Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| mevalonate pathway Accession ID: BioCyc:HUMAN_PWY-922 |
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| superpathway NAD/NADP - NADH/NADPH interconversion (yeast) Accession ID: BioCyc:META_PWY-7245 |
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Feng Y, Li W, Li J, Wang J, Ge J, Xu D, Liu Y, Wu K, Zeng Q, Wu JW, Tian C, Zhou B, Yang M. Structural insight into the type-II mitochondrial NADH dehydrogenases. Nature. 2012 Nov 15;491(7424):478–82. doi: 10.1038/nature11541. PMID: 23086143.; Gossmann TI, Ziegler M, Puntervoll P, de Figueiredo LF, Schuster S, Heiland I. NAD+ biosynthesis and salvage – a phylogenetic perspective. The FEBS Journal. 2012 Apr 04;279(18):3355–63. doi: 10.1111/j.1742-4658.2012.08559.x.; Lu S, Lin S. Phosphate-responsive Signaling Pathway Is a Novel Component of NAD+ Metabolism in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2011 Apr;286(16):14271–81. doi: 10.1074/jbc.m110.217885.; Miyagi H, Kawai S, Murata K. Two Sources of Mitochondrial NADPH in the Yeast Saccharomyces cerevisiae. Journal of Biological Chemistry. 2009 Mar;284(12):7553–60. doi: 10.1074/jbc.m804100200.; Koch-Nolte F, Haag F, Guse AH, Lund F, Ziegler M. Emerging Roles of NAD + and Its Metabolites in Cell SignalingA report on the NAD2008 symposium, Hamburg, Germany, 14 to 17 September 2008. Sci. Signal. 2009 Feb 10;2(57). doi: 10.1126/scisignal.257mr1.; Bieganowski P, Seidle HF, Wojcik M, Brenner C. Synthetic Lethal and Biochemical Analyses of NAD and NADH Kinases in Saccharomyces cerevisiae Establish Separation of Cellular Functions. Journal of Biological Chemistry. 2006 Aug;281(32):22439–45. doi: 10.1074/jbc.m513919200.; Minard KI, McAlister-Henn L. Sources of NADPH in Yeast Vary with Carbon Source. Journal of Biological Chemistry. 2005 Dec;280(48):39890–6. doi: 10.1074/jbc.m509461200.; Shi F, Kawai S, Mori S, Kono E, Murata K. Identification of ATP-NADH kinase isozymes and their contribution to supply of NADP(H) in Saccharomyces cerevisiae. The FEBS Journal. 2005 Jun 24;272(13):3337–49. doi: 10.1111/j.1742-4658.2005.04749.x.; Contreras-Shannon V, Lin A, McCammon MT, McAlister-Henn L. Kinetic Properties and Metabolic Contributions of Yeast Mitochondrial and Cytosolic NADP+-specific Isocitrate Dehydrogenases. Journal of Biological Chemistry. 2005 Feb;280(6):4469–75. doi: 10.1074/jbc.m410140200.; Strand MK, Stuart GR, Longley MJ, Graziewicz MA, Dominick OC, Copeland WC. POS5 Gene of Saccharomyces cerevisiae Encodes a Mitochondrial NADH Kinase Required for Stability of Mitochondrial DNA. Eukaryot Cell. 2003 Aug;2(4):809–20. doi: 10.1128/ec.2.4.809-820.2003.; Outten CE, Culotta VC. A novel NADH kinase is the mitochondrial source of NADPH in Saccharomyces cerevisiae. EMBO J. 2003 May 01;22(9):2015–24. PMID: 12727869; PMCID: PMC156083.; Grabowska D, Chelstowska A. The ALD6 Gene Product Is Indispensable for Providing NADPH in Yeast Cells Lacking Glucose-6-phosphate Dehydrogenase Activity. Journal of Biological Chemistry. 