Succinyl coenzyme A synthetase
Encyclopedia
Succinyl Coenzyme A Synthetase (SCS, also known as Succinyl-CoA Synthetase or Succinate Thiokinase or Succinate-CoA Ligase) is an enzyme that catalyzes
the reversible reaction of succinyl-CoA
to succinate. The enzyme facilitates the coupling of this reaction to the formation of a nucleoside triphosphate
molecule (either GTP
or ATP
) from an inorganic phosphate molecule and a nucleoside diphosphate molecule (either GDP
or ADP
). It plays a key role as one of the catalysts involved in the citric acid cycle
, a central pathway in cellular metabolism
, and it is located within the mitochondrial matrix
of a cell.
:
Where Pi denotes inorganic phosphate, NDP denotes nucleoside diphosphate (either GDP or ADP), and NTP denotes nucleoside triphosphate (either GTP or ATP). As mentioned, the enzyme facilitates coupling of the conversion of succinyl CoA to succinate with the formation of NTP from NDP and Pi. The reaction is has a biochemical standard state free energy
change of -3.4 kJ/mol. The reaction takes place by a three-step mechanism
which is depicted in Image 1. The first step involves displacement of CoA
from succinyl CoA by a nucleophilic
inorganic phosphate molecule to form succinyl phosphate. The enzyme then utilizes a histidine
residue to remove the phosphate group from succinyl CoA and generate succinate. Finally, the phosphorylated histidine transfers the phosphate group to a nucleoside diphosphate, which generates the high-energy carrying nucleoside triphosphate.
. In E. coli two αβ heterodimers
link together to form an α2β2 heterotetramer
ic structure. However, mammalian mitochondrial SCSs are active as αβ dimers and do not form a heterotramer.
The E. coli SCS heterotetramer has been crystallized and characterized in great detail. As can be seen in Image 2, the two α subunits (pink and green) reside on opposite sides of the structure and the two β subunits (yellow and blue) interact in the middle region of the protein. The two α subunits only interact with a single β unit, whereas the β units interact with a single α unit (to form the αβ dimer) and the β subunit of the other αβ dimer. A short amino acid chain links the two β subunits which gives rise to the tetrameric structure.
The crystal structure of Succinyl-CoA synthetase alpha subunit (succinyl-CoA-binding isoform) was determined by Joyce et al. to a resolution of 2.10 A, with PDB
code 1CQJ. http://www.rcsb.org/pdb/explore.do?structureId=1CQJ.
experiments have determined that two glutamate residues (one near the catalytic histidine, Glu208α and one near the ATP grasp domain, Glu197β) play a role in the phosphorylation and dephosphorylation of the histidine, but the exact mechanism by which the enzyme changes conformation is not fully understood.
s, one that specifies synthesis of ADP
, and one that synthesisesGDP
.
- ADP-forming - - GDP-forming - ,
The GTP form is the one more commonly used in the human citric acid cycle.
. Research studies have shown that E. coli SCSs can catalyze either GTP or ATP formation. However, mammals possess different types of SCSs that are specific for either GTP (G-SCS) or ATP (A-SCS) and are native to different types of tissue within the organism. An interesting study using pigeon cells showed that GTP specific SCSs were located in pigeon liver cells, and ATP specific SCSs were located in the pigeon breast muscle cells. Further research revealed a similar phenomenon of GTP and ATP specific SCSs in rat, mouse, and human tissue. It appears that tissue typically involved in anabolic metabolism
(like the liver and kidneys) express G-SCS, whereas tissue involved in catabolic metabolism
(like the brain, the heart, and muscular tissue) express A-SCS.
Formation of Metabolic Intermediates: SCS facilitates the flux of molecules into other metabolic pathways by controlling the interconversion between succinyl CoA and succinate. This is important because succinyl CoA is an intermediate necessary for porphyrin
, heme
, and ketone body biosynthesis
.
Regulation and Inhibition: Investigation into the regulation of SCS in E. coli has shown that the enzyme is regulated
at the transcriptional level. It has been demonstrated that the gene for SCS (sucCD) is transcribed
along with the gene for α-ketoglutarate dehydrogenase (sucAB) under the control of a promoter called sdhC, which is part of the succinate dehydrogenase operon
. This operon is up-regulated by the presence of oxygen and responds to a variety of carbon sources.
Antibacterial drugs that prevent phosphorylation of histidine, like the molecule LY26650, are potent inhibitors of bacterial SCSs.
Optimal Activity: Measurements (performed using a soy bean SCS) indicate an optimal temperature of 37°C and an optimal pH of 7.0-8.0.
