Serine dehydratase
Encyclopedia
Serine Dehydratase or L-Serine Ammonia Lyase
(SDH) is in the ß-family of Pyridoxal Phosphate-dependent (PLP) enzymes. SDH is found widely in nature, but its structural and chemical properties vary greatly among species. SDH is found in yeast
, bacteria, and the cytoplasm
of mammalian hepatocytes. The mechanism it catalyzes is the deamination
of L-serine to yield pyruvate, with the release of ammonia
.
This enzyme has 1 substrate
, L-Serine, and two product
s, pyruvate and NH3
, and uses 1 cofactor
, pyridoxal phosphate (PLP). The enzyme's main role is in gluconeogenesis
in the liver's
cytoplasm
. By orienting the substrates and utilizing the PLP coenzyme, SDH lowers the activation energy
to convert L-Serine
into pyruvate, which can then be converted into glucose
.
The holoenzyme SDH contains 319 residue
s, 1 PLP cofactor
molecule, and 131 water molecules. The overall fold of the monomer
is very similar to that of other PLP-dependent enzymes of the Beta-family. The enzyme contains a large domain
(catalytic domain or PLP- binding domain) and a small domain. The domains are joined by two peptide
linkers (residues 32-35 and 138-146), with the internal gap created being the space for the active site
(Figure 1).
Figure 1 shows the large catalytic domain in purple and cyan and the small regulatory domain in green in a monomer of Serine Dehydratase. Two monomers(left and right) are shown and the coenzyme PLP is placed in the crevice between the two domains.
Two Dimers:
Two monomers of hSDS (human SDH) come together to make a dimer
. The interface between the two monomers is formed through hydrogen bonds and hydrophobic interactions. The monomer–monomer contacts involve six pairs of hydrogen bonds formed between 10 residues (Arg98
-Asn
260, Leu310
-Asn
260, and Leu265
-Lys263
). Additional interactions include a number of hydrophobic contacts between the residues Met17
, Lys21
, Asn
101, Glu102
, Ser306
, Ile308
, Ser309
, and Ile264
in each monomer
. (Figure 2).
Figure 2 shows the PLP coenzyme situated in the active site of SDH. The purple dashes are the hydrogen bonds involved. Top view of the enzyme.
Cofactor Binding Site:
The PLP cofactor is positioned in between the Beta-strands 7 and 10 of the large domain and lies on the large internal gap made between small and large domain. The cofactor is covalently bonded through a Schiff base linkage
to Lys41
. The cofactor is sandwiched between the side chain of Phe
40 and the main chain of Ala222
. Each of the polar substituents of PLP is coordinated by functional groups: the pyridinium
nitrogen of PLP is hydrogen-bonded to the side chain of Cys
303, the C3-hydroxyl group of PLP is hydrogen-bonded to the side chain of Asn
67, and the phosphate group of PLP is coordinated by main chain amides from the tetraglycine loop. (Figure 3 and Figure 4).
Figure 3 shows the hydrogen bonding in the active site of SDH. Hydrogen bonds are (red) between protein, water (blue balls) and the cofactor PLP (purple).
Figure 4 shows the alpha helices (pink) and beta sheets (yellow) involved in the secondary structure of SDH.
to pyruvate is an example of a pyridoxal phosphate-dependent (PLP) catalyzed Beta-elimination
reaction. Beta-eliminations mediated by PLP yields products that have undergone a two-electron oxidation at C-alpha. In general, beta-eliminations involve the removal of a halide
and a proton from the adjacent beta-carbon
to give a double bond
; thus, the origin of the double bond pi electrons are from the C-H bond on the beta carbon of the substrate.
Beta eliminations occur with no net oxidation or reduction
of PLP. In overall terms, the reaction
catalyzed by serine dehydratase involves two steps: catalytic elimination and a nonenzymatic hydrolysis
reaction. The main role of SDH is to lower the activation energy
of this reaction by binding the coenzyme and substrate
in a particular conformational
geometry.
Mechanistic Steps :
(In panel 1 of Figure 5)
In the SDH enzyme’s active site
, Lys41
is located above the PLP molecule with its R group
NH2 connected to C4 of PLP by a Schiff base linkage
. The phosphate
group of PLP is located in a pocket of G residues. Serine
enters the active site and its positively charged amino group attracts the negatively charged phosphate group of PLP. The intermediate PLP-Ser aldimine is created. SDH's role is to orient the serine molecule’s Calpha-H parallel to the overlapping 2p orbitals of the PLP pi system
; in other words, SDH holds serine perpendicular to the plane of the PLP ring. ( See Figure 6 for orientation of substrate with PLP).
(In panel 2 of Figure 5)
The amino group of serine
protonates the PLP phosphate
by forming a H-bond. The deprotonated amino group of Serine is now a good nucleophile
that attacks the Lys-PLP Schiff base at the C4 carbon (shown in panel 1). The Lys41 is released from PLP.
(In panel 3 of Figure 5)
The COOH group of serine
is positioned tightly in the SDH enzyme so that the serine
molecule is perpendicular to the PLP pi system
. The R group OH group participates in two hydrogen bonds with SDH’s Ala222
and the protonated phosphate of PLP. The protonated phosphate of PLP then acts as an acid
and donates its proton to hydroxyl
of serine. In a concerted fashion, the R group hydrogen of serine
is removed by Lys41 and water is released. The intermediate created is PLP-aminoacrylate.