2003 Apr;278(16):13984–8. doi: 10.1074/jbc.m210076200.; Påhlman I, Larsson C, Averét N, Bunoust O, Boubekeur S, Gustafsson L, Rigoulet M. Kinetic Regulation of the Mitochondrial Glycerol-3-phosphate Dehydrogenase by the External NADH Dehydrogenase in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2002 Aug;277(31):27991–5. doi: 10.1074/jbc.m204079200.; Minard KI, McAlister-Henn L. Antioxidant function of cytosolic sources of NADPH in yeast. Free Radic Biol Med. 2001 Sep 15;31(6):832–43. doi: 10.1016/s0891-5849(01)00666-9. PMID: 11557322.; Kawai S, Suzuki S, Mori S, Murata K. Molecular cloning and identification of UTR1 of a yeast Saccharomyces cerevisiae as a gene encoding an NAD kinase. FEMS Microbiol Lett. 2001 Jun 25;200(2):181–4. doi: 10.1111/j.1574-6968.2001.tb10712.x. PMID: 11425472.; Overkamp KM, Bakker BM, Ko¨tter P, van Tuijl A, de Vries S, van Dijken JP, Pronk JT. In Vivo Analysis of the Mechanisms for Oxidation of Cytosolic NADH by Saccharomyces cerevisiae Mitochondria. J Bacteriol. 2000 May 15;182(10):2823–30. doi: 10.1128/jb.182.10.2823-2830.2000.; Luttik MAH, Overkamp KM, Kötter P, de Vries S, van Dijken JP, Pronk JT. The Saccharomyces cerevisiae NDE1 and NDE2 Genes Encode Separate Mitochondrial NADH Dehydrogenases Catalyzing the Oxidation of Cytosolic NADH. Journal of Biological Chemistry. 1998 Sep;273(38):24529–34. doi: 10.1074/jbc.273.38.24529.; Small WC, McAlister-Henn L. Identification of a Cytosolically Directed NADH Dehydrogenase in Mitochondria of Saccharomyces cerevisiae. J Bacteriol. 1998 Aug 15;180(16):4051–5. doi: 10.1128/jb.180.16.4051-4055.1998.; Tessier WD, Meaden PG, Dickinson FM, Midgley M. Identification and disruption of the gene encoding the K(+)-activated acetaldehyde dehydrogenase of Saccharomyces cerevisiae. FEMS Microbiol Lett. 1998 Jul 01;164(1):29–34. doi: 10.1111/j.1574-6968.1998.tb13063.x. PMID: 9675847.; Wang X, Mann CJ, Bai Y, Ni L, Weiner H. Molecular Cloning, Characterization, and Potential Roles of Cytosolic and Mitochondrial Aldehyde Dehydrogenases in Ethanol Metabolism in Saccharomyces cerevisiae. J Bacteriol. 1998 Feb 15;180(4):822–30. doi: 10.1128/jb.180.4.822-830.1998.; Meaden PG, Dickinson FM, Mifsud A, Tessier W, Westwater J, Bussey H, Midgley M. The ALD6 gene of Saccharomyces cerevisiae encodes a cytosolic, Mg(2+)-activated acetaldehyde dehydrogenase. Yeast. 1997 Nov;13(14):1319–27. doi: 10.1002/(sici)1097-0061(199711)13:14<1319::aid-yea183>3.0.co;2-t. PMID: 9392076.; Wang X, Bai Y, Ni L, Weiner H. Saccharomyces cerevisiae aldehyde dehydrogenases. Identification and expression. Adv Exp Med Biol. 1997;414():277–80. doi: 10.1007/978-1-4615-5871-2_32. PMID: 9059631.; Loftus TM, Hall LV, Anderson SL, McAlister-Henn L. Isolation, characterization, and disruption of the yeast gene encoding cytosolic NADP-specific isocitrate dehydrogenase. Biochemistry. 1994 Aug 16;33(32):9661–7. doi: 10.1021/bi00198a035. PMID: 8068643.; DE VRIES S, VAN WITZENBURG R, GRIVELL LA, MARRES CAM. Primary structure and import pathway of the rotenone-insensitive NADH-ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae. European Journal of Biochemistry. 1992 Feb;203(3):587–92. doi: 10.1111/j.1432-1033.1992.tb16587.x.; MARRES CAM, de VRIES S, GRIVELL LA. Isolation and inactivation of the nuclear gene encoding the rotenone-insensitive internal NADH: ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae. European Journal of Biochemistry. 1991 Feb;195(3):857–62. doi: 10.1111/j.1432-1033.1991.tb15775.x.; Nogae I, Johnston M. Isolation and characterization of the ZWF1 gene of Saccharomyces cerevisiae, encoding glucose-6-phosphate dehydrogenase. Gene. 1990 Dec 15;96(2):161–9. doi: 10.1016/0378-1119(90)90248-p. PMID: 2269430.; de VRIES S, GRIVELL LA. Purification and characterization of a rotenone-insensitive NADH: Q6 oxidoreductase from mitochondria of Saccharomyces cerevisiae. European Journal of Biochemistry. 1988 Sep;176(2):377–84. doi: 10.1111/j.1432-1033.1988.tb14292.x.; Bruinenberg PM. The NADP(H) redox couple in yeast metabolism. Antonie Van Leeuwenhoek. 1986;52(5):411–29. doi: 10.1007/bf00393469. PMID: 3789705. |
