Sandbox Wabash 09 Fumarase

<StructureSection load='1YFE_mm1.pdb' size='340' side='right' caption='Quaternary Structure of Fumarase (provided by Dr. Taylor)' scene=''>

<StructureSection load='1YFE_mm1.pdb' size='340' side='right' caption='Quaternary Structure of Fumarase (provided by Dr. Taylor)' scene=''>

Fumarase C, which is found in E. coli, is a enzyme homologous with some eurkaryotic enzymes found in both the cytosol and mitochondria. Fumarase catalyzes the dehydration of L-malate to form fumarate, as well as the reverse hydration reaction. Two basic groups play a role in the overall catalytic process of fumarase. The first basic group is responsible for the removal of a proton from the C3 carbon of L-malate, forming a carbanion. The carbanion is stabilized by an aci-carobxylate intermediate which is formed at C4. The carboxyl group on C4 has a negative two formal charge, stabilizing the substrate after the removal of the proton. The second basic group is protonated, for the creation of fumarate, and leads to the formation of a water molecule as a hydroxyl group is removed from C2. Interestingly, fumarase contains two possible sites at which catalysis occurs, prompting researchers to determine which of the sites is the true active site of the enzyme <ref>Weaver T, Lees M, Banaszak L. 1997. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site. Protein Science 6:834-842.ref>.

Fumarase C, which is found in E. coli, is a enzyme homologous with some eurkaryotic enzymes found in both the cytosol and mitochondria. Fumarase catalyzes the dehydration of L-malate to form fumarate, as well as the reverse hydration reaction. Two basic groups play a role in the overall catalytic process of fumarase. The first basic group is responsible for the removal of a proton from the C3 carbon of L-malate, forming a carbanion. The carbanion is stabilized by an aci-carobxylate intermediate which is formed at C4. The carboxyl group on C4 has a negative two formal charge, stabilizing the substrate after the removal of the proton. The second basic group is protonated, for the creation of fumarate, and leads to the formation of a water molecule as a hydroxyl group is removed from C2. Interestingly, fumarase contains two possible sites at which catalysis occurs, prompting researchers to determine which of the sites is the true active site of the enzyme <ref>Weaver T, Lees M, Banaszak L. 1997. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site. Protein Science 6:834-842.ref>.

== Determining the Active Site ==

== Determining the Active Site ==

The two possible active sites of fumarase that were studied to determine the actual active site are termed the A-site and the B-site. The A-site is comprised of residues from three of the four subunits, while the <scene name='72/726377/B-site_fumarase/1'>B-site</scene> consists of residues only from one chain. No active monomeric fumarase has been found, and this was one of observations supporting the A-site. Another observation was the fact that citrate, a known competitive inhibitor of fumarase, bound to fumarase at the A-site. Unlike the A-site, however, the B-site is closer to the surface of the enzyme and not in a deep pit containing an unknown water molecule. The two sites are actually linked by a single subunit at residues 131-140, and there are some important interactions that occur between the B-site and a ligand.

The two possible active sites of fumarase that were studied to determine the actual active site are termed the A-site and the B-site. The A-site is comprised of residues from three of the four subunits, while the <scene name='72/726377/B-site_fumarase/1'>B-site</scene> consists of residues only from one chain. No active monomeric fumarase has been found, and this was one of observations supporting the A-site. Another observation was the fact that citrate, a known competitive inhibitor of fumarase, bound to fumarase at the A-site. Unlike the A-site, however, the B-site is closer to the surface of the enzyme and not in a deep pit containing an unknown water molecule. The two sites are actually linked by a single subunit at residues 131-140, and there are some important interactions that occur between the B-site and a ligand.