In the reaction as the water leaves from the Beta-carbon of the substrate, the SDH orients the newly created double bond
perpendicular to the PLP plane (Figure 6). This allows the new pi bonds between Calpha and Cbeta to form resonance
with the PLP pi system. (Figure 6)
(In panel 4 of Figure 5)
Lys41
from SDH's active site attacks C4 of PLP, forming a tetrahedral intermediate.
(In panel 5 of Figure 5)
A Schiff base linkage
is then made and the aminoacrylate group is released as pyruvate.
(In panel 6 of Figure 5)
The aminoacrylate released from PLP is unstable in aqueous solution
and rapidly tautomer
izes to the preferred imine
form; this is spontaneously hydrolyzed to yield alpha-keto acid product of pyruvate. The aminoacrylate is nonezymatically deaminated
to pyruvate by hydrolysis
. The enzyme-PLP Schiff base linkage is reformed.
Figure 5 shows the mechanism of converting L-Serine into Pyruvate. The Figure displays the SDH active site, PLP coenzyme and substrate.
Figure 6 shows the role of SDH in orienting the PLP molecule perpendicular to the substrate Serine.
and D-serine
competitively inhibit the enzyme SDH. The reason that SDH activity is inhibited by L-cysteine is because an inorganic sulfur
is created from L-Cysteine
via Cystine Desulfrase and sulfur-containing groups are known to promote inhibition. In addition, researchers have shown that L-threonine competitively inhibits Serine Dehydratase as well.
Moreover, insulin is known to accelerate glycolysis
and repress induction of liver serine dehydratase in adult diabetic rats. Studies have been conducted to show insulin
causes a 40-50% inhibition of the induction serine dehydratase by glucagon
in hepatocytes of rats. Studies have also shown that insulin
and epinephrine
inhibit Serine Dehydratase activity by inhibiting transcription
of the SDH gene in the hepatocytes. Similarly, increasing levels of glucagon
, increase the activity of SDH because this hormone
up-regulates the SDH enzyme. This makes sense in the context of gluconeogenesis
. The main role of SDH is to create pyruvate that can be converted into free glucose. And glucagon
gives the signal to up-regulate gluconeogenesis and increase the amount of free glucose in the blood.
Homocysteine
, a compound that SDH combines with Serine to create cystathionine
, also noncompetitively inhibits the action of SDH. Studies have shown that homocysteine reacts with SDH's PLP coenzyme to create a complex. This complex is devoid of coenzyme activity and SDH is not able to function (See Enzyme Mechanism Section).
In general, homocysteine is an amino acid and metabolite of methionine
; increased levels of homocysteine can lead to homocystinuria
(see section Disease Relevance).
cleavage enzymes rather than SDH.
Studies show that the SDH enzyme from rat hepatocytes plays an important role in gluconeogenesis; its activity is augmented by high-protein diets and starvation. During periods of low carbohydrates, serine is converted into pyruvate via SDH. This pyruvate enters the mitochondria where it can be converted into oxaloacetate, and, thus, glucose.
Figure 7 shows the possible routes of L-Serine conversion into glucose during gluconeogenesis.
However, interestingly, little is known about the properties and the function of human SDH because human liver has low SDH activity. In a study done by Yoshida and Kikuchi, routes of glycine breakdown were measured. Glycine can be converted into serine and either become pyruvate via serine dehydratase or undergo oxidative cleavage into methylene-THF, ammonia
, and carbon dioxide. Results showed the secondary importance of the SDH pathway.
hyperglycemia
is due to the deficiency of threonine dehydratase, a close corollary to serine dehydratase. Serine dehydratase has also been found to be absent in human colon carcinoma and rat sarcoma
. The observed enzyme imbalance in these tumors shows that an increased capacity for the synthesis of serine is coupled to its utilization for nucleotide
biosynthesis as a part of the biochemical commitment to cellular replication in cancer cells. This pattern is found in sarcomas and carcinomas, and in tumors of human and rodent origin Thus, SDH is significant in the development of hyperglycemia
and tumors.
In addition, homocystinuria
is a hereditary disease caused by the deficiency of L-serine dehydratase. Its symptoms include mental retardation, death, atherosclerosis
, and coronary thrombosis as well as dislocation of the eye lens. Homocystinuria is a disease characterized by high urine and plasma levels of homocysteine. L-Serine dehydratase condenses homocysteine with serine to form cystathionine
.
between rat SDH and human SDH is 81% in the nucleotide sequence and 84% in the amino acid sequence. Similarities have also been shown between yeast and E.Coli threonine dehydratase and human serine dehydratase. Human SDH shows sequence homology of 27% with the yeast enzyme and 27% with the E. Coli enzyme.
Additionally, the primary structures are shown to be similar between mammalian SDH and microbial threonine dehydratase, especially in the sequences surrounding the PLP cofactor and the G-residues surrounding the PLP’s phosphate group. Thus, in PLP enzymes, there is high conservation of the active site residues during evolution. With active site sequence conservation, it is suggested that dehydratase enzymes originated from a common ancestor.
Figure 8 shows the sequence similarities of the amino acid sequence of human SDH with those of rat SDH, and yeast and E. coli threonine dehydratases. Asteriks and crosses represent sequence similarity to human SDH.
