Fumarase 2: Difference between revisions

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FumaraseFumarase

Overview

Fumarase, also known as fumarate hydratase, is an enzyme in the citric acid cycle. In the seventh step of the reaction pathway, fumarase catalyzes the reversible hydration reaction that converts fumarate to malate and vice versa. Fumarase is classified as an which belongs to the L-aspartase/fumarase family. It forms a tetramer of identical subunits that . Each subunit is comprised of .

Structure: will the real active site please stand?

Crystal structures of fumarase C revealed that the enzyme has two dicarboxylate binding sites; one was called the A site, and the second, the B site. This raises the question: which of the two sites is the active site of the enzyme? The A site shows relatively little change upon substrate binding, while the B site shifts substantially. ^[1]. But these changes could account for regulation...so which site is the true active site?

In order to answer this question, an experiment that tested each of the sites independently was conducted. Both sites contain histidine residues: in the A-site and in the B-site. These sites were mutated to asparagine in separate experiments, and the effect on kinetics was measured. The results of the experiment showed that the H129N mutation had little effect on the enzymatic activity of the enzyme, as the specific activity of the enzyme was comparable to the wild-type enzyme. In contrast, the mutation dramatically reduced the specific activity of the catalytic reaction. These data strongly suggested that the H188 residue had a direct role in the catalytic mechanism of the enzyme and, therefore, that the H188 residue was located in the active site of the enzyme. This lead to the conclusion that that the A-site was in fact the active site of the enzyme^[2].

Active Site Characteristics

The active site (A-site) of the fumarase enzyme is formed by residues from three of the enzyme’s four subunits (shown in ) and is located in a relatively deep pit that is removed from bulk solvent ^[3]. The residues that form the include N141b, T100b, S98b, E331c, K324c, N326c, His 188c, (the letter indicates the chain) and a water molecule. It is speculated that the is the most important active site residue, activating the water through a , which increases the basicity of the water molecule. This electron-withdrawing hydrogen bond allows the water molecule to remove the C3 proton of malate, though this model has in the active site. Complex hydrogen bonding patterns in the active site also help stabilize the aci-carboxylate intermediate^[2]. By increasing the stabilization if the intermediate, the fumarase enzyme can effectively catalyze the hydration/dehydration reaction between L-malate and fumarate.

ReferencesReferences

↑ Weaver,T. Structure of free fumarase C from Escherichia coli. Acta Crystallographica (2005), D61, 1395-1401. [http://dx.doi.org/10.1107/S0907444905024194 doi:10.1107/S0907444905024194]
↑ ^2.0 ^2.1 Weaver T, Lees M, Banaszak L. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site. Protein Sci. 1997 Apr;6(4):834-42. PMID:9098893
↑ Weaver TM, Levitt DG, Donnelly MI, Stevens PP, Banaszak LJ. The multisubunit active site of fumarase C from Escherichia coli. Nat Struct Biol. 1995 Aug;2(8):654-62. PMID:7552727

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Ann Taylor, Michal Harel, Jaime Prilusky, Karsten Theis

[Weaver,_et_al.-1] Weaver,T. Structure of free fumarase C from Escherichia coli. Acta Crystallographica (2005), D61, 1395-1401. [http://dx.doi.org/10.1107/S0907444905024194 doi:10.1107/S0907444905024194]

[Weaver-2] 2.0 ^2.1 Weaver T, Lees M, Banaszak L. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site. Protein Sci. 1997 Apr;6(4):834-42. PMID:9098893

[3] Weaver TM, Levitt DG, Donnelly MI, Stevens PP, Banaszak LJ. The multisubunit active site of fumarase C from Escherichia coli. Nat Struct Biol. 1995 Aug;2(8):654-62. PMID:7552727

