Succinyl coenzyme A synthetase

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Succinate—CoA ligase (GDP-forming)
2fp4.png
Pig GTP-specific succinyl-CoA synthetase with GTP. PDB 2fp4 [1]
Identifiers
EC no. 6.2.1.4
CAS no. 9014-36-2
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Succinate—CoA ligase (ADP-forming)
2scu.png
Succinyl-COA synthetase from Escherichia coli. PDB 2scu [2]
Identifiers
EC no. 6.2.1.5
CAS no. 9080-33-5
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO
Search
PMC articles
PubMed articles
NCBI proteins

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. [3] 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. [4]

Contents

Chemical reaction and enzyme mechanism

Succinyl CoA synthetase catalyzes the following reversible reaction:

Succinyl CoA + Pi + NDP ↔ Succinate + CoA + NTP

where Pi denotes inorganic phosphate, NDP denotes nucleotide diphosphate (either GDP or ADP), and NTP denotes nucleotide 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 has a biochemical standard state free energy change of -3.4 kJ/mol. [4] The reaction takes place by a three-step mechanism [3] which is depicted in the image below. 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 phosphate and generate succinate. Finally, the phosphorylated histidine transfers the phosphate group to a nucleoside diphosphate, which generates the high-energy carrying nucleoside triphosphate.

Succinyl CoA Synthetase Mechanism Revised.png

Structure

Subunits

Bacterial and mammalian SCSs are made up of α and β subunits. [5] In E. coli two αβ heterodimers link together to form an α2β2 heterotetrameric structure. However, mammalian mitochondrial SCSs are active as αβ dimers and do not form a heterotetramer. [6] The E. coli SCS heterotetramer has been crystallized and characterized in great detail. [6] [7] 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. [6] A short amino acid chain links the two β subunits which gives rise to the tetrameric structure.

Image 2: The E. coli Succinyl-CoA Synthetase Heterotetramer; a subunits: pink and green, b subunits: yellow and blue. Pink and yellow form the one dimer and green and blue form the other dimer. PDB ID: 1CQG SCS heterotetramer with ligands GNU.png
Image 2: The E. coli Succinyl-CoA Synthetase Heterotetramer; α subunits: pink and green, β subunits: yellow and blue. Pink and yellow form the one dimer and green and blue form the other dimer. PDB ID: 1CQG

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. . [8]

Catalytic residues

Crystal structures for the E. coli SCS provide evidence that the coenzyme A binds within each α-subunit (within a Rossmann fold) in close proximity to a histidine residue (His246α). [7] This histidine residue becomes phosphorylated during the succinate forming step in the reaction mechanism. The exact binding location of succinate is not well-defined. [9] The formation of the nucleotide 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. [8] 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. Mutagenesis 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. [9]

Isoforms

Johnson et al. describe two isoforms of succinyl-CoA synthetase in amniotes, one that specifies synthesis of ATP, and one that synthesises GTP. [10]

In amniotes, the enzyme is a heterodimer of an α- and a β-subunit. The specificity for either adenosine or guanosine phosphates is defined by the β-subunit, [10] which is encoded by 2 genes. SUCLG2 is GTP-specific and SUCLA2 is ATP-specific, while SUCLG1 encodes the common α-subunit. β variants are produced at different amounts in different tissues, [10] causing GTP or ATP substrate requirements.

Mostly consuming tissues such as heart and brain have more ATP-specific succinyl-CoA synthetase (ATPSCS), while synthetic tissues such as kidney and liver have the more GTP-specific form (GTPSCS). [11] Kinetics analysis of ATPSCS from the breast muscle of pigeons and GTPSCS from pigeon liver showed that their apparent Michaelis constants were similar for CoA, but different for the nucleotides, phosphate, and succinate. The largest difference was for succinate: Kmapp of ATPSCS = 5mM versus that of GTPSCS = 0.5mM. [10]

Function

Generation of nucleotide triphosphates

SCS is the only enzyme in the citric acid cycle that catalyzes a reaction in which a nucleotide triphosphate (GTP or ATP) is formed by substrate-level phosphorylation. [4] Research studies have shown that E. coli SCSs can catalyze either GTP or ATP formation. [7] 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. [12] 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. [11]

Formation of metabolic intermediates

SCS facilitates the flux of molecules into other metabolic pathways by controlling the interconversion between succinyl CoA and succinate. [13] This is important because succinyl CoA is an intermediate necessary for porphyrin, heme, [14] and ketone body biosynthesis. [15]

Regulation and inhibition

In some bacteria, the enzyme is regulated at the transcriptional level. [16] 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. [17]

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. [18]

Role in disease

Fatal infantile lactic acidosis: Defective SCS has been implicated as a cause of fatal infantile lactic acidosis, 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. [19] 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. [19] 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.