In an analysis done by Mehta and Christen from the Center for Bioinformatics and Biotechnology, the pyridoxal-5-phosphate (vitamin B6)-dependent enzymes that act on amino acid substrates have multiple evolutionary origins. The overall B6 enzymes
diverged into four independent evolutionary lines: α family (i.e. aspartate aminotransferase
), β family (serine dehydratase),D-alanine aminotransferase family and the alanine racemase
family. An example of the evolutionary similarity in the Beta family is seen in the mechanism. The β enzymes are all lyases
and catalyze reactions where Cα and Cβ participate. Overall, in the PLP
-dependent enzymes, the PLP in every case is covalently attached via an imine bond to the amino group in the active site.
Figure 9 displays the evolutionary lineage of enzymes from PLP-dependent enzyme to the Beta family to SDH.
L-serine ammonia-lyase
In enzymology, a L-serine ammonia-lyase is an enzyme that catalyzes the chemical reactionHence, this enzyme has one substrate, L-serine, and two products, pyruvate and NH3....
(SDH) is in the ß-family of Pyridoxal Phosphate-dependent (PLP) enzymes. SDH is found widely in nature, but its structural and chemical properties vary greatly among species. SDH is found in yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
, bacteria, and the cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...
of mammalian hepatocytes. The mechanism it catalyzes is the deamination
Deamination
Deamination is the removal of an amine group from a molecule. Enzymes which catalyse this reaction are called deaminases.In the human body, deamination takes place primarily in the liver, however glutamate is also deaminated in the kidneys. Deamination is the process by which amino acids are...
of L-serine to yield pyruvate, with the release of ammonia
Ammonia
Ammonia is a compound of nitrogen and hydrogen with the formula . It is a colourless gas with a characteristic pungent odour. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or...
.
This enzyme has 1 substrate
Substrate (biochemistry)
In biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate. In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or...
, L-Serine, and two product
Product (chemistry)
Product are formed during chemical reactions as reagents are consumed. Products have lower energy than the reagents and are produced during the reaction according to the second law of thermodynamics. The released energy comes from changes in chemical bonds between atoms in reagent molecules and...
s, pyruvate and NH3
Ammonia
Ammonia is a compound of nitrogen and hydrogen with the formula . It is a colourless gas with a characteristic pungent odour. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or...
, and uses 1 cofactor
Cofactor (biochemistry)
A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations....
, pyridoxal phosphate (PLP). The enzyme's main role is in gluconeogenesis
Gluconeogenesis
Gluconeogenesis is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids....
in the liver's
Liver
The liver is a vital organ present in vertebrates and some other animals. It has a wide range of functions, including detoxification, protein synthesis, and production of biochemicals necessary for digestion...
cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...
. By orienting the substrates and utilizing the PLP coenzyme, SDH lowers the activation energy
Activation energy
In chemistry, activation energy is a term introduced in 1889 by the Swedish scientist Svante Arrhenius that is defined as the energy that must be overcome in order for a chemical reaction to occur. Activation energy may also be defined as the minimum energy required to start a chemical reaction...
to convert L-Serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
into pyruvate, which can then be converted into glucose
Glucose
Glucose is a simple sugar and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate...
.
Nomenclature
Serine Dehydratase is also known as:- L-serine ammonia-lyase
- Serine deaminase
- L-hydroxyaminoacid dehydratase
- L-serine deaminase
- L-serine dehydratase
- L-serine hydro-lyase
Enzyme structure
HoloEnzyme:The holoenzyme SDH contains 319 residue
Residue (chemistry)
In chemistry, residue is the material remaining after a distillation or an evaporation, or to a portion of a larger molecule, such as a methyl group. It may also refer to the undesired byproducts of a reaction....
s, 1 PLP cofactor
Cofactor (biochemistry)
A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations....
molecule, and 131 water molecules. The overall fold of the monomer
Monomer
A monomer is an atom or a small molecule that may bind chemically to other monomers to form a polymer; the term "monomeric protein" may also be used to describe one of the proteins making up a multiprotein complex...
is very similar to that of other PLP-dependent enzymes of the Beta-family. The enzyme contains a large domain
Protein domain
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...
(catalytic domain or PLP- binding domain) and a small domain. The domains are joined by two peptide
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...
linkers (residues 32-35 and 138-146), with the internal gap created being the space for the active site
Active site
In biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues that...
(Figure 1).
Figure 1 shows the large catalytic domain in purple and cyan and the small regulatory domain in green in a monomer of Serine Dehydratase. Two monomers(left and right) are shown and the coenzyme PLP is placed in the crevice between the two domains.
Two Dimers:
Two monomers of hSDS (human SDH) come together to make a dimer
Protein dimer
In biochemistry, a dimer is a macromolecular complex formed by two, usually non-covalently bound, macromolecules like proteins or nucleic acids...
. The interface between the two monomers is formed through hydrogen bonds and hydrophobic interactions. The monomer–monomer contacts involve six pairs of hydrogen bonds formed between 10 residues (Arg98
Arginine
Arginine is an α-amino acid. The L-form is one of the 20 most common natural amino acids. At the level of molecular genetics, in the structure of the messenger ribonucleic acid mRNA, CGU, CGC, CGA, CGG, AGA, and AGG, are the triplets of nucleotide bases or codons that codify for arginine during...