, which is a disease in infants that is characterized by the build-up of toxic levels of lactic acid. The condition (when it is most severe) results in death usually within 2–4 days after birth. It has been determined that patients with the condition display a two base pair
deletion within the gene known as SUCLG1
that encodes the α subunit of SCS. As a result, functional SCS is absent in metabolism causing a major imbalance in flux between glycolysis
and the citric acid cycle. Since the cells do not have a functional citric acid cycle, acidosis results because cells are forced to choose lactic acid production
as the primary means of producing ATP.
Succinate dehydrogenase
Succinate-CoA ligase (ADP-forming)
Succinate-CoA ligase (GDP-forming)
Catalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
the reversible reaction of succinyl-CoA
Succinyl-CoA
Succinyl-Coenzyme A, abbreviated as Succinyl-CoA or SucCoA, is a combination of succinic acid and coenzyme A.-Source:It is an important intermediate in the citric acid cycle, where it is synthesized from α-Ketoglutarate by α-ketoglutarate dehydrogenase through decarboxylation...
to succinate. The enzyme facilitates the coupling of this reaction to the formation of a nucleoside triphosphate
Nucleoside triphosphate
Nucleoside triphosphate is a nucleoside with three phosphates. Natural nucleoside triphosphates include adenosine triphosphate , guanosine triphosphate , cytidine triphosphate , 5-methyluridine triphosphate , and uridine triphosphate . These terms refer to those nucleoside triphosphates that...
molecule (either GTP
Guanosine triphosphate
Guanosine-5'-triphosphate is a purine nucleoside triphosphate. It can act as a substrate for the synthesis of RNA during the transcription process...
or ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
) from an inorganic phosphate molecule and a nucleoside diphosphate molecule (either GDP
Guanosine diphosphate
Guanosine diphosphate, abbreviated GDP, is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside guanosine. GDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase guanine....
or ADP
Adenosine diphosphate
Adenosine diphosphate, abbreviated ADP, is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside adenosine. ADP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase adenine....
). It plays a key role as one of the catalysts involved in the citric acid cycle
Citric acid cycle
The citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or the Szent-Györgyi-Krebs cycle — is a series of chemical reactions which is used by all aerobic living organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and...
, a central pathway in cellular metabolism
Metabolism
Metabolism is the set of chemical reactions that happen in the cells of living organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories...
, and it is located within the mitochondrial matrix
Mitochondrial matrix
In the mitochondrion, the matrix contains soluble enzymes that catalyze the oxidation of pyruvate and other small organic molecules.The mitochondrial matrix also contains the mitochondria's DNA and ribosomes. The word "matrix" stems from the fact that this space is viscous, compared to the...
of a cell.
Chemical Reaction and Enzyme Mechanism
Succinyl CoA Synthetase catalyzes the following reversible reactionReversible reaction
A reversible reaction is a chemical reaction that results in an equilibrium mixture of reactants and products. For a reaction involving two reactants and two products this can be expressed symbolically as...
:
- Succinyl CoA + Pi + NDP ↔ Succinate + CoA + NTP
Where Pi denotes inorganic phosphate, NDP denotes nucleoside diphosphate (either GDP or ADP), and NTP denotes nucleoside triphosphate (either GTP or ATP). As mentioned, the enzyme facilitates coupling of the conversion of succinyl CoA to succinate with the formation of NTP from NDP and Pi. The reaction is has a biochemical standard state free energy
Gibbs free energy
In thermodynamics, the Gibbs free energy is a thermodynamic potential that measures the "useful" or process-initiating work obtainable from a thermodynamic system at a constant temperature and pressure...
change of -3.4 kJ/mol. The reaction takes place by a three-step mechanism
Reaction mechanism
In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical change occurs.Although only the net chemical change is directly observable for most chemical reactions, experiments can often be designed that suggest the possible sequence of steps in...
which is depicted in Image 1. The first step involves displacement of CoA
Coenzyme A
Coenzyme A is a coenzyme, notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in the citric acid cycle. All sequenced genomes encode enzymes that use coenzyme A as a substrate, and around 4% of cellular enzymes use it as a substrate...
from succinyl CoA by a nucleophilic
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...
inorganic phosphate molecule to form succinyl phosphate. The enzyme then utilizes a histidine
Histidine
Histidine Histidine, an essential amino acid, has a positively charged imidazole functional group. It is one of the 22 proteinogenic amino acids. Its codons are CAU and CAC. Histidine was first isolated by German physician Albrecht Kossel in 1896. Histidine is an essential amino acid in humans...
residue to remove the phosphate group from succinyl CoA and generate succinate. Finally, the phosphorylated histidine transfers the phosphate group to a nucleoside diphosphate, which generates the high-energy carrying nucleoside triphosphate.