| superpathway of glycol metabolism and degradation Accession ID: BioCyc:META_GLYCOL-GLYOXDEG-PWY |
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| chitin biosynthesis Accession ID: BioCyc:META_PWY-6981 |
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Merzendorfer H. The cellular basis of chitin synthesis in fungi and insects: Common principles and differences. European Journal of Cell Biology. 2011 Sep;90(9):759–69. doi: 10.1016/j.ejcb.2011.04.014.; Lenardon MD, Munro CA, Gow NA. Chitin synthesis and fungal pathogenesis. Current Opinion in Microbiology. 2010 Aug;13(4):416–23. doi: 10.1016/j.mib.2010.05.002.; Merzendorfer H. Insect chitin synthases: a review. Journal of Comparative Physiology B. 2005 Aug 02;176(1):1–15. doi: 10.1007/s00360-005-0005-3.; Merzendorfer H, Zimoch L. Chitin metabolism in insects: structure, function and regulation of chitin synthases and chitinases. J Exp Biol. 2003 Dec;206(Pt 24):4393–412. doi: 10.1242/jeb.00709. PMID: 14610026. |
| superpathay of heme b biosynthesis from glutamate Accession ID: BioCyc:META_PWY-5918 |
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Oborník M, Green BR. Mosaic origin of the heme biosynthesis pathway in photosynthetic eukaryotes. Mol Biol Evol. 2005 Dec;22(12):2343–53. doi: 10.1093/molbev/msi230. PMID: 16093570. |
| pyrimidine deoxyribonucleotides de novo biosynthesis II Accession ID: BioCyc:META_PWY-7187 |
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| superpathway of C1 compounds oxidation to CO2 Accession ID: BioCyc:META_PWY-1882 |
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Acharya P, Goenrich M, Hagemeier CH, Demmer U, Vorholt JA, Thauer RK, Ermler U. How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. J Biol Chem. 2005 Apr 08;280(14):13712–9. doi: 10.1074/jbc.m412320200. PMID: 15632161.; Ermler U, Hagemeier CH, Roth A, Demmer U, Grabarse W, Warkentin E, Vorholt JA. Structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens AM1. Structure. 2002 Aug;10(8):1127–37. doi: 10.1016/s0969-2126(02)00802-x. PMID: 12176390.; Vorholt JA, Chistoserdova L, Lidstrom ME, Thauer RK. The NADP-Dependent Methylene Tetrahydromethanopterin Dehydrogenase in Methylobacterium extorquens AM1. J Bacteriol. 1998 Oct 15;180(20):5351–6. doi: 10.1128/jb.180.20.5351-5356.1998. |
| superpathway of Clostridium acetobutylicum acidogenic fermentation Accession ID: BioCyc:META_PWY-6590 |
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Thorpe C, Kim JP. Structure and mechanism of action of the Acyl-CoA dehydrogenases 1. The FASEB Journal. 1995 Jun;9(9):718–25. doi: 10.1096/fasebj.9.9.7601336.; Jones DT, Woods DR. Acetone-butanol fermentation revisited. Microbiol Rev. 1986 Dec;50(4):484–524. doi: 10.1128/mr.50.4.484-524.1986.; Hauge JG, Crane FL, Beinert H. ON THE MECHANISM OF DEHYDROGENATION OF FATTY ACYL DERIVATIVES OF COENZYME A. Journal of Biological Chemistry. 1956 Apr;219(2):727–33. doi: 10.1016/s0021-9258(18)65732-1.; Green DE, Mii S, Mahler HR, Bock RM. STUDIES ON THE FATTY ACID OXIDIZING SYSTEM OF ANIMAL TISSUES. Journal of Biological Chemistry. 1954 Jan;206(1):1–12. doi: 10.1016/s0021-9258(18)71290-8.; MAHLER HR. Studies on the fatty acid oxidizing system of animal tissues. IV. The prosthetic group of butyryl coenzyme A dehydrogenase. J Biol Chem. 1954 Jan;206(1):13–26. PMID: 13130522. |