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@@ Line 1: / Line 1: @@
-=Fumarase=
+==Fumarase==
+<StructureSection load='1fuo' size='340' side='right' caption='Fumarase with citrate bound to the active site (PDB profile: 1fuo)' scene = ''>
 ===Overview===
-Fumarase, also known as fumarate hydratase, functions as an enzyme in the metabolic pathway known as the Kreb’s cycle, or citric acid cycle.  As the seventh step in the pathway, fumarase catalyzes the reversible reaction converting fumarate to S-malate.  It metabolizes Fumarate in the cytosol, which becomes a byproduct of the urea cycle and amino acid catabolism. It catalyzes the addition of water to make S-Malate; therefore, the mechanism of fumarase in the reaction involves hydration of fumarate in order to form S-malate.
+'''Fumarase''', also known as fumarate hydratase, is an enzyme in the citric acid cycle. In the seventh step of the reaction pathway, fumarase catalyzes the reversible hydration reaction that converts fumarate to malate and vice versa.  Fumarase is classified as an <scene name='44/446278/Secondary_structure/2'>alpha helical protein</scene> which belongs to the L-aspartase/fumarase family. It forms a tetramer of identical subunits that <scene name='44/446278/Rainbow_subunits/1'>alternate in orientation</scene>. Each subunit is comprised of <scene name='44/446278/Domains/1'>three domains</scene>.
-===Stucture and Classification===
-Fumarase is classified as an all alpha protein which belongs to the L-aspartase/fumarase family, and the enzyme specifically consists of four identical subunits which form a tetramer.  From the four subunits, fumarase has three domains which comprise two binding sites: the active site and B site.  Although the active site has a mostly solid structure and shifts very little when it binds, the B site shifts substantially more upon binding, and this shift helps regulate affinity for molecule binding at the active site (Weaver 2005).
-[[Image:Fumarase biological unit.JPG]]
-===Mechanism of Reaction===
-Fumarase has the ability to catalyze the hydration of fumarate to malate or the dehydration of malate to fumarate.  The mechanism of fumarase in the hydration and dehydration reaction pathways remains simple, only involving three steps.  In the dehydration reaction, fumarase deprotonates a carbon atom on malate to form a carbanion (Beechmans 1998).  This deprotonation results in an aci-carboxylate intermediate (Weaver 2005).  After the intermediate forms, the acidic proton from the initial step removes the hydroxide group from the aci-carboxylate intermediate to form fumarase which then detaches from the active site of fumarase, completing the reaction (Rose, Weaver, 2004).  In the active site, amino acid residues involved in binding the substrate are located on three subunits: Thr100, Ser139, Ser140, and Asn141 from the b-subunit, Thr187 and His188 on the d-subunit, and Lys324 and Asn326 of the c-subunit (Beechmans 198).  The B site is located in a π-helix turn between the active site and solvent, and it includes residues Arg126, Lys127, Val128, His129, Pro130, Asn131, and  Asp132 all on the b-subunit.  Two hydrogen bonds initiate the binding of Asn131 and Asp132 residues with S-malate (Rose, Weaver, 2004).
-<Structure load='1fuo' size='500' frame='true' align='right' caption='fumarase bound to citrate' scene='Insert optional scene name here' />
-===Enzyme Kinetics===
-Fumarase catalyzes the reversible reaction between S-malate and fumarate in the citric acid cycle for cellular metabolism.  When it catalyzes the addition of water to S-malate in order to form fumarate, the Km and Vmax values are 0.30 mM and 129 s^-1, respectively.  The reverse reaction (dehydration of fumarate to form S-malate) has a Km of 0.10 mM and Vmax of 60 s^-1 (Rose, Weaver 2004).  Thus, the forward pathway (fumarate to S-malate) is favored because of its higher Km and Vmax values.  According to Beechmans (1998), fumarase kinetics normally follows Michaelis-Menten kinetic plots with low concentrations of substrate, but high concentrations influence the enzyme’s activity.  Enzyme kinetics studies with fumarase mutants differ from wild type fumarase kinetics when the mutations alter amino acid residues involved in binding at the active site and B site.  Also, the Michaelis-Menten kinetics plots for fumarase mutants exhibit a sigmoidal curve which suggests the presence of cooperativity in the enzymes activity.
-===Regulation===
-Similar to numerous other enzymes involved in biological processes, fumarase can be regulated in several different ways.  Allosteric effects commonly regulate fumarase activity via substrate and inhibitor binding to the active site.  Fumarase activity is both positively and negatively regulated by substrate concentration.  When the concentration of a substrate is five times the Km value, it activates fumarase’s activity; however, substrate concentrations above 0.1 M result in inhibition of fumarase function (Beeckmans 1998).  The concentration of substrate influences cooperativity of fumarase, depending on the availability of substrate to bind to domains.