Subunits
Bacterial and mammalian SCSs are made up of α and β subunitsProtein subunit
In structural biology, a protein subunit or subunit protein is a single protein molecule that assembles with other protein molecules to form a protein complex: a multimeric or oligomeric protein. Many naturally occurring proteins and enzymes are multimeric...
. In E. coli two αβ heterodimers
Protein dimer
In biochemistry, a dimer is a macromolecular complex formed by two, usually non-covalently bound, macromolecules like proteins or nucleic acids...
link together to form an α2β2 heterotetramer
Heterotetramer
A heterotetramer is protein containing four non-covalently bound subunits, wherein the subunits are not all identical. A homotetramer contains four identical subunits....
ic structure. However, mammalian mitochondrial SCSs are active as αβ dimers and do not form a heterotramer.
The E. coli SCS heterotetramer has been crystallized and characterized in great detail. As can be seen in Image 2, the two α subunits (pink and green) reside on opposite sides of the structure and the two β subunits (yellow and blue) interact in the middle region of the protein. The two α subunits only interact with a single β unit, whereas the β units interact with a single α unit (to form the αβ dimer) and the β subunit of the other αβ dimer. A short amino acid chain links the two β subunits which gives rise to the tetrameric structure.
The crystal structure of Succinyl-CoA synthetase alpha subunit (succinyl-CoA-binding isoform) was determined by Joyce et al. to a resolution of 2.10 A, with PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
code 1CQJ. http://www.rcsb.org/pdb/explore.do?structureId=1CQJ.
Catalytic Residues
Crystal structures for the E. coli SCS provide evidence that the coenzyme A binds within each α-subunit (within a Rossman fold) in close proximity to a histidine residue (His246α). This histidine residue becomes phosphorylated during the succinate forming step in the reaction mechanism. The exact binding location of succinate is not well-defined. The formation of the nucleoside triphosphate occurs in an ATP grasp domain, which is located near the N-terminus of the each β subunit. However, this grasp domain is located about 35 Å away from the phosphorylated histidine residue. This leads researchers to believe that the enzyme must undergo a major change in conformation to bring the histidine to the grasp domain and facilitate the formation of the nucleoside triphosphate. MutagenesisMutagenesis
Mutagenesis is a process by which the genetic information of an organism is changed in a stable manner, resulting in a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using laboratory procedures...
experiments have determined that two glutamate residues (one near the catalytic histidine, Glu208α and one near the ATP grasp domain, Glu197β) play a role in the phosphorylation and dephosphorylation of the histidine, but the exact mechanism by which the enzyme changes conformation is not fully understood.
Isoforms
Johnson et al. describe two isoforms of succinyl-CoA synthetase in mammalMammal
Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...
s, one that specifies synthesis of ADP
Adenosine diphosphate
Adenosine diphosphate, abbreviated ADP, is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside adenosine. ADP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase adenine....
, and one that synthesisesGDP
Guanosine diphosphate
Guanosine diphosphate, abbreviated GDP, is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside guanosine. GDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase guanine....
.
- ADP-forming - - GDP-forming - ,
The GTP form is the one more commonly used in the human citric acid cycle.
Biological Function
Generation of Nucleoside Triphosphates: SCS is the only enzyme in the citric acid cycle that catalyzes a reaction in which a nucleoside triphosphate (GTP or ATP) is formed by substrate-level phosphorylationSubstrate-level phosphorylation
Substrate-level phosphorylation is a type of metabolism that results in the formation and creation of adenosine triphosphate or guanosine triphosphate by the direct transfer and donation of a phosphoryl group to adenosine diphosphate or guanosine diphosphate from a phosphorylated reactive...
. Research studies have shown that E. coli SCSs can catalyze either GTP or ATP formation. However, mammals possess different types of SCSs that are specific for either GTP (G-SCS) or ATP (A-SCS) and are native to different types of tissue within the organism. An interesting study using pigeon cells showed that GTP specific SCSs were located in pigeon liver cells, and ATP specific SCSs were located in the pigeon breast muscle cells. Further research revealed a similar phenomenon of GTP and ATP specific SCSs in rat, mouse, and human tissue. It appears that tissue typically involved in anabolic metabolism
Anabolism
Anabolism is the set of metabolic pathways that construct molecules from smaller units. These reactions require energy. One way of categorizing metabolic processes, whether at the cellular, organ or organism level is as 'anabolic' or as 'catabolic', which is the opposite...