-Asn
ASN
ASN may refer to:Organisations:* ASN Bank in the Netherlands* American Society of Nephrology* American Society for Neurochemistry* American Society of Neuroimaging* American Society for Nutrition...
260, Leu310
Leucine
Leucine is a branched-chain α-amino acid with the chemical formula HO2CCHCH2CH2. Leucine is classified as a hydrophobic amino acid due to its aliphatic isobutyl side chain. It is encoded by six codons and is a major component of the subunits in ferritin, astacin and other 'buffer' proteins...
-Asn
ASN
ASN may refer to:Organisations:* ASN Bank in the Netherlands* American Society of Nephrology* American Society for Neurochemistry* American Society of Neuroimaging* American Society for Nutrition...
260, and Leu265
Leucine
Leucine is a branched-chain α-amino acid with the chemical formula HO2CCHCH2CH2. Leucine is classified as a hydrophobic amino acid due to its aliphatic isobutyl side chain. It is encoded by six codons and is a major component of the subunits in ferritin, astacin and other 'buffer' proteins...
-Lys263
Lysine
Lysine is an α-amino acid with the chemical formula HO2CCH4NH2. It is an essential amino acid, which means that the human body cannot synthesize it. Its codons are AAA and AAG....
). Additional interactions include a number of hydrophobic contacts between the residues Met17
Methionine
Methionine is an α-amino acid with the chemical formula HO2CCHCH2CH2SCH3. This essential amino acid is classified as nonpolar. This amino-acid is coded by the codon AUG, also known as the initiation codon, since it indicates mRNA's coding region where translation into protein...
, Lys21
Lysine
Lysine is an α-amino acid with the chemical formula HO2CCH4NH2. It is an essential amino acid, which means that the human body cannot synthesize it. Its codons are AAA and AAG....
, Asn
ASN
ASN may refer to:Organisations:* ASN Bank in the Netherlands* American Society of Nephrology* American Society for Neurochemistry* American Society of Neuroimaging* American Society for Nutrition...
101, Glu102
Glutamic acid
Glutamic acid is one of the 20 proteinogenic amino acids, and its codons are GAA and GAG. It is a non-essential amino acid. The carboxylate anions and salts of glutamic acid are known as glutamates...
, Ser306
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
, Ile308
Isoleucine
Isoleucine is an α-amino acid with the chemical formula HO2CCHCHCH2CH3. It is an essential amino acid, which means that humans cannot synthesize it, so it must be ingested. Its codons are AUU, AUC and AUA....
, Ser309
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
, and Ile264
Isoleucine
Isoleucine is an α-amino acid with the chemical formula HO2CCHCHCH2CH3. It is an essential amino acid, which means that humans cannot synthesize it, so it must be ingested. Its codons are AUU, AUC and AUA....
in each monomer
Monomer
A monomer is an atom or a small molecule that may bind chemically to other monomers to form a polymer; the term "monomeric protein" may also be used to describe one of the proteins making up a multiprotein complex...
. (Figure 2).
Figure 2 shows the PLP coenzyme situated in the active site of SDH. The purple dashes are the hydrogen bonds involved. Top view of the enzyme.
Cofactor Binding Site:
The PLP cofactor is positioned in between the Beta-strands 7 and 10 of the large domain and lies on the large internal gap made between small and large domain. The cofactor is covalently bonded through a Schiff base linkage
Schiff base
A Schiff base, named after Hugo Schiff, is a compound with a functional group that contains a carbon-nitrogen double bond with the nitrogen atom connected to an aryl or alkyl group, not hydrogen....
to Lys41
Lysine
Lysine is an α-amino acid with the chemical formula HO2CCH4NH2. It is an essential amino acid, which means that the human body cannot synthesize it. Its codons are AAA and AAG....
. The cofactor is sandwiched between the side chain of Phe
PHE
PHE may refer to:* Population Health and Environment , an approach to development that integrates health or family planning with conservation efforts* Paramount Home Entertainment* BitTorrent protocol encryption...
40 and the main chain of Ala222
Alanine
Alanine is an α-amino acid with the chemical formula CH3CHCOOH. The L-isomer is one of the 20 amino acids encoded by the genetic code. Its codons are GCU, GCC, GCA, and GCG. It is classified as a nonpolar amino acid...
. Each of the polar substituents of PLP is coordinated by functional groups: the pyridinium
Pyridinium
Pyridinium refers to the cationic form of pyridine. This can either be due to protonation of the ring nitrogen or because of addition of a substituent to the ring nitrogen, typically via alkylation. The lone pair of electrons on the nitrogen atom of pyridine is not delocalized, and thus pyridine...
nitrogen of PLP is hydrogen-bonded to the side chain of Cys
CYS
CYS may refer to:* Cysteine an amino-acid* IATA airport code for Cheyenne Regional Airport.* California Youth Symphony, a San Francisco Bay Area symphony orchestra for young musicians* Count Your Sheep, a webcomic by Adrian Ramos...
303, the C3-hydroxyl group of PLP is hydrogen-bonded to the side chain of Asn
ASN
ASN may refer to:Organisations:* ASN Bank in the Netherlands* American Society of Nephrology* American Society for Neurochemistry* American Society of Neuroimaging* American Society for Nutrition...
67, and the phosphate group of PLP is coordinated by main chain amides from the tetraglycine loop. (Figure 3 and Figure 4).