| superpathway of tetrahydrofolate biosynthesis and salvage Accession ID: BioCyc:META_FOLSYN-PWY |
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| L-phenylalanine degradation IV (mammalian, via side chain) Accession ID: BioCyc:META_PWY-6318 |
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Williams RA, Mamotte CD, Burnett JR. Phenylketonuria: an inborn error of phenylalanine metabolism. Clin Biochem Rev. 2008 Feb;29(1):31–41. PMID: 18566668; PMCID: PMC2423317.; Wada M. Measurement of hepatic phenylalanine metabolism in children using the [(13)C]-phenylalanine breath test and gas chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Jun 25;806(1):5–10. doi: 10.1016/j.jchromb.2004.02.023. PMID: 15149604.; Bier DM. Amino acid pharmacokinetics and safety assessment. J Nutr. 2003 Jun;133(6 Suppl 1):2034S–2039S. doi: 10.1093/jn/133.6.2034s. PMID: 12771361.; Kaufman S. A model of human phenylalanine metabolism in normal subjects and in phenylketonuric patients. Proc. Natl. Acad. Sci. U.S.A. 1999 Mar 16;96(6):3160–4. doi: 10.1073/pnas.96.6.3160.; Lindblad B, Lindstedt G, Lindstedt S, Rundgren M. Purification and some properties of human 4-hydroxyphenylpyruvate dioxygenase (I). Journal of Biological Chemistry. 1977 Jul;252(14):5073–84. doi: 10.1016/s0021-9258(17)40160-8.; Yang H-T, Neff NH. ß-PHENYLETHYLAMINE: A SPECIFIC SUBSTRATE FOR TYPE B MONOAMINE OXIDASE OF BRAIN. The Journal of Pharmacology and Experimental Therapeutics. 1973 Nov;187(2):365–71. doi: 10.1016/s0022-3565(25)29682-3.; Fellman JH, Fujita TS, Roth ES. Assay, properties and tissue distribution of p-hydroxyphenylpyruvate hydroxylase. Biochimica et Biophysica Acta (BBA) - Enzymology. 1972 Sep;284(1):90–100. doi: 10.1016/0005-2744(72)90048-4. |
| superpathway of L-homoserine and L-methionine biosynthesis Accession ID: BioCyc:META_METSYN-PWY |
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Banerjee RV, Matthews RG. Cobalamin-dependent methionine synthase. FASEB J. 1990 Mar;4(5):1450–9. doi: 10.1096/fasebj.4.5.2407589. PMID: 2407589.; Smith DA. S-amino acid metabolism and its regulation in Escherichia coli and Salmonella typhimurium. Adv Genet. 1971;16():141–65. doi: 10.1016/s0065-2660(08)60357-0. PMID: 4947102. |
| ketogenesis Accession ID: BioCyc:META_PWY66-367 |
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Fukao T, Lopaschuk GD, Mitchell GA. Pathways and control of ketone body metabolism: on the fringe of lipid biochemistry. Prostaglandins Leukot Essent Fatty Acids. 2004 Mar;70(3):243–51. doi: 10.1016/j.plefa.2003.11.001. PMID: 14769483. |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis I Accession ID: BioCyc:META_P4-PWY |
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Devenish SR, Blunt JW, Gerrard JA. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem. 2010 Jun 24;53(12):4808–12. doi: 10.1021/jm100349s. PMID: 20503968.; Farkas W, Gilvarg C. The Reduction Step in Diaminopimelic Acid Biosynthesis. Journal of Biological Chemistry. 1965 Dec;240(12):4717–22. doi: 10.1016/s0021-9258(18)97014-6. |