-The regulation of fumarase via allosteric effects involves conformational changes that occur when a substrate binds to the active site.  Studies of the active site and B site amino acid residue manipulation show that the B site helps regulate the binding affinity for the active site by allosteric effects (Rose & Weaver 2004, Beeckmans 1998).  According to Weaver (2004), the active site and B site are located 12 Å apart which suggests that the conformational changes resulting from the B site binding influence the active site affinity to bind with the substrate.  Inhibitors also regulate the activity of an enzyme via binding to the active site.  Both citrate and succinate are known as competitive inhibitors of fumarase since they negatively influence the enzyme’s activity.  They are competitive inhibitors because they have structural similarity to the substrate; therefore, the inhibitors compete with substrates to bind with the active site.
+==Structure:  will the real active site please stand?==
+Crystal structures of fumarase C revealed that the enzyme has two dicarboxylate binding sites; one was called the A site, and the second, the B site.  This raises the question: which of the two sites is the active site of the enzyme?  The A site shows relatively little change upon substrate binding, while the B site shifts substantially. <ref name="Weaver, et al."> Weaver,T.  Structure of free fumarase C from ''Escherichia coli''. ''Acta Crystallographica'' (2005), '''D61''', 1395-1401. ['''http://dx.doi.org/10.1107/S0907444905024194''' doi:10.1107/S0907444905024194]</ref>. But these changes could account for regulation...so which site is the true active site?
+In order to answer this question, an experiment that tested each of the sites independently was conducted. Both sites contain histidine residues: <scene name='44/446278/His_188/1'>His 188</scene> in the A-site and <scene name='44/446278/His_129/1'>His 129</scene> in the B-site.  These sites were mutated to asparagine in separate experiments, and the effect on kinetics was measured. The results of the experiment showed that the H129N mutation had little effect on the enzymatic activity of the enzyme, as the specific activity of the enzyme was comparable to the wild-type enzyme. In contrast, the <scene name='72/726367/Ans_188_mutant/1'>H188N</scene> mutation dramatically reduced the specific activity of the catalytic reaction. These data strongly suggested that the H188 residue had a direct role in the catalytic mechanism of the enzyme and, therefore, that the H188 residue was located in the active site of the enzyme.  This lead to the conclusion that that the A-site was in fact the active site of the enzyme<ref name= "Weaver">PMID:9098893</ref>.
-===Other Interesting Information===
+== Active Site Characteristics ==
-Fumarase expression mainly occurs in skin, parathyroid, lymph, and colon tissues, and it is present throughout all life stages, from early development to mature adults. Fumarase comprises two specific classes which relate to the enzyme's: arrangement of subunits, metal ion requirement, and thermal stability. Class I fumarase isozymes  can change their state, become inactive upon exposure to heat or radiation, are sensitive to superoxide anions, and Fe2+ dependent.  Class II includes fumarase found in eukaryotes and prokaryotes, and they are iron-independent and thermally stable.
+The active site (A-site) of the fumarase enzyme is formed by residues from three of the enzyme’s four subunits (shown in <scene name='44/446278/Active_site_chains/3'>different colors</scene>) and is located in a relatively deep pit that is removed from bulk solvent <ref>PMID: 7552727</ref>. The residues that form the <scene name='44/446278/Active_site_residues/6'>active site</scene> include N141b, T100b, S98b, E331c, K324c, N326c, His 188c, (the letter indicates the chain) and a water molecule. It is speculated that the <scene name='44/446278/His_188_active_site/2'>H188</scene> is the most important active site residue, activating the water through a <scene name='44/446278/Short_h_bond/2'>short hydrogen bond</scene>, which increases the basicity of the water molecule. This electron-withdrawing hydrogen bond allows the water molecule to remove the C3 proton of malate, though this model has <scene name='44/446278/Citrate/2'>citrate</scene> in the active site. Complex hydrogen bonding patterns in the active site also help stabilize the aci-carboxylate intermediate<ref name= "Weaver">PMID:9098893</ref>. By increasing the stabilization if the intermediate, the fumarase enzyme can effectively catalyze the hydration/dehydration reaction between L-malate and fumarate.
-Mutations in the gene that encodes fumarase can lead to a deficiency in fumarase enzyme in the citric acid cycle which is known to cause certain diseases.  Autosomal recessive mutants can result in fumarase deficiency, a metabolic disorder distinguished by excess fumaric acid in the body (Remes 1992). Inheritance of this autosomal recessive mutation has serious effects on early neural and brain development and can be fatal.  Also, heterozygous fumarase mutations play a role in cancerous tumor development; specifically, the mutant H153R has identified as a factor in three families of malignant tumor growths (Kokko 2006).
+</StructureSection>
+===References===
+<references/>