Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| CMP-N-acetylneuraminate biosynthesis I (eukaryotes) Accession ID: BioCyc:HUMAN_PWY-6138 |
|
Ghaderi D, Strauss HM, Reinke S, Cirak S, Reutter W, Lucka L, Hinderlich S. Evidence for dynamic interplay of different oligomeric states of UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase by biophysical methods. J Mol Biol. 2007 Jun 08;369(3):746–58. doi: 10.1016/j.jmb.2007.03.037. PMID: 17448495.; Inoue S, Kitajima K. KDN (deaminated neuraminic acid): dreamful past and exciting future of the newest member of the sialic acid family. Glycoconj J. 2006 Jul;23(5-6):277–90. doi: 10.1007/s10719-006-6484-y. PMID: 16897172.; Tanner ME. The enzymes of sialic acid biosynthesis. Bioorg Chem. 2005 Jun;33(3):216–28. doi: 10.1016/j.bioorg.2005.01.005. PMID: 15888312. |
| protein citrullination Accession ID: BioCyc:HUMAN_PWY-4921 |
|
Curis E, Nicolis I, Moinard C, Osowska S, Zerrouk N, Bénazeth S, Cynober L. Almost all about citrulline in mammals. Amino Acids. 2005 Nov;29(3):177–205. doi: 10.1007/s00726-005-0235-4. PMID: 16082501. |
| 3-phosphoinositide biosynthesis Accession ID: BioCyc:HUMAN_PWY-6352 |
|
Kapeller R, Cantley LC. Phosphatidylinositol 3-kinase. Bioessays. 1994 Aug;16(8):565–76. doi: 10.1002/bies.950160810. PMID: 8086005. |
| polymethylated quercetin glucoside biosynthesis I - quercetin series (Chrysosplenium) Accession ID: BioCyc:META_PWY-7150 |
|
Anzellotti D, Ibrahim RK. Molecular characterization and functional expression of flavonol 6-hydroxylase. BMC Plant Biol. 2004 Dec 13;4():20. PMID: 15596008; PMCID: PMC544895.; Seguin J, Muzac I, Ibrahim RK. Purification and immunological characterization of a recombinant trimethylflavonol 3'-O-methyltransferase. Phytochemistry. 1998 Sep;49(2):319–25. doi: 10.1016/s0031-9422(98)00138-1. PMID: 9747535.; Gauthier A, Gulick PJ, Ibrahim RK. cDNA cloning and characterization of a 3'/5'-O-methyltransferase for partially methylated flavonols from Chrysosplenium americanum. Plant Mol Biol. 1996 Dec;32(6):1163–9. doi: 10.1007/bf00041401. PMID: 9002616.; Latchinian-Sadek L, Ibrahim RK. Flavonol ring B-specific O-glucosyltransferases: Purification, production of polyclonal antibodies, and immunolocalization. Archives of Biochemistry and Biophysics. 1991 Aug;289(1):230–6. doi: 10.1016/0003-9861(91)90466-v.; Khouri HE, De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. III. Purification and kinetic analysis of S-adenosyl-L-methionine:3-methylquercetin 7-O-methyltransferase. Arch Biochem Biophys. 1988 Aug 15;265(1):1–7. doi: 10.1016/0003-9861(88)90364-5. PMID: 3415239.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. I. Partial purification and some properties of S-adenosyl-l-methionine: Flavonol 3-, 6-, 7-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):596–605. doi: 10.1016/0003-9861(85)90205-x.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. II. Substrate interaction and product inhibition studies of flavonol 3-, 6-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):606–18. doi: 10.1016/0003-9861(85)90206-1.; KHOURI H, IBRAHIM RK. Kinetic mechanism of a flavonol-ring-B O-glucosyltransferase from Chrysosplenium americanum. European Journal of Biochemistry. 1984 Aug;142(3):559–64. doi: 10.1111/j.1432-1033.1984.tb08322.x.; Bajaj KL, de Luca V, Khouri H, Ibrahim RK. Purification and Properties of Flavonol-Ring B Glucosyltransferase from Chrysosplenium americanum. Plant Physiol. 1983 Jul 01;72(3):891–6. doi: 10.1104/pp.72.3.891. |
| polymethylated quercetin glucoside biosynthesis II - quercetagetin series (Chrysosplenium) Accession ID: BioCyc:META_PWY-7151 |
|
Anzellotti D, Ibrahim RK. Molecular characterization and functional expression of flavonol 6-hydroxylase. BMC Plant Biol. 2004 Dec 13;4():20. PMID: 15596008; PMCID: PMC544895.; Gauthier A, Gulick PJ, Ibrahim RK. cDNA cloning and characterization of a 3'/5'-O-methyltransferase for partially methylated flavonols from Chrysosplenium americanum. Plant Mol Biol. 1996 Dec;32(6):1163–9. doi: 10.1007/bf00041401. PMID: 9002616.; Latchinian-Sadek L, Ibrahim RK. Flavonol ring B-specific O-glucosyltransferases: Purification, production of polyclonal antibodies, and immunolocalization. Archives of Biochemistry and Biophysics. 