Succinyl CoA Synthase and Regulation of the Enzyme - Essay Example

Succinyl CoA synthase Introduction Succinyl-CoA synthetase is a major enzyme in carbohydrate metabolism. It catalyzes substrate level phosphorylation of nucleoside diphosphate which is the only reversible reaction in the citric acid cycle. Its role is however not limited to TCA cycle; it is also essential in ketone body metabolism and in the synthesis of haem. Its abnormal activities are associated with diabetes mellitus and neurodegenerative diseases (Schomburg, 2001). Structure and activity relationship Figure1.1: 3D E. coli Succinyl-CoA synthetase crystal (Harel, 2014) Key: α subunit (grey, yellow), β subunit (green, magenta), complex with CoA and phosphate The enzyme is a tetramer with an active site in each subunit as can be seen in the above presentation. The two subunits are usually denoted as alpha and beta. The amino acid responsible for activity is the phosphorylated histidine intermediate (HIS 246 alpha) which is the residue responsible for dephosphorylation of ATP and another site is suspected to be present in the beta subunit that ensures continued metabolism. It is also suspected that there is a nucleotide binding site at the N-terminal of beta subunit (Harel, 2014). This suggests that there are two active sites which are situated approximately 35A apart and that the HIS 246 alpha loop usually moves between them while catalysis is occurring. There is also GLU 208 alpha on the alpha subunit which interacts with the active HIS 246 residue in both the phosphorylated and dephosphorylated enzyme (Harel, 2014) Catalysis Process As indicated above the histidine residue is the one involved in dephosphorylation or phosphorylation of ATP or ADP respectively. It has been proposed that the process involves a cooperative binding catalysis. Thus binding of ATP at one site enhances catalysis at another catalytic site (Schürmann et al, 2011). Binding of ATP occurs only in the presence of magnesium ion (Mg++) forming a complex which contains two ATP residue plus 2 phosphoric acid residues. If incubation is done this complex is converted to another one with 4 phosphoric acid residues per given protein. The complex with 4 phosphoric acid residues is the only one with the capability to react with succinate and CoA to give Succinyl CoA complex (Harel, 2014). This complex then releases phosphoric residues as many as bound succinate. The transfer of this phosphoric residue from the first active site correlates with the transfer to the second active site supporting the cooperative binding mechanism. These therefore means that both ADP and ATP can both be activating or inhibiting depending on which stage of catalysis they bind to the enzyme(Harel, 2014). These therefore support the reversibility of the catalysis. After the phosphorylation of the Succinyl-CoA and subsequent dephosphorylation it is released and continues along the Krebs cycle as succinate. It is suggested that CoA thioester bond with Succinyl CoA is usually broken down when the orthophosphate bonds with Succinyl CoA thus resulting into Succinyl phosphate. The alpha histidine residue then removes the phosphate group, the phosphor-histidine group then moves to the beta group where the ADP is bound sometimes GDP as shown in the equation below and forms ATP sometimes GTP (Harel, 2014). The result is the production of succinate which as have been said above proceeds to Krebs cycle. The energy comes from the thioester bond which is broken between Succinyl CoA and CoA. In the case of GTP which is the most frequent product it is converted to ATP. The reaction is very important part of citric acid cycle and occurs in the mitochondria (Harel, 2014) Kinetics Succinyl CoA synthetase catalyzes a reversible reaction as shown below; each chemical reactant represents a sum of rapidly interconverting chemical species. GDP + SCoA + Pi ↔ GTP + SUC + CoA--------- (1) (Li, Wu & Beard, 2013) The corresponding chemical reaction is: GDP3− + SCoA− + P!2−↔ GTP4− + SUC2− + CoA− + H+-------------(2) (Li, Wu & Beard, 2013) From the equation (2) we can calculate Gibbs free energy using a series of given calculations. The value is found to be 56.55KJ/Mol (Li, Wu & Beard, 2013). The value is however not constant as it has been shown that in Escherichia coli the Succinyl CoA lacks a specific kinetic pattern. The pattern is only consistent with the sequential addition of all substrates which is rarely achieved in vivo to produce a quaternary structure before release of any product. This gives limits the initial kinetic rate due to limits in the order of substrate attachment. The reaction however is dependent on the amount of GDP and GTP or ATP and ADP present. In most of the case two Succinyl CoA gives two GTP or 2 ATP(GUEST & RUSSELL, 2014). The 2GTP are converted to 2ATP thus it generates the two of the ATP of the Krebs cycle. It gives an overall