substrate. The calculated rate constant for intermolecular proton transfer is 3 x 10(7) M(-1) s(-1). At saturating buffer concentrations and pH 8.5, k(cat) is 2.6-fold higher in H(2)O than in D(2)O, suggesting that an intramolecular proton transfer step is at least partially rate-determining. At high pH (pH > 8), k(cat)/K(m) is not dependent on buffer and no solvent hydrogen isotope effect was observed, consistent with a zinc hydroxide mechanism. Therefore, at high pH the catalytic mechanism of Cam appears to resemble that of human CAII, despite significant structural differences in the active sites of these two unrelated enzymes.

Catalysis and inhibition of human carbonic anhydrase IV.

Carbonic anhydrase IV (CA IV) is a membrane-bound form of carbonic anhydrase. We have characterized the catalytic activity and inhibition of recombinant human CA IV. CA IV is a high-activity isozyme in CO2 hydration with a pH-independent kcat value (1.1 x 10(6) s(-1)) comparable to that of CA II (8 x 10(5) s(-1)). Furthermore, CA IV is more active in HCO3- dehydration than is CA II as illustrated by the nearly 3-fold increase in kcat/K(M) to 3 x 10(7) M(-1) s(-1). However, the esterase activity of CA IV is decreased 150-fold compared to CA II. The catalytic mechanisms of CA II and CA IV are nearly identical. Both isozymes show similar dependence on buffer concentration with the rate-limiting step at high buffer concentration being intramolecular proton transfer, although the intramolecular proton transfer for CA IV is 3 times faster than that observed with CA II. Additional positive charges in the active site of CA IV stabilize anions as indicated by a decreased pKa for the Zn-bound water compared to CA II (6.2 vs 6.9), as well as lower inhibition constants for a variety of anions, including halides, sulfate, formate, acetate, and bicarbonate. CA IV is also activated by low concentrations (<20 mM) of chloride, bromide, and phosphate. Activation by phosphate suggests that the phospholipid anchor may be acting both as an extracellular tether and as a protein activator. Finally, the affinity of CA IV for sulfonamide inhibitors is decreased up to 65-fold compared to CA II as demonstrated by fluorescence titration. The increased bicarbonate activity and altered pH profile are consistent with the proposed physiological role of CA IV in renal bicarbonate reabsorption.

Structure-assisted redesign of a protein-zinc-binding site with femtomolar affinity.

We have inserted a fourth protein ligand into the zinc coordination polyhedron of carbonic anhydrase II (CAII) that increases metal affinity 200-fold (Kd = 20 fM). The three-dimensional structures of threonine-199-->aspartate (T199D) and threonine-199-->glutamate (T199E) CAIIs, determined by x-ray crystallographic methods to resolutions of 2.35 Angstrum and 2.2 Angstrum, respectively, reveal a tetrahedral metal-binding site consisting of H94, H96, H119, and the engineered carboxylate side chain, which displaces zinc-bound hydroxide. Although the stereochemistry of neither engineered carboxylate-zinc interaction is comparable to that found in naturally occurring protein zinc-binding sites, protein-zinc affinity is enhanced in T199E CAII demonstrating that ligand-metal separation is a significant determinant of carboxylate-zinc affinity. In contrast, the three-dimensional structure of threonine-199-->histidine (T199H) CAII, determined to 2.25-Angstrum resolution, indicates that the engineered imidazole side chain rotates away from the metal and does not coordinate to zinc; this results in a weaker zinc-binding site. All three of these substitutions nearly obliterate CO2 hydrase activity, consistent with the role of zinc-bound hydroxide as catalytic nucleophile. The engineering of an additional protein ligand represents a general approach for increasing protein-metal affinity if the side chain can adopt a reasonable conformation and achieve inner-sphere zinc coordination. Moreover, this structure-assisted design approach may be effective in the development of high-sensitivity metal ion biosensors.