1991 Aug;289(1):230–6. doi: 10.1016/0003-9861(91)90466-v.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. I. Partial purification and some properties of S-adenosyl-l-methionine: Flavonol 3-, 6-, 7-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):596–605. doi: 10.1016/0003-9861(85)90205-x.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. II. Substrate interaction and product inhibition studies of flavonol 3-, 6-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):606–18. doi: 10.1016/0003-9861(85)90206-1.; KHOURI H, IBRAHIM RK. Kinetic mechanism of a flavonol-ring-B O-glucosyltransferase from Chrysosplenium americanum. European Journal of Biochemistry. 1984 Aug;142(3):559–64. doi: 10.1111/j.1432-1033.1984.tb08322.x.; Bajaj KL, de Luca V, Khouri H, Ibrahim RK. Purification and Properties of Flavonol-Ring B Glucosyltransferase from Chrysosplenium americanum. Plant Physiol. 1983 Jul 01;72(3):891–6. doi: 10.1104/pp.72.3.891.; Schnitsky S. Own your own telephone system? Dent Manage. 1976 Jun;16(6):15–6, 19, 21. PMID: 1068865. |
| protein N-glycosylation processing phase (yeast) Accession ID: BioCyc:META_PWY-7918 |
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Herscovics A. Processing glycosidases of Saccharomyces cerevisiae. Biochimica et Biophysica Acta (BBA) - General Subjects. 1999 Jan;1426(2):275–85. doi: 10.1016/s0304-4165(98)00129-9.; Daniel PF, Winchester B, Warren CD. Mammalian alpha-mannosidases--multiple forms but a common purpose? Glycobiology. 1994 Oct;4(5):551–66. doi: 10.1093/glycob/4.5.551. PMID: 7881169. |
| homogalacturonan biosynthesis Accession ID: BioCyc:META_PWY-1061 |
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Sterling JD, Quigley HF, Orellana A, Mohnen D. The catalytic site of the pectin biosynthetic enzyme alpha-1,4-galacturonosyltransferase is located in the lumen of the Golgi. Plant Physiol. 2001 Sep;127(1):360–71. PMID: 11553763; PMCID: PMC117991.; Ishikawa M, Kuroyama H, Takeuchi Y, Tsumuraya Y. Characterization of pectin methyltransferase from soybean hypocotyls. Planta. 2000 Apr;210(5):782–91. doi: 10.1007/s004250050680. PMID: 10805450.; Goubet F, Mohnen D. Solubilization and partial characterization of homogalacturonan-methyltransferase from microsomal membranes of suspension-cultured tobacco cells. Plant Physiol. 1999 Sep;121(1):281–90. PMID: 10482684; PMCID: PMC59378. |
| berberine biosynthesis Accession ID: BioCyc:META_PWY-3901 |
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Samanani N, Park SU, Facchini PJ. Cell type-specific localization of transcripts encoding nine consecutive enzymes involved in protoberberine alkaloid biosynthesis. Plant Cell. 2005 Mar;17(3):915–26. PMID: 15722473; PMCID: PMC1069708.; Ikezawa N, Tanaka M, Nagayoshi M, Shinkyo R, Sakaki T, Inouye K, Sato F. Molecular Cloning and Characterization of CYP719, a Methylenedioxy Bridge-forming Enzyme That Belongs to a Novel P450 Family, from cultured Coptis japonica Cells. Journal of Biological Chemistry. 2003 Oct;278(40):38557–65. doi: 10.1074/jbc.m302470200.; Bock A, Wanner G, Zenk MH. Immunocytological localization of two enzymes involved in berberine biosynthesis. Planta. 2002 Nov;216(1):57–63. doi: 10.1007/s00425-002-0867-5. PMID: 12430014.; Facchini PJ. A |
| spermidine biosynthesis I Accession ID: BioCyc:META_BSUBPOLYAMSYN-PWY |
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Li Y, Hess S, Pannell LK, Tabor CW, Tabor H. In vivo mechanism-based inactivation of S -adenosylmethionine decarboxylases from Escherichia coli , Salmonella typhimurium , and Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 2001 Aug 28;98(19):10578–83. doi: 10.1073/pnas.181341198.; Hamasaki-Katagiri N, Tabor CW, Tabor H. Spermidine biosynthesis in Saccharomyces cerevisae: polyamine requirement of a null mutant of the SPE3 gene (spermidine synthase). Gene. 1997 Mar 10;187(1):35–43. doi: 10.1016/s0378-1119(96)00660-9. PMID: 9073064. |
| 3-phosphoinositide biosynthesis Accession ID: BioCyc:META_PWY-6352 |
|
Kapeller R, Cantley LC. Phosphatidylinositol 3-kinase. Bioessays. 1994 Aug;16(8):565–76. doi: 10.1002/bies.950160810. PMID: 8086005. |
| suberin monomers biosynthesis Accession ID: BioCyc:META_PWY-1121 |
|
