Fumarase 2: Difference between revisions

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===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 (see image on right). 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 <ref>Weaver,T. Structure of free fumarase C from 'Escherichia coli. Acta Crystallographica' (2005). [http://dx.doi.org/10.1107 ~~DOI~~: 10.1107 </ref>

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 (see image on right). 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 <ref name="Weaver"> 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>

===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 <scene name='Vas_Sandbox_1/Active_site/1'>active site</scene>, 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).

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. 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 <scene name='Vas_Sandbox_1/Active_site/1'>active site</scene>, 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).

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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 <scene name='Vas_Sandbox_1/Malate_interaction/1'>malate interactions</scene>

with the B site 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. The natural state of fumarase commonly involves <scene name='Vas_Sandbox_1/citrate_interactions/1'>citrate interaction</scene> with the active site in which similar amino acid residues responsible for binding with a substrate result in binding with a citrate molecule.

with the B site influence the active site affinity to bind with the substrate <ref name="Weaver"/>. 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. The natural state of fumarase commonly involves <scene name='Vas_Sandbox_1/citrate_interactions/1'>citrate interaction</scene> with the active site in which similar amino acid residues responsible for binding with a substrate result in binding with a citrate molecule.

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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.

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).

===References===

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@@ Line 8: / Line 8: @@
 ===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 (see image on right).  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 <ref>Weaver,T.  Structure of free fumarase C from 'Escherichia coli. Acta Crystallographica' (2005). [http://dx.doi.org/10.1107 DOI: 10.1107 </ref>
+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 (see image on right).  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 <ref name="Weaver"> 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>
 ===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 <scene name='Vas_Sandbox_1/Active_site/1'>active site</scene>, 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).
+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.  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 <scene name='Vas_Sandbox_1/Active_site/1'>active site</scene>, 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='400' frame='true' align='right' caption='Fumarase with substrates bound to active site and B site (PDB profile: 1fuo)'/>
@@ Line 24: / Line 24: @@
 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 <scene name='Vas_Sandbox_1/Malate_interaction/1'>malate interactions</scene>
-with the B site 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.  The natural state of fumarase commonly involves <scene name='Vas_Sandbox_1/citrate_interactions/1'>citrate interaction</scene> with the active site in which similar amino acid residues responsible for binding with a substrate result in binding with a citrate molecule.
+with the B site influence the active site affinity to bind with the substrate <ref name="Weaver"/>.  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.  The natural state of fumarase commonly involves <scene name='Vas_Sandbox_1/citrate_interactions/1'>citrate interaction</scene> with the active site in which similar amino acid residues responsible for binding with a substrate result in binding with a citrate molecule.
@@ Line 30: / Line 30: @@
 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.
 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).
+===References===
+<references />