| superpathway of cholesterol biosynthesis Accession ID: BioCyc:META_PWY66-5 |
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Mo C, Valachovic M, Randall SK, Nickels JT, Bard M. Protein-protein interactions among C-4 demethylation enzymes involved in yeast sterol biosynthesis. Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9739–44. PMID: 12119386; PMCID: PMC124998. |
| chorismate biosynthesis from 3-dehydroquinate Accession ID: BioCyc:META_PWY-6163 |
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Tzin V, Malitsky S, Zvi MMB, Bedair M, Sumner L, Aharoni A, Galili G. Expression of a bacterial feedback-insensitive 3-deoxy- |
| formaldehyde oxidation VI (H4MPT pathway) Accession ID: BioCyc:META_PWY-1723 |
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Acharya P, Goenrich M, Hagemeier CH, Demmer U, Vorholt JA, Thauer RK, Ermler U. How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. J Biol Chem. 2005 Apr 08;280(14):13712–9. doi: 10.1074/jbc.m412320200. PMID: 15632161.; Marx CJ, Chistoserdova L, Lidstrom ME. Formaldehyde-Detoxifying Role of theTetrahydromethanopterin-Linked Pathway in Methylobacteriumextorquens AM1. J Bacteriol. 2003 Dec 15;185(24):7160–8. doi: 10.1128/jb.185.23.7160-7168.2003.; Ermler U, Hagemeier CH, Roth A, Demmer U, Grabarse W, Warkentin E, Vorholt JA. Structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens AM1. Structure. 2002 Aug;10(8):1127–37. doi: 10.1016/s0969-2126(02)00802-x. PMID: 12176390.; Vorholt JA, Chistoserdova L, Lidstrom ME, Thauer RK. The NADP-Dependent Methylene Tetrahydromethanopterin Dehydrogenase in Methylobacterium extorquens AM1. J Bacteriol. 1998 Oct 15;180(20):5351–6. doi: 10.1128/jb.180.20.5351-5356.1998. |
| superpathway of L-threonine biosynthesis Accession ID: BioCyc:META_THRESYN-PWY |
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Chassagnole C, Raïs B, Quentin E, Fell DA, Mazat JP. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem J. 2001 Jun 01;356(Pt 2):415–23. PMID: 11368768; PMCID: PMC1221852.; Shames SL, Ash DE, Wedler FC, Villafranca JJ. Interaction of aspartate and aspartate-derived antimetabolites with the enzymes of the threonine biosynthetic pathway of Escherichia coli. Journal of Biological Chemistry. 1984 Dec;259(24):15331–9. doi: 10.1016/s0021-9258(17)42554-3.; Cohen GN, Hirsch M. THREONINE SYNTHASE, A SYSTEM SYNTHESIZING |
| Entner-Doudoroff pathway III (semi-phosphorylative) Accession ID: BioCyc:META_PWY-2221 |
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Siebers B, Schönheit P. Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Curr Opin Microbiol. 2005 Dec;8(6):695–705. doi: 10.1016/j.mib.2005.10.014. PMID: 16256419.; Tomlinson GA, Koch TK, Hochstein LI. The metabolism of carbohydrates by extremely halophilic bacteria: glucose metabolism via a modified Entner-Doudoroff pathway. Can. J. Microbiol. 1974 Aug 01;20(8):1085–91. doi: 10.1139/m74-170. |
| L-tryptophan degradation III (eukaryotic) Accession ID: BioCyc:META_TRYPTOPHAN-DEGRADATION-1 |
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| superpathway of S-adenosyl-L-methionine biosynthesis Accession ID: BioCyc:META_MET-SAM-PWY |
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