See also

Related Research Articles

<span class="mw-page-title-main">Adenosine triphosphate</span> Energy-carrying molecule in living cells

Adenosine triphosphate (ATP) is a nucleotide that provides energy to drive and support many processes in living cells, such as muscle contraction, nerve impulse propagation, condensate dissolution, and chemical synthesis. Found in all known forms of life, it is often referred to as the "molecular unit of currency" of intracellular energy transfer.

<span class="mw-page-title-main">Citric acid cycle</span> Interconnected biochemical reactions releasing energy

The citric acid cycle—also known as the Krebs cycle, Szent–Györgyi–Krebs cycle or the TCA cycle (tricarboxylic acid cycle)—is a series of biochemical reactions to release the energy stored in nutrients through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins. The chemical energy released is available under the form of ATP. The Krebs cycle is used by organisms that respire (as opposed to organisms that ferment) to generate energy, either by anaerobic respiration or aerobic respiration. In addition, the cycle provides precursors of certain amino acids, as well as the reducing agent NADH, that are used in numerous other reactions. Its central importance to many biochemical pathways suggests that it was one of the earliest components of metabolism. Even though it is branded as a "cycle", it is not necessary for metabolites to follow only one specific route; at least three alternative segments of the citric acid cycle have been recognized.

<span class="mw-page-title-main">Nucleotide</span> Biological molecules constituting nucleic acids

Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver.

<span class="mw-page-title-main">Guanosine triphosphate</span> Chemical compound

Guanosine-5'-triphosphate (GTP) is a purine nucleoside triphosphate. It is one of the building blocks needed for the synthesis of RNA during the transcription process. Its structure is similar to that of the guanosine nucleoside, the only difference being that nucleotides like GTP have phosphates on their ribose sugar. GTP has the guanine nucleobase attached to the 1' carbon of the ribose and it has the triphosphate moiety attached to ribose's 5' carbon.

DnaG is a bacterial DNA primase and is encoded by the dnaG gene. The enzyme DnaG, and any other DNA primase, synthesizes short strands of RNA known as oligonucleotides during DNA replication. These oligonucleotides are known as primers because they act as a starting point for DNA synthesis. DnaG catalyzes the synthesis of oligonucleotides that are 10 to 60 nucleotides long, however most of the oligonucleotides synthesized are 11 nucleotides. These RNA oligonucleotides serve as primers, or starting points, for DNA synthesis by bacterial DNA polymerase III. DnaG is important in bacterial DNA replication because DNA polymerase cannot initiate the synthesis of a DNA strand, but can only add nucleotides to a preexisting strand. DnaG synthesizes a single RNA primer at the origin of replication. This primer serves to prime leading strand DNA synthesis. For the other parental strand, the lagging strand, DnaG synthesizes an RNA primer every few kilobases (kb). These primers serve as substrates for the synthesis of Okazaki fragments.

Succinyl-coenzyme A, abbreviated as succinyl-CoA or SucCoA, is a thioester of succinic acid and coenzyme A.

A nucleoside triphosphate is a nucleoside containing a nitrogenous base bound to a 5-carbon sugar, with three phosphate groups bound to the sugar. They are the molecular precursors of both DNA and RNA, which are chains of nucleotides made through the processes of DNA replication and transcription. Nucleoside triphosphates also serve as a source of energy for cellular reactions and are involved in signalling pathways.

In molecular biology, biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined to form macromolecules. This process often consists of metabolic pathways. Some of these biosynthetic pathways are located within a single cellular organelle, while others involve enzymes that are located within multiple cellular organelles. Examples of these biosynthetic pathways include the production of lipid membrane components and nucleotides. Biosynthesis is usually synonymous with anabolism.

<span class="mw-page-title-main">Mitochondrial matrix</span> Space within the inner membrane of the mitochondrion

In the mitochondrion, the matrix is the space within the inner membrane. The word "matrix" stems from the fact that this space is viscous, compared to the relatively aqueous cytoplasm. The mitochondrial matrix contains the mitochondrial DNA, ribosomes, soluble enzymes, small organic molecules, nucleotide cofactors, and inorganic ions.[1] The enzymes in the matrix facilitate reactions responsible for the production of ATP, such as the citric acid cycle, oxidative phosphorylation, oxidation of pyruvate, and the beta oxidation of fatty acids.

<span class="mw-page-title-main">Adenylate kinase</span> Class of enzymes

Adenylate kinase is a phosphotransferase enzyme that catalyzes the interconversion of the various adenosine phosphates. By constantly monitoring phosphate nucleotide levels inside the cell, ADK plays an important role in cellular energy homeostasis.