free energy of -3.4kJ/mol ( Champe, Harvey & Ferrier, 2005). Role in Metabolism As have been discussed above, Succinyl CoA is very essential in the Krebs cycle. It catalyzes reaction that leads to generation of nucleosides triphosphates i.e. GTP or GDP which are high energy molecules (GUEST & RUSSELL, 2014). It also controls the flux of various metabolic intermediates; it controls flux of molecules into the metabolic pathway (Krebs cycle) and other metabolic pathways by catalyzing conversion of Succinyl CoA to succinate (Phillips et al, 2009). Succinate is substrate in the Krebs cycle and thus allows for continuation of the cycle which is the major source of energy in form of ATP for the body. The control of Succinyl CoA metabolism is very essential in other activities as Succinyl CoA is required in various pathways such as haem synthesis and metabolism of ketone bodies ( Champe, Harvey & Ferrier, 2005). Regulation of the enzyme It is not a major regulator in the citric cycle thus its regulation in the pathway depends on the prior step. Evidence is however accumulating that suggests that high affinity binding sites of GDP does not regulate the enzyme as was suggested in the earlier literatures (Nunes-Nesi et al, 2013). Binding of GDP to the allosteric sites on the other hand has been associated with increase in rate of phosphorylation of the enzyme (Harel, 2014). This believed to happen by the fact that GDP may be altering the affinity for GTP. The major co-factor and the compound that is required for binding of substrate is Mg++ ions, the absence of which the release of succinate is reduced and thus the metabolism of Succinyl CoA to succinate is severely hampered ( Champe, Harvey & Ferrier, 2005). Organisms and sub-cellular locations Succinyl CoA synthetase (SCS) is found in almost all organisms. Our discussion however has focused on E. coli as it is easy to isolate and produce. The human enzyme has been suggested to have differences from the E. coli one (Cohen, 2014). For example the mitochondrial SCS of humans are not heterotetramer and occur as αβ dimers the form in which they are active. This is opposed to E. coli SCS which we have established is heterotetramer and whose crystal structure was given above in figure 1.1. Another difference is lack of specificity in the E. coli enzyme as it can bind both GTP and ATP without selectivity unlike in humans where the enzymes are substrate specific. The sub-types that bind GTP can only bind it and not ATP and the vice versa is true (Joyce et al, 2012). It is mostly found in mitochondria of various tissues, whereas said it takes part in the citric acid cycle. Conclusion Various enzymes are specific in their action and take parts in significant reactions in the body. They catalyze various processes that are essential for life. As seen in the discussion Succinyl CoA synthase is a Step five Krebs cycle enzyme whose activity is very essential to the pathway as it produces succinate allowing for the continuation of the pathway. It also produces high energy nucleoside phosphates that provide energy to the body. It lacks strict regulation though it requires Mg++ to be optimally active. References Champe, P. C., Harvey, R. A., & Ferrier, D. R. (2005). Lippincott's illustrated reviews: Biochemistry. Philadelphia: Lippincott Williams & Wilkins. Cohen, G. N. (2014). Microbial biochemistry. GUEST, J. R., & RUSSELL, G. C. (2014). Complexes and complexities of the citric acid cycle in. From Metabolite, to Metabolism, to Metabolon: Current Topics in Cellular Regulation, 33, 231. Harel, M. (2014, December). Succinyl-CoA synthetase - Proteopedia, life in 3D. Retrieved from http://proteopedia.org/wiki/index.php/Succinyl-CoA_synthetase Joyce, M. A., Hayakawa, K., Wolodko, W. T., & Fraser, M. E. (2012). Biochemical and structural characterization of the GTP-preferring succinyl-CoA synthetase from Thermus aquaticus. Acta Crystallographica Section D: Biological Crystallography, 68(7), 751-762. Li, X., Wu, F., & Beard, D. A. (2013). Identification of the kinetic mechanism of succinyl-CoA synthetase. Bioscience reports, 33(1). Nunes-Nesi, A., Araújo, W. L., Obata, T., & Fernie, A. R. (2013). Regulation of the mitochondrial tricarboxylic acid cycle. Current opinion in plant biology, 16(3), 335-343. Phillips, D., Aponte, A. M., French, S. A., Chess, D. J., & Balaban, R. S. (2009). Succinyl-CoA synthetase is a phosphate target for the activation of mitochondrial metabolism. Biochemistry, 48(30), 7140-7149. Schomburg, D. (2001). Springer handbook of enzymes: 2. Berlin [u.a.: Springer. Schürmann, M., Wübbeler, J. H., Grote, J., & Steinbüchel, A. (2011). Novel reaction of succinyl coenzyme A (succinyl-CoA) synthetase: activation of 3-sulfinopropionate to 3-sulfinopropionyl-CoA in Advenella mimigardefordensis strain DPN7T during degradation of 3, 3′-dithiodipropionic acid. Journal of bacteriology, 193(12), 3078-3089. Read More