View source for Fumarase

{{Short description|Type of enzyme}}
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{{infobox_gene}}
{{Infobox enzyme|image=Fumarase.png|name=Fumarase|EC_number=4.2.1.2|CAS_number=9032-88-6|GO_code=0004333}}
'''Fumarase''' (or '''fumarate hydratase''') is an [[enzyme]] ({{EnzExplorer|4.2.1.2}}) that [[catalyzes]] the reversible [[Hydration reaction|hydration]]/[[Dehydration reaction|dehydration]] of [[fumarate]] to [[malate]]. Fumarase comes in two forms: [[mitochondrial]] and [[cytosolic]]. The mitochondrial [[isoenzyme]] is involved in the [[Krebs Cycle|Krebs cycle]] and the cytosolic isoenzyme is involved in the [[metabolism]] of [[amino acids]] and fumarate. Subcellular localization is established by the presence of a signal sequence on the amino terminus in the mitochondrial form, while subcellular localization in the cytosolic form is established by the absence of the signal sequence found in the mitochondrial variety.<ref>[http://atlasgeneticsoncology.org/Genes/FHID40573ch1q42.html FH (fumarate hydratase)<!-- Bot generated title -->]</ref>

This enzyme participates in 2 [[metabolism|metabolic pathways]]: [[citric acid cycle]] and [[reverse Krebs cycle|reductive citric acid cycle]] (CO<sub>2</sub> fixation), and is also important in [[renal cell carcinoma]]. Mutations in this gene have been associated with the  development of leiomyomas in the skin and uterus in combination with renal cell carcinoma ([[Hereditary leiomyomatosis and renal cell cancer syndrome|HLRCC]] syndrome).

== Nomenclature ==
This enzyme belongs to the family of [[lyase]]s, specifically the hydro-lyases, which cleave carbon-oxygen bonds.  The [[List of enzymes|systematic name]] of this enzyme class is '''(S)-malate hydro-lyase (fumarate-forming)'''. Other names in common use include:
* fumarase
* L-malate hydro-lyase
* (S)-malate hydro-lyase

== Structure ==
=== Gene ===
[[File: 1fuo2.jpg|thumb|326 px|Fumarase C tetramer, E.coli]]
In humans, the FH gene is localized to the chromosomal position 1q42.3-q43. The FH gene contains 10 exons. 
<!-- Unsourced image removed: [[Image:GeneStructure.png|thumb|center|600x800px|border|Genomic structure of FH. Exons are represented by purple boxes with base pair number above and exon number below. Gene mutation sites associated with diseases are highlighted.  These sites are sometimes monitored in [[genetic testing]]. The image is not drawn to scale.<ref name="url_FH_fumarate_hydratase"/>]] -->

=== Protein ===
Crystal structures of fumarase C from ''[[Escherichia coli]]'' have been observed to have two dicarboxylate [[binding sites]] close to one another. These are known as the [[active site]] and the B site. These sites are connected by a series of hydrogen bonds and the access to either site is only through an opening near the enzyme surface near the B site.<ref name="pmid16204892" /> Active site is made up of three domains. Even when no ligand is bound to the active site, the binding pocket created by surrounding residues is sufficient to bind water in its place.<ref name="pmid16204892" /> Crystallographic research on the B site of the enzyme has observed that there is a shift on His129 between free and occupied states. It also suggests that the use of an [[imidazole]]-[[imidazolium]] conversion controls access to the allosteric B site.<ref name="pmid16204892">{{cite journal | vauthors = Weaver T | title = Structure of free fumarase C from Escherichia coli | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 61 | issue = Pt 10 | pages = 1395–1401 | date = October 2005 | pmid = 16204892 | doi = 10.1107/S0907444905024194 }}</ref>

=== Subtypes ===
There are two classes of fumarases, class I and class II.<ref name="url_FH_fumarate_hydratase">{{cite web | url = http://atlasgeneticsoncology.org/Genes/FHID40573ch1q42.html | title = FH (fumarate hydratase). |vauthors=Lynch AM, Morton CC | date = 2006-07-01 | publisher = Atlas of Genetics and Cytogenetics in Oncology and Haematology }}</ref> Classification depends on the arrangement of their relative subunits, their metal ion requirement, and their thermal stability.  Class I fumarases are change state or become inactive when subjected to heat or radiation, are sensitive to [[superoxide]] anion, are iron (Fe<sup>2+</sup>) dependent, and are dimeric proteins with each subunit consisting of around 120 kD. Class II fumarases, found in prokaryotes as well as in eukaryotes, are tetrameric enzymes with subunits of 200 kD that contain three distinct segments of significantly homologous amino acids.  They are also iron-independent and thermally stable. Prokaryotes are known to have three different forms of fumarase:  Fumarase A, Fumarase B, and Fumarase C. Fumarase A and Fumarase B from ''[[Escherichia coli]]'' are classified as class I, whereas Fumarase C is a part of the class II fumarases.<ref name="pmid12021453"/>