Substrate-level phosphorylation is a metabolism reaction that results in the production of ATP or GTP supported by the energy released from another high-energy bond that leads to phosphorylation of ADP or GDP to ATP or GTP (note that the reaction catalyzed by creatine kinase is not considered as "substrate-level phosphorylation"). This process uses some of the released chemical energy, the Gibbs free energy, to transfer a phosphoryl (PO3) group to ADP or GDP. Occurs in glycolysis and in the citric acid cycle.

<span class="mw-page-title-main">Nucleoside-diphosphate kinase</span> Class of enzymes

Nucleoside-diphosphate kinases are enzymes that catalyze the exchange of terminal phosphate between different nucleoside diphosphates (NDP) and triphosphates (NTP) in a reversible manner to produce nucleotide triphosphates. Many NDP serve as acceptor while NTP are donors of phosphate group. The general reaction via ping-pong mechanism is as follows: XDP + YTP ←→ XTP + YDP. NDPK activities maintain an equilibrium between the concentrations of different nucleoside triphosphates such as, for example, when guanosine triphosphate (GTP) produced in the citric acid (Krebs) cycle is converted to adenosine triphosphate (ATP). Other activities include cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor, endocytosis, and gene expression.

<span class="mw-page-title-main">Cyclic nucleotide phosphodiesterase</span> Class of enzymes

3′,5′-cyclic-nucleotide phosphodiesterases (EC 3.1.4.17) are a family of phosphodiesterases. Generally, these enzymes hydrolyze a nucleoside 3′,5′-cyclic phosphate to a nucleoside 5′-phosphate:

<span class="mw-page-title-main">Nucleic acid metabolism</span> Process

Nucleic acid metabolism is a collective term that refers to the variety of chemical reactions by which nucleic acids are either synthesized or degraded. Nucleic acids are polymers made up of a variety of monomers called nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base. Degradation of nucleic acids is a catabolic reaction and the resulting parts of the nucleotides or nucleobases can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require multiple enzymes to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases.

<span class="mw-page-title-main">Ribose-phosphate diphosphokinase</span> Class of enzymes

Ribose-phosphate diphosphokinase is an enzyme that converts ribose 5-phosphate into phosphoribosyl pyrophosphate (PRPP). It is classified under EC 2.7.6.1.

<span class="mw-page-title-main">Succinate—CoA ligase (ADP-forming)</span>

In enzymology, a succinate-CoA ligase (ADP-forming) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Succinate—CoA ligase (GDP-forming)</span>

In enzymology, a succinate—CoA ligase (GDP-forming) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">SUCLA2</span> Protein-coding gene in the species Homo sapiens

Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial (SUCLA2), also known as ADP-forming succinyl-CoA synthetase (SCS-A), is an enzyme that in humans is encoded by the SUCLA2 gene on chromosome 13.

<span class="mw-page-title-main">SUCLG1</span> Protein-coding gene in the species Homo sapiens

Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial is an enzyme that in humans is encoded by the SUCLG1 gene.

<span class="mw-page-title-main">SUCLG2</span> Protein-coding gene in the species Homo sapiens

Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial is an enzyme that in humans is encoded by the SUCLG2 gene on chromosome 3.