Figure 3 shows the hydrogen bonding in the active site of SDH. Hydrogen bonds are (red) between protein, water (blue balls) and the cofactor PLP (purple).
Figure 4 shows the alpha helices (pink) and beta sheets (yellow) involved in the secondary structure of SDH.
Enzyme mechanism
The degradation of serineSerine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
to pyruvate is an example of a pyridoxal phosphate-dependent (PLP) catalyzed Beta-elimination
Elimination reaction
An elimination reaction is a type of organic reaction in which two substituents are removed from a molecule in either a one or two-step mechanism...
reaction. Beta-eliminations mediated by PLP yields products that have undergone a two-electron oxidation at C-alpha. In general, beta-eliminations involve the removal of a halide
Halide
A halide is a binary compound, of which one part is a halogen atom and the other part is an element or radical that is less electronegative than the halogen, to make a fluoride, chloride, bromide, iodide, or astatide compound. Many salts are halides...
and a proton from the adjacent beta-carbon
Carbon
Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...
to give a double bond
Double bond
A double bond in chemistry is a chemical bond between two chemical elements involving four bonding electrons instead of the usual two. The most common double bond, that between two carbon atoms, can be found in alkenes. Many types of double bonds between two different elements exist, for example in...
; thus, the origin of the double bond pi electrons are from the C-H bond on the beta carbon of the substrate.
Beta eliminations occur with no net oxidation or reduction
Redox
Redox reactions describe all chemical reactions in which atoms have their oxidation state changed....
of PLP. In overall terms, the reaction
Chemical reaction
A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. Chemical reactions can be either spontaneous, requiring no input of energy, or non-spontaneous, typically following the input of some type of energy, such as heat, light or electricity...
catalyzed by serine dehydratase involves two steps: catalytic elimination and a nonenzymatic hydrolysis
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...
reaction. The main role of SDH is to lower the activation energy
Activation energy
In chemistry, activation energy is a term introduced in 1889 by the Swedish scientist Svante Arrhenius that is defined as the energy that must be overcome in order for a chemical reaction to occur. Activation energy may also be defined as the minimum energy required to start a chemical reaction...
of this reaction by binding the coenzyme and substrate
Substrate (biochemistry)
In biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate. In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or...
in a particular conformational
Chemical structure
A chemical structure includes molecular geometry, electronic structure and crystal structure of molecules. Molecular geometry refers to the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together. Molecular geometry can range from the very simple, such as...
geometry.
Mechanistic Steps :
(In panel 1 of Figure 5)
In the SDH enzyme’s active site
Active site
In biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues that...
, Lys41
Lysine
Lysine is an α-amino acid with the chemical formula HO2CCH4NH2. It is an essential amino acid, which means that the human body cannot synthesize it. Its codons are AAA and AAG....
is located above the PLP molecule with its R group
Side chain
In organic chemistry and biochemistry, a side chain is a chemical group that is attached to a core part of the molecule called "main chain" or backbone. The placeholder R is often used as a generic placeholder for alkyl group side chains in chemical structure diagrams. To indicate other non-carbon...
NH2 connected to C4 of PLP by a Schiff base linkage
Schiff base
A Schiff base, named after Hugo Schiff, is a compound with a functional group that contains a carbon-nitrogen double bond with the nitrogen atom connected to an aryl or alkyl group, not hydrogen....
. The phosphate
Phosphate
A phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
group of PLP is located in a pocket of G residues. Serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
enters the active site and its positively charged amino group attracts the negatively charged phosphate group of PLP. The intermediate PLP-Ser aldimine is created. SDH's role is to orient the serine molecule’s Calpha-H parallel to the overlapping 2p orbitals of the PLP pi system
Pi system
In mathematics, a π-system on a set Ω is a set P, consisting of certain subsets of Ω, such that* P is non-empty.* A ∩ B ∈ P whenever A and B are in P....
; in other words, SDH holds serine perpendicular to the plane of the PLP ring. ( See Figure 6 for orientation of substrate with PLP).
(In panel 2 of Figure 5)
The amino group of serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
protonates the PLP phosphate
Phosphate
A phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
by forming a H-bond. The deprotonated amino group of Serine is now a good nucleophile
Nucleophile
A nucleophile is a species that donates an electron-pair to an electrophile to form a chemical bond in a reaction. All molecules or ions with a free pair of electrons can act as nucleophiles. Because nucleophiles donate electrons, they are by definition Lewis bases.Nucleophilic describes the...
that attacks the Lys-PLP Schiff base at the C4 carbon (shown in panel 1). The Lys41 is released from PLP.
(In panel 3 of Figure 5)
The COOH group of serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
is positioned tightly in the SDH enzyme so that the serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
molecule is perpendicular to the PLP pi system
Pi system
In mathematics, a π-system on a set Ω is a set P, consisting of certain subsets of Ω, such that* P is non-empty.* A ∩ B ∈ P whenever A and B are in P....
