Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

MetaCyc Compound: Na+

Synonyms: Sodium, sodium ion

Superclasses: an ion a cation

Component of:
sodium dodecyl sulfate
sodium tetraborate decahydrate
disodium phosphate
monosodium phosphate
sodium citrate trihydrate
sodium sulfate
NaF
tiron (summary available)
acidulated phosphate fluoride (summary available)
sodium tetrahydridoborate
sodium pyruvate
sodium acetate
sodium chloride
disodium phosphate heptahydrate
sodium nitrate

Chemical Formula: Na

Molecular Weight: 22.99 Daltons

Monoisotopic Molecular Weight: 22.98976967 Daltons

SMILES: [Na+]

InChI: InChI=1S/Na/q+1

InChIKey: InChIKey=FKNQFGJONOIPTF-UHFFFAOYSA-N

Unification Links: CAS:7440-23-5 , ChEBI:29101 , ChemSpider:899 , HMDB:HMDB00588 , IAF1260:37376 , KEGG:C01330 , MetaboLights:MTBLC29101 , PubChem:923

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -0.3120594 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

malonate degradation II (biotin-dependent) :
[a carboxylated biotinylated MadF protein] + n Na+[in] + H+ → CO2 + [a biotinylated MadF protein] + n Na+[extracellular space]

Reactions known to produce the compound:

Not in pathways:
sodium dodecyl sulfate + H2O → 1-dodecanol + sulfate + Na+ + H+

In Transport reactions:
choline[extracellular space] + Na+[extracellular space] → choline[cytosol] + Na+[cytosol] ,
K+[extracellular space] + Na+[cytosol] → K+[cytosol] + Na+[extracellular space] ,
Na+[in]Na+[out] ,
Na+[periplasmic space] + 2,3-dioxo-L-gulonate[periplasmic space]Na+[cytosol] + 2,3-dioxo-L-gulonate[cytosol] ,
Na+[in] + NADH + an ubiquinone + H+Na+[out] + NAD+ + an ubiquinol ,
Na+[cytosol] + ATP + H2O ↔ Na+[extracellular space] + ADP + phosphate + H+ ,
2 K+[extracellular space] + 3 Na+[cytosol] + ATP + H2O → 2 K+[cytosol] + 3 Na+[extracellular space] + ADP + phosphate + H+ ,
Na+[periplasmic space] + L-isoleucine[periplasmic space]Na+[cytosol] + L-isoleucine[cytosol] ,
methyl-β-D-galactoside[periplasmic space] + Na+[periplasmic space] → methyl-β-D-galactoside[cytosol] + Na+[cytosol] ,
Na+[periplasmic space] + L-proline[periplasmic space]Na+[cytosol] + L-proline[cytosol] ,
Na+[cytosol] + 2 H+[periplasmic space]Na+[periplasmic space] + 2 H+[cytosol] ,
Na+[periplasmic space] + L-valine[periplasmic space]Na+[cytosol] + L-valine[cytosol] ,
Na+[cytosol] + H+[periplasmic space]Na+[periplasmic space] + H+[cytosol] ,
2 Na+[cytosol] + 3 H+[periplasmic space] → 2 Na+[periplasmic space] + 3 H+[cytosol] ,
Na+[periplasmic space] + L-serine[periplasmic space]Na+[cytosol] + L-serine[cytosol] ,
Na+[periplasmic space] + L-leucine[periplasmic space]Na+[cytosol] + L-leucine[cytosol] ,
Na+[periplasmic space] + L-alanine[periplasmic space]Na+[cytosol] + L-alanine[cytosol] ,
2 Na+[periplasmic space] + L-glutamate[periplasmic space] → 2 Na+[cytosol] + L-glutamate[cytosol] ,
Na+[periplasmic space] + (R)-pantothenate[periplasmic space]Na+[cytosol] + (R)-pantothenate[cytosol] ,
Na+[periplasmic space] + melibiose[periplasmic space]Na+[cytosol] + melibiose[cytosol] ,
Na+[in] + ATP + H2O ↔ Na+[out] + ADP + phosphate + H+

Enzymes activated by Na+, sorted by the type of activation, are:

Activator (Allosteric) of: acetyl-CoA acetyltransferase [Haapalainen07] , malonate decarboxylase [Hilbi94] , glucose dehydrogenase [Bonete96] , NADP-dependent glyceraldehyde-3-phosphate dehydrogenase [Crow79]

Activator (Non-allosteric) of: methenyltetrahydropterin cyclohydrolase [Pomper99]

Activator (Mechanism unknown) of: glyoxylate carboligase [Gupta66, Comment 1] , glycerophosphocholine cholinephosphodiesterase [Sugimori13] , 8-hydroxy-5-deazaflavin:NADPH oxidoreductase [Eker89] , neocarrabiose sulfate 4-sulfatase [GalperinLemaitr75] , phenylacetyl-coenzyme A:glycine N-acyltransferase [Nandi79] , V-type Na+-translocating ATPase [Murata97] , asparaginase [Sodek80] , formyltransferase/hydrolase complex [Pomper01] , trehalose-6-phosphate synthase [Lippert93] , 5-enolpyruvoylshikimate-3-phosphate synthase [Comment 2]

