| Succinate--CoA ligase (GDP-forming) |
Pig GTP-specific succinyl-CoA synthetase with GTP. PDB 2fp4 [1]
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| Identifiers |
| EC number |
6.2.1.4 |
| CAS number |
9014-36-2 |
| 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 / EGO |
| Search |
| PMC |
articles |
| PubMed |
articles |
| NCBI |
proteins |
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| Succinate--CoA ligase (ADP-forming) |
Succinyl-COA synthetase from Escherichia coli. PDB 2scu [2]
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| Identifiers |
| EC number |
6.2.1.5 |
| CAS number |
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 / EGO |
| 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
- 1 Chemical Reaction and Enzyme Mechanism
- 2 Enzyme structure
- 2.1 Subunits
- 2.2 Catalytic Residues
- 2.3 Isoforms
- 3 Biological Function
- 4 Role in Disease
- 5 See also
- 6 References
- 7 External links
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 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 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.
Enzyme 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; 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. [1].[8]
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).[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 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.[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 mammals, one that specifies synthesis of ADP, and one that synthesises GDP.[10]
- EC 6.2.1.5 - ADP-forming - SUCLA2
- EC 6.2.1.4 - GDP-forming - SUCLG1, SUCLG2
The GTP form is the one more commonly used in the human citric acid cycle.[citation needed]
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 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.[11] 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.[12]
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: Investigation into the regulation of SCS in E. coli has shown that 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 implemented 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
Citric Acid Cycle
Succinate dehydrogenase
Succinate-CoA ligase (ADP-forming)
Succinate-CoA ligase (GDP-forming)
References
- ^ Fraser, M. E.; Hayakawa, K.; Hume, M. S.; Ryan, D. G.; Brownie, E. R. (2006). "Interactions of GTP with the ATP-grasp Domain of GTP-specific Succinyl-CoA Synthetase". Journal of Biological Chemistry 281 (16): 11058–11065. doi:10.1074/jbc.M511785200. PMID 16481318. edit
- ^ Fraser, M. E.; James, M. N. G.; Bridger, W. A.; Wolodko, W. T. (1999). "A detailed structural description of Escherichia coli succinyl-CoA synthetase1". Journal of Molecular Biology 285 (4): 1633–1653. doi:10.1006/jmbi.1998.2324. PMID 9917402. edit
- ^ a b Voet, Donald J. (2011). Biochemistry / Donald J. Voet ; Judith G. Voet. New York, NY: Wiley, J. ISBN 978-0-470-57095-1.
- ^ a b c 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.
- ^ Nishimura, JS. (1986). "Succinyl-CoA synthetase structure-function relationships and other considerations.". Adv Enzymol Relat Areas Mol Biol 58: 141–72. PMID 3521216.
- ^ a b c 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.
- ^ a b c Fraser, ME.; James, MN.; Bridger, WA.; Wolodko, J. (May 1999). "A detailed structural description of escherichia coli succinly-CoA synthetase". J Mol Biol 288 (3): 501. doi:10.1006/jmbi.1999.2773. PMID 10329157.
- ^ a b 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.
- ^ a b 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.
- ^ Johnson JD, Mehus JG, Tews K, Milavetz BI, Lambeth DO (1998). "Genetic evidence for the expression of ATP- and GTP-specific succinyl-CoA synthetases in multicellular eucaryotes". J Biol Chem 273 (42): 27580–6. doi:10.1074/jbc.273.42.27580. PMID 9765291.
- ^ 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.". J Biol Chem 273 (42): 27573–9. doi:10.1074/jbc.273.42.27573. PMID 9765290.
- ^ 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.". J Biol Chem 279 (35): 36621–4. doi:10.1074/jbc.M406884200. PMID 15234968.
- ^ Labbe, RF.; Kurumada, T.; Onisawa, J. (Dec 1965). "The role of succinyl-CoA synthetase in the control of heme biosynthesis.". Biochim Biophys Acta 111 (2): 403–15. PMID 5879477.
- ^ Ottaway, JH.; McClellan, JA.; Saunderson, CL. (1981). "Succinic thiokinase and metabolic control.". Int J Biochem 13 (4): 401–10. PMID 6263728.
- ^ 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 Lett 205 (2): 215–8. doi:10.1016/0014-5793(86)80900-0. PMID 2943604.
- ^ Park, SJ.; Chao, G.; Gunsalus, RP. (Jul 1997). "Aerobic regulation of the sucABCD genes of Escherichia coli, which encode alpha-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter.". J Bacteriol 179 (13): 4138–42. PMC 179232. PMID 9209026.
- ^ 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.". Mol Biochem Parasitol 100 (1): 53–9. PMID 10376993.
- ^ Wider de Xifra, EA.; del C Batlle, AM. (Mar 1978). "Porphyrin biosynthesis: immobilized enzymes and ligands. VI. Studies on succinyl CoA synthetase from cultured soya bean cells.". Biochim Biophys Acta 523 (1): 245–9. PMID 564714.
- ^ a b 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.". Am J Hum Genet 81 (2): 383–7. doi:10.1086/519222. PMC 1950792. PMID 17668387.