. The R group OH group participates in two hydrogen bonds with SDH’s Ala222
Alanine
Alanine is an α-amino acid with the chemical formula CH3CHCOOH. The L-isomer is one of the 20 amino acids encoded by the genetic code. Its codons are GCU, GCC, GCA, and GCG. It is classified as a nonpolar amino acid...
and the protonated phosphate of PLP. The protonated phosphate of PLP then acts as an acid
Acid
An acid is a substance which reacts with a base. Commonly, acids can be identified as tasting sour, reacting with metals such as calcium, and bases like sodium carbonate. Aqueous acids have a pH of less than 7, where an acid of lower pH is typically stronger, and turn blue litmus paper red...
and donates its proton to hydroxyl
Hydroxyl
A hydroxyl is a chemical group containing an oxygen atom covalently bonded with a hydrogen atom. In inorganic chemistry, the hydroxyl group is known as the hydroxide ion, and scientists and reference works generally use these different terms though they refer to the same chemical structure in...
of serine. In a concerted fashion, the R group hydrogen of serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
is removed by Lys41 and water is released. The intermediate created is PLP-aminoacrylate.
In the reaction as the water leaves from the Beta-carbon of the substrate, the SDH orients the newly created double bond
Double bond
A double bond in chemistry is a chemical bond between two chemical elements involving four bonding electrons instead of the usual two. The most common double bond, that between two carbon atoms, can be found in alkenes. Many types of double bonds between two different elements exist, for example in...
perpendicular to the PLP plane (Figure 6). This allows the new pi bonds between Calpha and Cbeta to form resonance
Resonance
In physics, resonance is the tendency of a system to oscillate at a greater amplitude at some frequencies than at others. These are known as the system's resonant frequencies...
with the PLP pi system. (Figure 6)
(In panel 4 of Figure 5)
Lys41
Lysine
Lysine is an α-amino acid with the chemical formula HO2CCH4NH2. It is an essential amino acid, which means that the human body cannot synthesize it. Its codons are AAA and AAG....
from SDH's active site attacks C4 of PLP, forming a tetrahedral intermediate.
(In panel 5 of Figure 5)
A Schiff base linkage
Schiff base
A Schiff base, named after Hugo Schiff, is a compound with a functional group that contains a carbon-nitrogen double bond with the nitrogen atom connected to an aryl or alkyl group, not hydrogen....
is then made and the aminoacrylate group is released as pyruvate.
(In panel 6 of Figure 5)
The aminoacrylate released from PLP is unstable in aqueous solution
Aqueous solution
An aqueous solution is a solution in which the solvent is water. It is usually shown in chemical equations by appending aq to the relevant formula, such as NaCl. The word aqueous means pertaining to, related to, similar to, or dissolved in water...
and rapidly tautomer
Tautomer
Tautomers are isomers of organic compounds that readily interconvert by a chemical reaction called tautomerization. This reaction commonly results in the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond...
izes to the preferred imine
Imine
An imine is a functional group or chemical compound containing a carbon–nitrogen double bond, with the nitrogen attached to a hydrogen atom or an organic group. If this group is not a hydrogen atom, then the compound is known as a Schiff base...
form; this is spontaneously hydrolyzed to yield alpha-keto acid product of pyruvate. The aminoacrylate is nonezymatically deaminated
Deamination
Deamination is the removal of an amine group from a molecule. Enzymes which catalyse this reaction are called deaminases.In the human body, deamination takes place primarily in the liver, however glutamate is also deaminated in the kidneys. Deamination is the process by which amino acids are...
to pyruvate by hydrolysis
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...
. The enzyme-PLP Schiff base linkage is reformed.
Figure 5 shows the mechanism of converting L-Serine into Pyruvate. The Figure displays the SDH active site, PLP coenzyme and substrate.
Figure 6 shows the role of SDH in orienting the PLP molecule perpendicular to the substrate Serine.
Inhibitors
According to the series of assays performed by Cleland (1967), the linear rate of pyruvate formation at various concentrations of inhibitors demonstrated that L-cysteineCysteine
Cysteine is an α-amino acid with the chemical formula HO2CCHCH2SH. It is a non-essential amino acid, which means that it is biosynthesized in humans. Its codons are UGU and UGC. The side chain on cysteine is thiol, which is polar and thus cysteine is usually classified as a hydrophilic amino acid...
and D-serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
competitively inhibit the enzyme SDH. The reason that SDH activity is inhibited by L-cysteine is because an inorganic sulfur
Sulfur
Sulfur or sulphur is the chemical element with atomic number 16. In the periodic table it is represented by the symbol S. It is an abundant, multivalent non-metal. Under normal conditions, sulfur atoms form cyclic octatomic molecules with chemical formula S8. Elemental sulfur is a bright yellow...
is created from L-Cysteine
Cysteine
Cysteine is an α-amino acid with the chemical formula HO2CCHCH2SH. It is a non-essential amino acid, which means that it is biosynthesized in humans. Its codons are UGU and UGC. The side chain on cysteine is thiol, which is polar and thus cysteine is usually classified as a hydrophilic amino acid...
via Cystine Desulfrase and sulfur-containing groups are known to promote inhibition. In addition, researchers have shown that L-threonine competitively inhibits Serine Dehydratase as well.