Enzymes inhibited by Na+, sorted by the type of inhibition, are:

Inhibitor (Noncompetitive) of: ribonuclease [Venkov71]

Inhibitor (Mechanism unknown) of: aspartate semialdehyde dehydrogenase [Helmward89, Hegeman70] , dTMP kinase [Helmward89] , guanosine-5'-triphosphate, 3'-diphosphate pyrophosphatase [Keasling93] , dihydrofolate reductase [Baccanari75, Comment 3] , trimethylamine N-oxide reductase [Shimokawa79, Silvestro88] , tryptophanase [HogbergRaibaud75, Comment 4] , nitrate reductase [Iobbi87] , propionyl-CoA carboxylase [Hardewig94] , NADH kinase [Shi05c] , NAD(+) kinase [Shi05c] , trehalase [Lee01d] , farnesoic acid carboxyl methyltransferase [Yang06c] , phosphotransacetylase [Hartmanis84a] , porphobilinogen deaminase [Jones94] , D-tagatose-6-phosphate kinase [Bissett80] , phosphotransacetylase [Lundie89] , hydrogenase [Schneider76] , L-lysine monooxygenase [Flashner74]


References

Baccanari75: Baccanari D, Phillips A, Smith S, Sinski D, Burchall J (1975). "Purification and properties of Escherichia coli dihydrofolate reductase." Biochemistry 1975;14(24);5267-73. PMID: 46

Bissett80: Bissett DL, Anderson RL (1980). "Lactose and D-galactose metabolism in Staphylococcus aureus. III. Purification and properties of D-tagatose-6-phosphate kinase." J Biol Chem 255(18);8745-9. PMID: 6251066

Bonete96: Bonete MJ, Pire C, LLorca FI, Camacho ML (1996). "Glucose dehydrogenase from the halophilic Archaeon Haloferax mediterranei: enzyme purification, characterisation and N-terminal sequence." FEBS Lett 383(3);227-9. PMID: 8925901

Crow79: Crow VL, Wittenberger CL (1979). "Separation and properties of NAD+- and NADP+-dependent glyceraldehyde-3-phosphate dehydrogenases from Streptococcus mutans." J Biol Chem 254(4);1134-42. PMID: 33184

Eker89: Eker AP, Hessels JK, Meerwaldt R (1989). "Characterization of an 8-hydroxy-5-deazaflavin:NADPH oxidoreductase from Streptomyces griseus." Biochim Biophys Acta 990(1);80-6. PMID: 2492438

Fischer87: Fischer RS, Rubin JL, Gaines CG, Jensen RA (1987). "Glyphosate sensitivity of 5-enol-pyruvylshikimate-3-phosphate synthase from Bacillus subtilis depends upon state of activation induced by monovalent cations." Arch Biochem Biophys 1987;256(1);325-34. PMID: 3111378

Flashner74: Flashner MI, Massey V (1974). "Purification and properties of L-lysine monooxygenase from Pseudomonas fluorescens." J Biol Chem 249(8);2579-86. PMID: 4207122

GalperinLemaitr75: Galperin-Lemaitre H, Kirsch-Volders M, Levi S (1975). "Letter: Ultrasound and mammalian D.N.A." Lancet 2(7936);662. PMID: 52031

Gupta66: Gupta NK, Vennesland B (1966). "Glyoxylate carboligase of Escherichia coli: some properties of the enzyme." Arch Biochem Biophys 1966;113(2);255-64. PMID: 5328735

Haapalainen07: Haapalainen AM, Merilainen G, Pirila PL, Kondo N, Fukao T, Wierenga RK (2007). "Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase: the importance of potassium and chloride ions for its structure and function." Biochemistry 46(14);4305-21. PMID: 17371050

Hardewig94: Hardewig I, Portner HO, Grieshaber MK (1994). "Interactions of anaerobic propionate formation and acid-base status in Arenicola marina: an analysis of propionyl-CoA carboxylase." Physiol. Zool. 67(4):892-909.

Hartmanis84a: Hartmanis MGN, Gatenbeck S (1984). "Intermediary Metabolism in Clostridium acetobutylicum: Levels of Enzymes Involved in the Formation of Acetate and Butyrate." Applied and Environmental Microbiology 47:1277-1283. PMID: 16346566

Hegeman70: Hegeman G, Cohen G, Morgan R "Aspartic semialdehyde dehydrogenase (Escherichia coli K12)." Methods in Enzymology 1970; 17A:708-713.

