Sandbox Wabash 02 Fumarase

Determination of the True Active Site of Fumarase C from E. Coli.

Fumarase C from E. coli is an enzyme homologous with the cytosolic and mitochondrial enzymes found in eukaryotic cells. It catalyzes the hydration/dehydration reaction between the metabolites L-malate and fumarate. Eukaryotic fumarases have been studied extensively by classical kinetic and isotope labeling methods (Hill & Teipel, 1971; Cleveland,1977). Fumarase from E. coli is less well characterized. Two basic groups are thought to be involved in the overall catalytic process. The first (B1) is responsible for the removal of a proton from the C3 position of L-malate, resulting in a carbanion stabilized by an acid-carboxylate intermediate formed at C4. The last stage of the catalytic process is thought to involve a second basic group on the protein labeled B2. In the direction of fumarate production, this basic group would be protonated and the removal of the -OH from C2 results in the formation of a water molecule.The proton at B1 in Figure 1 has unusual properties and is believed to be removed as the next substrate molecule binds (Rose et al., 1992). The crystallographic studies of wild-type fumarase indicated that the enzyme had an unusual subunit arrangement with a core of 20 alpha-helices, 5 from each of the subunits (Weaver et al., 1995). Subsequent crystallographic studies with several inhibitors including pyromellitic acid and beta-trimethylsilyl maleate produced some unexpected results. Although both are related to the normal substrate, they are bound at different sites. The original tungstate site, a heavy atom derivative, was also the binding site of the inhibitors citrate and pyromellitic acid. This was labeled the A-site and is comprised of atoms from three of the four subunits (Weaver & Banaszak, 1996). The second site contained L-malate in the native crystals and beta-trimethylsilyl maleate in another crystallographic study (Weaver & Banaszak, 1996), and was labeled the B-site and was formed by atoms from a single subunit. The results led to the dilemma as to which of the two sites was the active site.

It was suspected that the A-site was the active site because of the observation that no active monomeric form of fumarase has ever been described, and the A-site was formed by residues from three of the four subunits. Because the biochemical data suggested that a histidine side chain was one of the bases participating in the catalytic reaction (Brant et al.. 1963), testing whether H129 or H188 affected catalytic activity appeared to offer a way of resolving the two site dilemma. Evidence as to which of the two ligand binding sites was indeed the catalytic site should be obtainable by mutating the histidines at the two different sites. If the A-site was the active site, changing H188 should dramatically affect the catalytic activity. Conversely, if the B-site was the active site then a mutation at H129 should affect catalysis.

Structure of the Active Site of Fumarase. A number of stereochemical factors describing the two sites were examined in the wild-type crystal structures (Weaver & Banaszak, 1996). Site A was in a relatively deep pit removed from bulk solvent. It also contained an unusual bound water, although there was no obvious way of linking this directly to the catalytic process. One of the side chains interacting with this water molecule is H188. In the crystallographic coordinates of the wildtype enzyme, the water molecule forms a short hydrogen bond, 2.5 A, with the imidazole ring of H188. The side chain of H188 is also within hydrogen bonding distance to an oxygen atom of bound citrate or pyromellitic acid. The B-site is closer to the surface of the enzyme (Weaver & Banaszak, 1996). There are three principal interactions between the ligand and wild-type fumarase at the B-site, and in an indirect fashion the A- and B-sites are linked by residues 131 to 140 in a single subunit. Main chain hydrogen bonds between the oxygen atoms of the bound ligand and main chain -NHs of D132 and N131 on the N-terminal end of the pi-helix are important to stabilization at the B-site. Oxygen atoms of the other carboxylate of the ligand at the B-site are hydrogen bonded to R126-NE and H129-NDI. The hydrogen bonds between side chain atoms of N135 and N103, and between N103 and SI40 form an indirect connection between the B- and the A-site. HI29 is the only basic group close to a ligand bound at the B-site.

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