Moreover, insulin is known to accelerate glycolysis
Glycolysis
Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+...
and repress induction of liver serine dehydratase in adult diabetic rats. Studies have been conducted to show insulin
Insulin
Insulin is a hormone central to regulating carbohydrate and fat metabolism in the body. Insulin causes cells in the liver, muscle, and fat tissue to take up glucose from the blood, storing it as glycogen in the liver and muscle....
causes a 40-50% inhibition of the induction serine dehydratase by glucagon
Glucagon
Glucagon, a hormone secreted by the pancreas, raises blood glucose levels. Its effect is opposite that of insulin, which lowers blood glucose levels. The pancreas releases glucagon when blood sugar levels fall too low. Glucagon causes the liver to convert stored glycogen into glucose, which is...
in hepatocytes of rats. Studies have also shown that insulin
Insulin
Insulin is a hormone central to regulating carbohydrate and fat metabolism in the body. Insulin causes cells in the liver, muscle, and fat tissue to take up glucose from the blood, storing it as glycogen in the liver and muscle....
and epinephrine
Epinephrine
Epinephrine is a hormone and a neurotransmitter. It increases heart rate, constricts blood vessels, dilates air passages and participates in the fight-or-flight response of the sympathetic nervous system. In chemical terms, adrenaline is one of a group of monoamines called the catecholamines...
inhibit Serine Dehydratase activity by inhibiting transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
of the SDH gene in the hepatocytes. Similarly, increasing levels of glucagon
Glucagon
Glucagon, a hormone secreted by the pancreas, raises blood glucose levels. Its effect is opposite that of insulin, which lowers blood glucose levels. The pancreas releases glucagon when blood sugar levels fall too low. Glucagon causes the liver to convert stored glycogen into glucose, which is...
, increase the activity of SDH because this hormone
Hormone
A hormone is a chemical released by a cell or a gland in one part of the body that sends out messages that affect cells in other parts of the organism. Only a small amount of hormone is required to alter cell metabolism. In essence, it is a chemical messenger that transports a signal from one...
up-regulates the SDH enzyme. This makes sense in the context of gluconeogenesis
Gluconeogenesis
Gluconeogenesis is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids....
. The main role of SDH is to create pyruvate that can be converted into free glucose. And glucagon
Glucagon
Glucagon, a hormone secreted by the pancreas, raises blood glucose levels. Its effect is opposite that of insulin, which lowers blood glucose levels. The pancreas releases glucagon when blood sugar levels fall too low. Glucagon causes the liver to convert stored glycogen into glucose, which is...
gives the signal to up-regulate gluconeogenesis and increase the amount of free glucose in the blood.
Homocysteine
Homocysteine
Homocysteine is a non-protein amino acid with the formula HSCH2CH2CHCO2H. It is a homologue of the amino acid cysteine, differing by an additional methylene group. It is biosynthesized from methionine by the removal of its terminal Cε methyl group...
, a compound that SDH combines with Serine to create cystathionine
Cystathionine
Cystathionine is an intermediate in the synthesis of cysteine.It is generated from homocysteine and serine by cystathionine beta synthase.It is cleaved into cysteine and α-ketobutyrate by cystathionine gamma-lyase....
, also noncompetitively inhibits the action of SDH. Studies have shown that homocysteine reacts with SDH's PLP coenzyme to create a complex. This complex is devoid of coenzyme activity and SDH is not able to function (See Enzyme Mechanism Section).
In general, homocysteine is an amino acid and metabolite of methionine
Methionine
Methionine is an α-amino acid with the chemical formula HO2CCHCH2CH2SCH3. This essential amino acid is classified as nonpolar. This amino-acid is coded by the codon AUG, also known as the initiation codon, since it indicates mRNA's coding region where translation into protein...
; increased levels of homocysteine can lead to homocystinuria
Homocystinuria
Homocystinuria, also known as cystathionine beta synthase deficiency or CBS deficiency, is an inherited disorder of the metabolism of the amino acid methionine, often involving cystathionine beta synthase...
(see section Disease Relevance).
Biological function
In general, SDH levels decrease with increasing mammalian size. In fact, mammals catabolize serine into pyruvate with the enzymes serine hydroxymethyltransferase and glycineGlycine
Glycine is an organic compound with the formula NH2CH2COOH. Having a hydrogen substituent as its 'side chain', glycine is the smallest of the 20 amino acids commonly found in proteins. Its codons are GGU, GGC, GGA, GGG cf. the genetic code.Glycine is a colourless, sweet-tasting crystalline solid...
cleavage enzymes rather than SDH.
Studies show that the SDH enzyme from rat hepatocytes plays an important role in gluconeogenesis; its activity is augmented by high-protein diets and starvation. During periods of low carbohydrates, serine is converted into pyruvate via SDH. This pyruvate enters the mitochondria where it can be converted into oxaloacetate, and, thus, glucose.
Figure 7 shows the possible routes of L-Serine conversion into glucose during gluconeogenesis.
However, interestingly, little is known about the properties and the function of human SDH because human liver has low SDH activity. In a study done by Yoshida and Kikuchi, routes of glycine breakdown were measured. Glycine can be converted into serine and either become pyruvate via serine dehydratase or undergo oxidative cleavage into methylene-THF, ammonia
Ammonia
Ammonia is a compound of nitrogen and hydrogen with the formula . It is a colourless gas with a characteristic pungent odour. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or...
, and carbon dioxide. Results showed the secondary importance of the SDH pathway.