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

Hilbi94: Hilbi H, Dimroth P (1994). "Purification and characterization of a cytoplasmic enzyme component of the Na+-activated malonate decarboxylase system of Malonomonas rubra: acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase." Arch Microbiol 162(1-2);48-56. PMID: 18251085

HogbergRaibaud75: Hogberg-Raibaud A, Raibaud O, Goldberg ME (1975). "Kinetic and equilibrium studies on the activation of Escherichia coli K12 tryptophanase by pyridoxal 5'-phosphate and monovalent cations." J Biol Chem 250(9);3352-8. PMID: 1091651

Iobbi87: Iobbi C, Santini CL, Bonnefoy V, Giordano G (1987). "Biochemical and immunological evidence for a second nitrate reductase in Escherichia coli K12." Eur J Biochem 1987;168(2);451-9. PMID: 3311749

Jones94: Jones RM, Jordan PM (1994). "Purification and properties of porphobilinogen deaminase from Arabidopsis thaliana." Biochem J 299 ( Pt 3);895-902. PMID: 8192681

Keasling93: Keasling JD, Bertsch L, Kornberg A (1993). "Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase." Proc Natl Acad Sci U S A 1993;90(15);7029-33. PMID: 8394006

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Lee01d: Lee JH, Tsuji M, Nakamura M, Nishimoto M, Okuyama M, Mori H, Kimura A, Matsui H, Chiba S (2001). "Purification and identification of the essential ionizable groups of honeybee, Apis mellifera L., trehalase." Biosci Biotechnol Biochem 65(12);2657-65. PMID: 11826961

Lippert93: Lippert K, Galinski EA, Truper HG (1993). "Biosynthesis and function of trehalose in Ectothiorhodospira halochloris." Antonie Van Leeuwenhoek 63(1);85-91. PMID: 8480996

Lundie89: Lundie LL, Ferry JG (1989). "Activation of acetate by Methanosarcina thermophila. Purification and characterization of phosphotransacetylase." J Biol Chem 1989;264(31);18392-6. PMID: 2808380

Murata97: Murata T, Takase K, Yamato I, Igarashi K, Kakinuma Y (1997). "Purification and reconstitution of Na+-translocating vacuolar ATPase from Enterococcus hirae." J Biol Chem 272(40);24885-90. PMID: 9312089

Nandi79: Nandi DL, Lucas SV, Webster LT (1979). "Benzoyl-coenzyme A:glycine N-acyltransferase and phenylacetyl-coenzyme A:glycine N-acyltransferase from bovine liver mitochondria. Purification and characterization." J Biol Chem 254(15);7230-7. PMID: 457678

Pomper01: Pomper BK, Vorholt JA (2001). "Characterization of the formyltransferase from Methylobacterium extorquens AM1." Eur J Biochem 268(17);4769-75. PMID: 11532013

Pomper99: Pomper BK, Vorholt JA, Chistoserdova L, Lidstrom ME, Thauer RK (1999). "A methenyl tetrahydromethanopterin cyclohydrolase and a methenyl tetrahydrofolate cyclohydrolase in Methylobacterium extorquens AM1." Eur J Biochem 261(2);475-80. PMID: 10215859

Schneider76: Schneider K, Schlegel HG (1976). "Purification and properties of soluble hydrogenase from Alcaligenes eutrophus H 16." Biochim Biophys Acta 1976;452(1);66-80. PMID: 186126

Shi05c: Shi F, Kawai S, Mori S, Kono E, Murata K (2005). "Identification of ATP-NADH kinase isozymes and their contribution to supply of NADP(H) in Saccharomyces cerevisiae." FEBS J 272(13);3337-49. PMID: 15978040

Shimokawa79: Shimokawa O, Ishimoto M (1979). "Purification and some properties of inducible tertiary amine N-oxide reductase from Escherichia coli." J Biochem (Tokyo) 1979;86(6);1709-17. PMID: 393699

Silvestro88: Silvestro A, Pommier J, Giordano G (1988). "The inducible trimethylamine-N-oxide reductase of Escherichia coli K12: biochemical and immunological studies." Biochim Biophys Acta 1988;954(1);1-13. PMID: 3282544

Snell75: Snell EE (1975). "Tryptophanase: structure, catalytic activities, and mechanism of action." Adv Enzymol Relat Areas Mol Biol 1975;42;287-333. PMID: 236639

Sodek80: Sodek, Ladaslav, Lea, Peter, Miflin, Benjamin "Distribution and properties of a potassium-dependdent asparaginase isolated from developing seeds of Pisum sativa and other plants." Plant Physiology, 1980, 65:22-26.

Sugimori13: Sugimori D, Ogasawara J, Okuda K, Murayama K (2013). "Purification, characterization, molecular cloning, and extracellular production of a novel bacterial glycerophosphocholine cholinephosphodiesterase from Streptomyces sanglieri." J Biosci Bioeng. PMID: 24211038

Venkov71: Venkov P, Schlessinger D, Longo D (1971). "Inhibition of ribonuclease II of Escherichia coli by sodium ions, adenosine-5'-triphosphate, and transfer ribonucleic acid." J Bacteriol 108(1);601-3. PMID: 4941574

Yang06c: Yang Y, Yuan JS, Ross J, Noel JP, Pichersky E, Chen F (2006). "An Arabidopsis thaliana methyltransferase capable of methylating farnesoic acid." Arch Biochem Biophys 448(1-2);123-32. PMID: 16165084


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 28, 2014, BIOCYC13B.