This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
Sandbox Wabash 28 Fumarase
From Proteopedia
(→Theoretical mechanism) |
(→Theoretical mechanism) |
||
| Line 4: | Line 4: | ||
==Theoretical mechanism== | ==Theoretical mechanism== | ||
L-malate is believed to be dehydrated by fumarase into fumarate using basic residues in its active site. | L-malate is believed to be dehydrated by fumarase into fumarate using basic residues in its active site. | ||
| - | [[Image:Fumarase mechanism.jpg|thumb| | + | [[Image:Fumarase mechanism.jpg|thumb|Fumarase mechanism]] |
| + | One of the bases deprotonates the γ-C producing an anion stabilized by the aci-carboxylate carbanion intermediate. The hydrogenation of the alcohol by a second, previously protonated base renders the alcohol a good leaving group. The closing of the aci-carboxylate into a carboxylate and alkene by pushing off the water produces fumarate. | ||
| + | |||
| + | The mechanism can also work in reverse as it is the aci-carboxylate intermediate that is believed to be most stabilized by fumarase. In this direction, a water molecule attacks the alkene to produce the aci-carboxylate carbanion. This high energy structure quickly deprotonates a local, protonated base to produce L-malate. | ||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 00:23, 28 February 2016
Fumarase's debated active site
is a highly conserved enzyme found in bacteria as well as mitochondria of eukaryotes which catalyzes the hydration/dehydration of fumarate and L-malate, respectively. The protein, which consists of two dimers laden with α-helices, initially crystalized as a dimer making conclusions about its active site problematic. However, subsequent crystalizations with various inhibitors showed two potential active sites - the locations at which the inhibitors bound: the first discovered theoretical active site is located deep in the interior of the tetramer and was inhibited by pyromelletic acid and citrate - the latter of which is found in the potential active site; β-trimethylsilyl maleate inhibition resulted in the discover of found at the exterior of each subunit. In either case, a basic His residue is believed to be the origin of catalytic function and two such residues were found (His 188 in site A and His 129 in site B). To conclusively determine whether A or B is the active site, site-directed mutagenesis in E. coli was conducted.
Theoretical mechanism
L-malate is believed to be dehydrated by fumarase into fumarate using basic residues in its active site.
One of the bases deprotonates the γ-C producing an anion stabilized by the aci-carboxylate carbanion intermediate. The hydrogenation of the alcohol by a second, previously protonated base renders the alcohol a good leaving group. The closing of the aci-carboxylate into a carboxylate and alkene by pushing off the water produces fumarate.
The mechanism can also work in reverse as it is the aci-carboxylate intermediate that is believed to be most stabilized by fumarase. In this direction, a water molecule attacks the alkene to produce the aci-carboxylate carbanion. This high energy structure quickly deprotonates a local, protonated base to produce L-malate.