External links
- Succinyl Coenzyme A Synthetases at the US National Library of Medicine Medical Subject Headings (MeSH)
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Enzymes: CO CS and CN ligases (EC 6.1-6.3)
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| 6.1: Carbon-Oxygen |
- Aminoacyl tRNA synthetase
- Tyrosine
- Tryptophan
- Threonine
- Leucine
- Isoleucine
- Lysine
- Alanine
- Valine
- Methionine
- Serine
- Aspartate
- D-alanine-poly(phosphoribitol) ligase
- Glycine
- Proline
- Cysteine
- Glutamate
- Glutamine
- Arginine
- Phenylalanine
- Histidine
- Asparagine
- Aspartate
- Glutamate
- Lysine
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| 6.2: Carbon-Sulfur |
- Succinyl coenzyme A synthetase - Acetyl Co-A synthetase - Long fatty acyl CoA synthetase
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| 6.3: Carbon-Nitrogen |
- Glutamine synthetase
- Ubiquitin ligase
- Cullin
- Von Hippel-Lindau tumor suppressor
- UBE3A
- Mdm2
- Anaphase-promoting complex
- UBR1
- Glutathione synthetase
- CTP synthase
- Adenylosuccinate synthase
- Argininosuccinate synthetase
- Holocarboxylase synthetase
- GMP synthase
- Asparagine synthetase
- Carbamoyl phosphate synthetase
- Gamma-glutamylcysteine synthetase
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- B
- enzm
- 1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
- 2.1
- 3.1
- 4.1
- 5.1
- 6.1-3
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Ligases: carbon-carbon ligases (EC 6.4)
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| Biotin dependent carboxylase |
- Pyruvate carboxylase
- Acetyl-CoA carboxylase
- Propionyl-CoA carboxylase
- Methylcrotonyl-CoA carboxylase
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| Other |
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- B
- enzm
- 1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
- 2.1
- 3.1
- 4.1
- 5.1
- 6.1-3
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Enzymes: Phosphoric ester and nitrogen-metal ligases (EC 6.5-6.6)
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| 6.5: Phosphoric Ester |
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| 6.6: Nitrogen-Metal |
- Magnesium chelatase
- Cobaltochelatase
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- B
- enzm
- 1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
- 2.1
- 3.1
- 4.1
- 5.1
- 6.1-3
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Metabolism: Citric acid cycle enzymes
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| Cycle |
- Citrate synthase
- Aconitase
- Isocitrate dehydrogenase
- Oxoglutarate dehydrogenase
- Succinyl CoA synthetase
- Succinate dehydrogenase (SDHA)
- Fumarase
- Malate dehydrogenase and ETC
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| Anaplerotic |
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to acetyl-CoA
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- Pyruvate dehydrogenase complex (E1, E2, E3)
- (regulated by Pyruvate dehydrogenase kinase and Pyruvate dehydrogenase phosphatase)
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to α-ketoglutaric acid
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to succinyl-CoA
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to oxaloacetate
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- Pyruvate carboxylase
- Aspartate transaminase
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Mitochondrial
electron transport chain/
oxidative phosphorylation |
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Primary
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- Complex I/NADH dehydrogenase
- Complex II/Succinate dehydrogenase
- Coenzyme Q
- Complex III/Coenzyme Q - cytochrome c reductase
- Cytochrome c
- Complex IV/Cytochrome c oxidase
- Coenzyme Q10 synthesis: COQ2
- COQ3
- COQ4
- COQ5
- COQ6
- COQ7
- COQ9
- COQ10A
- COQ10B
- PDSS1
- PDSS2
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Other
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- Alternative oxidase
- Electron-transferring-flavoprotein dehydrogenase
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mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m
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k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon
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m (A16/C10), i (k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)
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Mitochondrial proteins
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| Outer membrane |
| fatty acid degradation |
- Carnitine palmitoyltransferase I
- Long-chain-fatty-acid—CoA ligase
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| tryptophan metabolism |
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monoamine neurotransmitter
metabolism |
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| Intermembrane space |
- Adenylate kinase
- Creatine kinase
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| Inner membrane |
| oxidative phosphorylation |
- Coenzyme Q – cytochrome c reductase
- Cytochrome c
- NADH dehydrogenase
- Succinate dehydrogenase
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| pyrimidine metabolism |
- Dihydroorotate dehydrogenase
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| mitochondrial shuttle |
- Malate-aspartate shuttle
- Glycerol phosphate shuttle
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| other |
- Glutamate aspartate transporter
- Glycerol-3-phosphate dehydrogenase
- ATP synthase
- Carnitine palmitoyltransferase II
- Uncoupling protein
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| Matrix |
| citric acid cycle |
- Citrate synthase
- Aconitase
- Isocitrate dehydrogenase
- Oxoglutarate dehydrogenase complex
- Succinyl coenzyme A synthetase
- Fumarase
- Malate dehydrogenase
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| anaplerotic reactions |
- Aspartate transaminase
- Glutamate dehydrogenase
- Pyruvate dehydrogenase complex
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| urea cycle |
- Carbamoyl phosphate synthetase I
- Ornithine transcarbamylase
- N-Acetylglutamate synthase
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| alcohol metabolism |
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| Other/to be sorted |
| steroidogenesis |
- Cholesterol side-chain cleavage enzyme
- Steroid 11-beta-hydroxylase
- Aldosterone synthase
- Frataxin
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- Mitochondrial membrane transport protein
- Mitochondrial permeability transition pore
- Mitochondrial carrier
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| Mitochondrial DNA |
| Complex I |
- MT-ND1
- MT-ND2
- MT-ND3
- MT-ND4
- MT-ND4L
- MT-ND5
- MT-ND6
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| Complex III |
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| Complex IV |
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| ATP synthase |
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| tRNA |
- MT-TA
- MT-TC
- MT-TD
- MT-TE
- MT-TF
- MT-TG
- MT-TH
- MT-TI
- MT-TK
- MT-TL1
- MT-TL2
- MT-TM
- MT-TN
- MT-TP
- MT-TQ
- MT-TR
- MT-TS1
- MT-TS2
- MT-TT
- MT-TV
- MT-TW
- MT-TY
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see also mitochondrial diseases
B strc: edmb (perx), skel (ctrs), epit, cili, mito, nucl (chro)
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