== Function ==
=== Mechanism ===
[[Image:FumaraseMechanismE1CB.png|thumb|right|400px|Figure 1: Conversion of fumarate to S-malate by fumarase through a carbanion intermediate.]]
Figure 1 depicts the fumarase reaction mechanism. Two residues catalyze proton transfer and the ionization state of these residues is in part defined by two forms of the enzyme, E<sub>1</sub> and E<sub>2</sub>. In E<sub>1</sub>, the groups exist in an internally neutralized AH/B: state, while in E<sub>2</sub>, they occur in a [[zwitterion]]ic A<sup>−</sup>/BH<sup>+</sup> state. E<sub>1</sub> binds fumarate and facilitates its transformation into malate, and E<sub>2</sub> binds malate and facilitates its transformation into fumarate. The two forms must undergo isomerization with each catalytic turnover.<ref name="isbn0-19-512258-5">{{cite book | vauthors = Hegemony AD, Frey PA | title = Enzymatic reaction mechanisms | publisher = Oxford University Press | location = Oxford [Oxfordshire] | year = 2007 | isbn = 978-0-19-512258-9 }}</ref>

[[Image:Reaction1.png|thumb|right|400px|Figure 2: Conversion of fumarate to S-malate.]]
Despite its biological significance, the reaction mechanism of fumarase is not completely understood. The reaction itself can be monitored in either direction; however, it is the formation of fumarate from S-malate in particular that is less understood due to the high [[acid dissociation constant|pK<sub>a</sub>]] value of the H<sup>R</sup> atom (Fig. 2) that is removed without the aid of any [[Cofactor (biochemistry)|cofactors]] or [[coenzymes]]. The reaction from fumarate to S-malate is better understood, and involves a [[stereospecific]] hydration of fumarate to produce S-malate by trans-addition of a [[hydroxyl]] group and a hydrogen atom. Early research into this reaction suggested that the formation of fumarate from S-malate involved dehydration of malate to a carbocationic intermediate, which then loses the alpha proton to form fumarate. This led to the conclusion that the formation of S-malate proceeds as [[E1 elimination]] - protonation of fumarate to create a carbocation was followed by the addition of a hydroxyl group from H<sub>2</sub>O. However, more recent trials have provided evidence that the mechanism actually takes place through an acid-base catalyzed elimination by means of a carbanionic intermediate, meaning it proceeds as [[E1cB elimination reaction|E1cB elimination]] (Figure 1).<ref name="isbn0-19-512258-5" /><ref name="isbn0-9747077-1-6">{{cite book | vauthors = Begley TP, McMurry J | title = The organic chemistry of biological pathways | publisher = Roberts and Co. Publishers | year = 2005 | isbn = 978-0-9747077-1-6 }}</ref><ref name="isbn0-7167-0070-0">{{cite book | vauthors = Walsh C | title = Enzymatic reaction mechanisms | publisher = W. H. Freeman | location = San Francisco | year = 1979 | isbn = 978-0-7167-0070-8 }}</ref>

=== Biochemical pathway ===
The function of fumarase in the [[citric acid cycle]] is to facilitate a transition step in the production of energy in the form of [[NADH]].<ref name="pmid21929734">{{cite journal | vauthors = Yogev O, Naamati A, Pines O | title = Fumarase: a paradigm of dual targeting and dual localized functions | journal = The FEBS Journal | volume = 278 | issue = 22 | pages = 4230–4242 | date = November 2011 | pmid = 21929734 | doi = 10.1111/j.1742-4658.2011.08359.x | doi-access = free }}</ref> In the [[cytosol]], the enzyme functions to metabolize fumarate, which is a byproduct of the [[urea cycle]] as well as amino acid catabolism. Studies have revealed that the active site is composed of amino acid residues from three of the four subunits within the tetrameric enzyme.<ref name="pmid12021453">{{cite journal | vauthors = Estévez M, Skarda J, Spencer J, Banaszak L, Weaver TM | title = X-ray crystallographic and kinetic correlation of a clinically observed human fumarase mutation | journal = Protein Science | volume = 11 | issue = 6 | pages = 1552–1557 | date = June 2002 | pmid = 12021453 | pmc = 2373640 | doi = 10.1110/ps.0201502 }}</ref><ref name="isbn0-19-512258-5"/><ref name="isbn0-9747077-1-6"/><ref name="isbn0-7167-0070-0"/>