(like the liver and kidneys) express G-SCS, whereas tissue involved in catabolic metabolism
Catabolism
Catabolism is the set of metabolic pathways that break down molecules into smaller units and release energy. In catabolism, large molecules such as polysaccharides, lipids, nucleic acids and proteins are broken down into smaller units such as monosaccharides, fatty acids, nucleotides, and amino...
(like the brain, the heart, and muscular tissue) express A-SCS.
Formation of Metabolic Intermediates: SCS facilitates the flux of molecules into other metabolic pathways by controlling the interconversion between succinyl CoA and succinate. This is important because succinyl CoA is an intermediate necessary for porphyrin
Porphyrin
Porphyrins are a group of organic compounds, many naturally occurring. One of the best-known porphyrins is heme, the pigment in red blood cells; heme is a cofactor of the protein hemoglobin. Porphyrins are heterocyclic macrocycles composed of four modified pyrrole subunits interconnected at...
, heme
Heme
A heme or haem is a prosthetic group that consists of an iron atom contained in the center of a large heterocyclic organic ring called a porphyrin. Not all porphyrins contain iron, but a substantial fraction of porphyrin-containing metalloproteins have heme as their prosthetic group; these are...
, and ketone body biosynthesis
Biosynthesis
Biosynthesis is an enzyme-catalyzed process in cells of living organisms by which substrates are converted to more complex products. The biosynthesis process often consists of several enzymatic steps in which the product of one step is used as substrate in the following step...
.
Regulation and Inhibition: Investigation into the regulation of SCS in E. coli has shown that the enzyme is regulated
Transcriptional regulation
Transcriptional regulation is the change in gene expression levels by altering transcription rates. -Regulation of transcription:Regulation of transcription controls when transcription occurs and how much RNA is created...
at the transcriptional level. It has been demonstrated that the gene for SCS (sucCD) is transcribed
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...
along with the gene for α-ketoglutarate dehydrogenase (sucAB) under the control of a promoter called sdhC, which is part of the succinate dehydrogenase operon
Operon
In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal or promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo trans-splicing to create...
. This operon is up-regulated by the presence of oxygen and responds to a variety of carbon sources.
Antibacterial drugs that prevent phosphorylation of histidine, like the molecule LY26650, are potent inhibitors of bacterial SCSs.
Optimal Activity: Measurements (performed using a soy bean SCS) indicate an optimal temperature of 37°C and an optimal pH of 7.0-8.0.
Role in Disease
Fatal Infantile Lactic Acidosis: Defective SCS has been implemented as a cause of Fatal Infantile Lactic AcidosisLactic acidosis
Lactic acidosis is a physiological condition characterized by low pH in body tissues and blood accompanied by the buildup of lactate especially D-lactate, and is considered a distinct form of metabolic acidosis. The condition typically occurs when cells receive too little oxygen , for example...
, which is a disease in infants that is characterized by the build-up of toxic levels of lactic acid. The condition (when it is most severe) results in death usually within 2–4 days after birth. It has been determined that patients with the condition display a two base pair
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
deletion within the gene known as SUCLG1
SUCLG1
Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial is an enzyme that in humans is encoded by the SUCLG1 gene.- Interactive pathway map :-Further reading:...
that encodes the α subunit of SCS. As a result, functional SCS is absent in metabolism causing a major imbalance in flux between glycolysis
Glycolysis
Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+...
and the citric acid cycle. Since the cells do not have a functional citric acid cycle, acidosis results because cells are forced to choose lactic acid production
Lactic acid fermentation
Lactic acid fermentation is a biological process by which sugars such as glucose, fructose, and sucrose, are converted into cellular energy and the metabolic byproduct lactate. It is an anaerobic fermentation reaction that occurs in some bacteria and animal cells, such as muscle cells, in the...
as the primary means of producing ATP.
See also
Citric Acid CycleCitric acid cycle
The citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or the Szent-Györgyi-Krebs cycle — is a series of chemical reactions which is used by all aerobic living organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and...
Succinate dehydrogenase
Succinate-CoA ligase (ADP-forming)
Succinate-CoA ligase (ADP-forming)
In enzymology, a succinate-CoA ligase is an enzyme that catalyzes the chemical reactionThe 3 substrates of this enzyme are ATP, succinate, and CoA, whereas its 3 products are ADP, phosphate, and succinyl-CoA....
Succinate-CoA ligase (GDP-forming)
Succinate-CoA ligase (GDP-forming)
In enzymology, a succinate-CoA ligase is an enzyme that catalyzes the chemical reactionThe 3 substrates of this enzyme are GTP, succinate, and CoA, whereas its 3 products are GDP, phosphate, and succinyl-CoA....