References

  1. ↑ Fraser ME, Hayakawa K, Hume MS, Ryan DG, Brownie ER (Apr 2006). "Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase". The Journal of Biological Chemistry. 281 (16): 11058–65. doi: 10.1074/jbc.M511785200 . PMID   16481318.
  2. ↑ Fraser ME, James MN, Bridger WA, Wolodko WT (Jan 1999). "A detailed structural description of Escherichia coli succinyl-CoA synthetase". Journal of Molecular Biology. 285 (4): 1633–53. doi:10.1006/jmbi.1998.2324. PMID   9917402.
  3. 1 2 Voet, Donald J. (2011). Biochemistry / Donald J. Voet ; Judith G. Voet. New York, NY: Wiley, J. ISBN   978-0-470-57095-1.
  4. 1 2 3 Berg, Jeremy M. (Jeremy M.); Tymoczko, John L.; Stryer, Lubert.; Stryer, Lubert. Biochemistry. (2002). Biochemistr . New York: W.H. Freeman. pp.  475–477. ISBN   0-7167-3051-0.
  5. ↑ Nishimura JS (1986). "Succinyl-CoA synthetase structure-function relationships and other considerations". Advances in Enzymology and Related Areas of Molecular Biology. Advances in Enzymology and Related Areas of Molecular Biology. Vol. 58. pp. 141–72. doi:10.1002/9780470123041.ch4. ISBN   9780470123041. PMID   3521216.
  6. 1 2 3 Wolodko WT, Kay CM, Bridger WA (Sep 1986). "Active enzyme sedimentation, sedimentation velocity, and sedimentation equilibrium studies of succinyl-CoA synthetases of porcine heart and Escherichia coli". Biochemistry. 25 (19): 5420–5. doi:10.1021/bi00367a012. PMID   3535876.
  7. 1 2 3 Fraser ME, James MN, Bridger WA, Wolodko J (May 1999). "A detailed structural description of escherichia coli succinly-CoA synthetase". Journal of Molecular Biology. 288 (3): 501. doi: 10.1006/jmbi.1999.2773 . PMID   10329157.
  8. 1 2 Joyce MA, Fraser ME, James MN, Bridger WA, Wolodko WT (Jan 2000). "ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography". Biochemistry. 39 (1): 17–25. doi:10.1021/bi991696f. PMID   10625475.
  9. 1 2 Fraser ME, Joyce MA, Ryan DG, Wolodko WT (Jan 2002). "Two glutamate residues, Glu 208 alpha and Glu 197 beta, are crucial for phosphorylation and dephosphorylation of the active-site histidine residue in succinyl-CoA synthetase". Biochemistry. 41 (2): 537–46. doi:10.1021/bi011518y. PMID   11781092.
  10. 1 2 3 4 Johnson JD, Mehus JG, Tews K, Milavetz BI, Lambeth DO (Oct 1998). "Genetic evidence for the expression of ATP- and GTP-specific succinyl-CoA synthetases in multicellular eucaryotes". The Journal of Biological Chemistry. 273 (42): 27580–6. doi: 10.1074/jbc.273.42.27580 . PMID   9765291.
  11. 1 2 Lambeth DO, Tews KN, Adkins S, Frohlich D, Milavetz BI (Aug 2004). "Expression of two succinyl-CoA synthetases with different nucleotide specificities in mammalian tissues". The Journal of Biological Chemistry. 279 (35): 36621–4. doi: 10.1074/jbc.M406884200 . PMID   15234968.
  12. ↑ Johnson JD, Muhonen WW, Lambeth DO (Oct 1998). "Characterization of the ATP- and GTP-specific succinyl-CoA synthetases in pigeon. The enzymes incorporate the same alpha-subunit". The Journal of Biological Chemistry. 273 (42): 27573–9. doi: 10.1074/jbc.273.42.27573 . PMID   9765290.
  13. ↑ Labbe RF, Kurumada T, Onisawa J (Dec 1965). "The role of succinyl-CoA synthetase in the control of heme biosynthesis". Biochimica et Biophysica Acta (BBA) - General Subjects. 111 (2): 403–15. doi:10.1016/0304-4165(65)90050-4. PMID   5879477.
  14. ↑ Ottaway JH, McClellan JA, Saunderson CL (1981). "Succinic thiokinase and metabolic control". The International Journal of Biochemistry. 13 (4): 401–10. doi:10.1016/0020-711x(81)90111-7. PMID   6263728.
  15. ↑ Jenkins TM, Weitzman PD (Sep 1986). "Distinct physiological roles of animal succinate thiokinases. Association of guanine nucleotide-linked succinate thiokinase with ketone body utilization". FEBS Letters. 205 (2): 215–8. doi: 10.1016/0014-5793(86)80900-0 . PMID   2943604. S2CID   23667115.
  16. ↑ Kruspl W, Streitmann B (Feb 1975). "[Knotty reticulosis with keloid formation]". Zeitschrift für Hautkrankheiten. 50 (3): 117–25. PMID   179232.
  17. ↑ Hunger-Glaser I, Brun R, Linder M, Seebeck T (May 1999). "Inhibition of succinyl CoA synthetase histidine-phosphorylation in Trypanosoma brucei by an inhibitor of bacterial two-component systems". Molecular and Biochemical Parasitology. 100 (1): 53–9. doi:10.1016/s0166-6851(99)00032-8. PMID   10376993.
  18. ↑ Wider de Xifra E, del C Batlle AM (Mar 1978). "Porphyrin biosynthesis: immobilized enzymes and ligands. VI. Studies on succinyl CoA synthetase from cultured soya bean cells". Biochimica et Biophysica Acta. 523 (1): 245–9. doi:10.1016/0005-2744(78)90027-x. PMID   564714.
  19. 1 2 Ostergaard E, Christensen E, Kristensen E, Mogensen B, Duno M, Shoubridge EA, Wibrand F (Aug 2007). "Deficiency of the alpha subunit of succinate-coenzyme A ligase causes fatal infantile lactic acidosis with mitochondrial DNA depletion". American Journal of Human Genetics. 81 (2): 383–7. doi:10.1086/519222. PMC   1950792 . PMID   17668387.
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