Disease relevance
Although there is much controversy over the role of SDH in human hepatocytes, studies have shown that nonketoticKetosis
Ketosis is a state of elevated levels of ketone bodies in the body. It is almost always generalized throughout the body, with hyperketonemia, that is, an elevated level of ketone bodies in the blood. Ketone bodies are formed by ketogenesis when the liver glycogen stores are depleted...
hyperglycemia
Hyperglycemia
Hyperglycemia or Hyperglycæmia, or high blood sugar, is a condition in which an excessive amount of glucose circulates in the blood plasma. This is generally a glucose level higher than 13.5mmol/l , but symptoms may not start to become noticeable until even higher values such as 15-20 mmol/l...
is due to the deficiency of threonine dehydratase, a close corollary to serine dehydratase. Serine dehydratase has also been found to be absent in human colon carcinoma and rat sarcoma
Sarcoma
A sarcoma is a cancer that arises from transformed cells in one of a number of tissues that develop from embryonic mesoderm. Thus, sarcomas include tumors of bone, cartilage, fat, muscle, vascular, and hematopoietic tissues...
. The observed enzyme imbalance in these tumors shows that an increased capacity for the synthesis of serine is coupled to its utilization for nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
biosynthesis as a part of the biochemical commitment to cellular replication in cancer cells. This pattern is found in sarcomas and carcinomas, and in tumors of human and rodent origin Thus, SDH is significant in the development of hyperglycemia
Hyperglycemia
Hyperglycemia or Hyperglycæmia, or high blood sugar, is a condition in which an excessive amount of glucose circulates in the blood plasma. This is generally a glucose level higher than 13.5mmol/l , but symptoms may not start to become noticeable until even higher values such as 15-20 mmol/l...
and tumors.
In addition, homocystinuria
Homocystinuria
Homocystinuria, also known as cystathionine beta synthase deficiency or CBS deficiency, is an inherited disorder of the metabolism of the amino acid methionine, often involving cystathionine beta synthase...
is a hereditary disease caused by the deficiency of L-serine dehydratase. Its symptoms include mental retardation, death, atherosclerosis
Atherosclerosis
Atherosclerosis is a condition in which an artery wall thickens as a result of the accumulation of fatty materials such as cholesterol...
, and coronary thrombosis as well as dislocation of the eye lens. Homocystinuria is a disease characterized by high urine and plasma levels of homocysteine. L-Serine dehydratase condenses homocysteine with serine to form cystathionine
Cystathionine
Cystathionine is an intermediate in the synthesis of cysteine.It is generated from homocysteine and serine by cystathionine beta synthase.It is cleaved into cysteine and α-ketobutyrate by cystathionine gamma-lyase....
.
Evolution
Comparing human and rat serine dehydratase using a cDNA library was identical except for a 36 amino acid residue. The overall homologyHomology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
between rat SDH and human SDH is 81% in the nucleotide sequence and 84% in the amino acid sequence. Similarities have also been shown between yeast and E.Coli threonine dehydratase and human serine dehydratase. Human SDH shows sequence homology of 27% with the yeast enzyme and 27% with the E. Coli enzyme.
Additionally, the primary structures are shown to be similar between mammalian SDH and microbial threonine dehydratase, especially in the sequences surrounding the PLP cofactor and the G-residues surrounding the PLP’s phosphate group. Thus, in PLP enzymes, there is high conservation of the active site residues during evolution. With active site sequence conservation, it is suggested that dehydratase enzymes originated from a common ancestor.
Figure 8 shows the sequence similarities of the amino acid sequence of human SDH with those of rat SDH, and yeast and E. coli threonine dehydratases. Asteriks and crosses represent sequence similarity to human SDH.
In an analysis done by Mehta and Christen from the Center for Bioinformatics and Biotechnology, the pyridoxal-5-phosphate (vitamin B6)-dependent enzymes that act on amino acid substrates have multiple evolutionary origins. The overall B6 enzymes
Vitamin B6
Vitamin B6 is a water-soluble vitamin and is part of the vitamin B complex group. Several forms of the vitamin are known, but pyridoxal phosphate is the active form and is a cofactor in many reactions of amino acid metabolism, including transamination, deamination, and decarboxylation...
diverged into four independent evolutionary lines: α family (i.e. aspartate aminotransferase
Vitamin B6
Vitamin B6 is a water-soluble vitamin and is part of the vitamin B complex group. Several forms of the vitamin are known, but pyridoxal phosphate is the active form and is a cofactor in many reactions of amino acid metabolism, including transamination, deamination, and decarboxylation...
), β family (serine dehydratase),D-alanine aminotransferase family and the alanine racemase
Alanine racemase
In enzymology, an alanine racemase is an enzyme that catalyzes the chemical reactionHence, this enzyme has one substrate, L-alanine, and one product, D-alanine....
family. An example of the evolutionary similarity in the Beta family is seen in the mechanism. The β enzymes are all lyases
Vitamin B6
Vitamin B6 is a water-soluble vitamin and is part of the vitamin B complex group. Several forms of the vitamin are known, but pyridoxal phosphate is the active form and is a cofactor in many reactions of amino acid metabolism, including transamination, deamination, and decarboxylation...
and catalyze reactions where Cα and Cβ participate. Overall, in the PLP
Vitamin B6
Vitamin B6 is a water-soluble vitamin and is part of the vitamin B complex group. Several forms of the vitamin are known, but pyridoxal phosphate is the active form and is a cofactor in many reactions of amino acid metabolism, including transamination, deamination, and decarboxylation...
-dependent enzymes, the PLP in every case is covalently attached via an imine bond to the amino group in the active site.
Figure 9 displays the evolutionary lineage of enzymes from PLP-dependent enzyme to the Beta family to SDH.