=== Other substrates ===
The main substrates for fumarase are malate and fumarate. However, the enzyme can also catalyze the dehydration of <small>D</small>-[[tartrate]] which results in enol-[[oxaloacetate]]. Enol-oxaloacetate can then izomerize into keto-oxaloacetate. Both Fumarase A and Fumarase B have essentially the same [[Enzyme kinetics|kinetics]] for the reversible malate to fumarase conversion, but Fumarase B has a much higher catalytic efficiency for the conversion of <small>D</small>-tartrate to oxaloacetate compared to Fumarase A.<ref name = "van Vugt-Lussenburg_2021">{{cite journal | vauthors = van Vugt-Lussenburg BM, van der Weel L, Hagen WR, Hagedoorn PL | title = Biochemical similarities and differences between the catalytic [4Fe-4S] cluster containing fumarases FumA and FumB from Escherichia coli | journal = PLOS ONE | volume = 8 | issue = 2 | pages = e55549 | date = February 26, 2021 | pmid = 23405168 | pmc = 3565967 | doi = 10.1371/journal.pone.0055549 | doi-access = free }}</ref> This allows bacteria such as ''E. coli'' use <small>D</small>-tartrate for their growth; the growth of mutants with a disruptive gene ''fumB'' encoding Fumarase B on <small>D</small>-tartrate was severely impaired.<ref name = "van Vugt-Lussenburg_2021" />

== Clinical significance ==
[[Fumarase deficiency]] is characterized by [[polyhydramnios]] and fetal brain abnormalities. In the newborn period, findings include severe neurologic abnormalities, poor feeding, failure to thrive, and [[hypotonia]]. Fumarase deficiency is suspected in infants with multiple severe neurologic abnormalities in the absence of an acute metabolic crisis. Inactivity of both cytosolic and mitochondrial forms of fumarase are potential causes. Isolated, increased concentration of [[fumaric acid]] on urine organic acid analysis is highly suggestive of fumarase deficiency. Molecular genetic testing for fumarase deficiency is currently available.<ref name="url_FH_fumarate_hydratase"/>

Fumarase is prevalent in both fetal and adult tissues.  A large percentage of the enzyme is expressed in the [[skin]], [[parathyroid]], [[lymph]], and [[Colon (anatomy)|colon]]. Mutations in the production and development of fumarase have led to the discovery of several fumarase-related diseases in humans.  These include [[benign]] [[mesenchymal]] tumors of the uterus, [[leiomyomatosis]] and renal cell [[carcinoma]], and [[fumarase deficiency]].  [[Germinal mutation]]s in fumarase are associated with two distinct conditions.  If the enzyme has [[missense]] mutation and in-frame deletions from the 3’ end, fumarase deficiency results.  If it contains [[heterozygous]] 5’ missense mutation and deletions (ranging from one base pair to the whole gene), then leiomyomatosis and renal cell carcinoma/Reed’s syndrome ([[Multiple cutaneous leiomyoma|multiple cutaneous]] and uterine [[leiomyomatosis]]) could result.<ref name="pmid12021453"/><ref name="url_FH_fumarate_hydratase"/>

== Interactive pathway map ==
{{TCACycle_WP78|highlight=Fumarase}}

== See also ==
* [[Fumarase deficiency]]

== References ==
{{reflist|33em}}

== External links ==
* {{MeshName|Fumarase}}
* [https://web.archive.org/web/20061011220752/http://www.biocheminfo.org/klotho/html/fumarate.html  Structure of Fumarate]
* [https://web.archive.org/web/20061011234603/http://www.biocheminfo.org/klotho/html/L-malate.html  Structure of S-Malate]
* [http://www.biology.pomona.edu/hoopes/bio147/Fumarate%20Hydratase%20(final).doc Link to Breakdown of Citric Acid Cycle]
* [http://www.johnkyrk.com/krebs.html Video of Fumarate → (S)L-Malate] {{Webarchive|url=https://web.archive.org/web/20050625074113/http://www.johnkyrk.com/krebs.html |date=2005-06-25 }}

{{Citric acid cycle enzymes}}
{{Mitochondrial enzymes}}
{{Carbon-oxygen lyases}}
{{Enzymes}}
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[[Category:EC 4.2.1]]