Compagnon V, Diehl P, Benveniste I, Meyer D, Schaller H, Schreiber L, Franke R, Pinot F. CYP86B1 is required for very long chain omega-hydroxyacid and alpha, omega -dicarboxylic acid synthesis in root and seed suberin polyester. Plant Physiol. 2009 Aug;150(4):1831–43. PMID: 19525321; PMCID: PMC2719127. |
| protein N-glycosylation initial phase (eukaryotic) Accession ID: BioCyc:META_MANNOSYL-CHITO-DOLICHOL-BIOSYNTHESIS |
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Helenius A, Aebi M. Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem. 2004;73():1019–49. doi: 10.1146/annurev.biochem.73.011303.073752. PMID: 15189166.; Chantret I, Dancourt J, Dupré T, Delenda C, Bucher S, Vuillaumier-Barrot S, Ogier de Baulny H, Peletan C, Danos O, Seta N, Durand G, Oriol R, Codogno P, Moore SE. A deficiency in dolichyl-P-glucose:Glc1Man9GlcNAc2-PP-dolichyl alpha3-glucosyltransferase defines a new subtype of congenital disorders of glycosylation. J Biol Chem. 2003 Mar 14;278(11):9962–71. doi: 10.1074/jbc.m211950200. PMID: 12480927.; Burda P, Aebi M. The dolichol pathway of N-linked glycosylation. Biochimica et Biophysica Acta (BBA) - General Subjects. 1999 Jan;1426(2):239–57. doi: 10.1016/s0304-4165(98)00127-5.; Runge KW, Robbins PW. A new yeast mutation in the glucosylation steps of the asparagine-linked glycosylation pathway. Formation of a novel asparagine-linked oligosaccharide containing two glucose residues. Journal of Biological Chemistry. 1986 Nov;261(33):15582–90. doi: 10.1016/s0021-9258(18)66754-7. |
| NADH to cytochrome bo oxidase electron transfer I Accession ID: BioCyc:META_PWY0-1335 |
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| Lipid A-core biosynthesis (E. coli K-12) Accession ID: BioCyc:META_LIPA-CORESYN-PWY |
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Raetz CRH, Whitfield C. Lipopolysaccharide Endotoxins. Annu. Rev. Biochem. 2002 Jun;71(1):635–700. doi: 10.1146/annurev.biochem.71.110601.135414. |
| pyrimidine deoxyribonucleotides de novo biosynthesis III Accession ID: BioCyc:META_PWY-6545 |
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Leduc D, Graziani S, Meslet-Cladiere L, Sodolescu A, Liebl U, Myllykallio H. Two distinct pathways for thymidylate (dTMP) synthesis in (hyper)thermophilic Bacteria and Archaea. Biochem Soc Trans. 2004 Apr;32(Pt 2):231–5. doi: 10.1042/bst0320231. PMID: 15046578.; Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science. 2002 Jul 05;297(5578):105–7. doi: 10.1126/science.1072113. PMID: 12029065. |
| γ-butyrobetaine degradation Accession ID: BioCyc:META_PWY-3621 |
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Lindstedt G, Lindstedt S, Midtvedt T, Tofft M. Inducible ?-Butyrobetaine-Degrading Enzymes in Pseudomonas Species AK 1. J Bacteriol. 1970 Mar;101(3):1094–5. doi: 10.1128/jb.101.3.1094-1095.1970. |
| dopamine degradation Accession ID: BioCyc:META_PWY6666-2 |
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Eisenhofer G, Kopin IJ, Goldstein DS. Catecholamine metabolism: a contemporary view with implications for physiology and medicine. Pharmacol Rev. 2004 Sep;56(3):331–49. doi: 10.1124/pr.56.3.1. PMID: 15317907. |
| aromatic biogenic amine degradation (bacteria) Accession ID: BioCyc:META_PWY-7431 |
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Arcos M, Olivera ER, Arias S, Naharro G, Luengo JM. The 3,4-dihydroxyphenylacetic acid catabolon, a catabolic unit for degradation of biogenic amines tyramine and dopamine in Pseudomonas putida U. Environmental Microbiology. 2010 Jun;12(6):1684–704. doi: 10.1111/j.1462-2920.2010.02233.x.; Díaz E, Ferrández A, Prieto MA, García JL. Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev. 2001 Dec;65(4):523–69, table of contents. PMID: 11729263; PMCID: PMC99040.; Roh JH, Suzuki H, Azakami H, Yamashita M, Murooka Y, Kumagai H. Purification, Characterization, and Crystallization of Monoamine Oxidase fromEscherichia coliK-12. Bioscience, Biotechnology, and Biochemistry. 1994 Jan;58(9):1652–6. doi: 10.1271/bbb.58.1652.; Cuskey SM, Olsen RH. Catabolism of aromatic biogenic amines by Pseudomonas aeruginosa PAO1 via meta cleavage of homoprotocatechuic acid. J Bacteriol. 1988 Jan;170(1):393–9. doi: 10.1128/jb.170.1.393-399.1988.; Cuskey SM, Peccoraro V, Olsen RH. Initial catabolism of aromatic biogenic amines by Pseudomonas aeruginosa PAO: pathway description, mapping of mutations, and cloning of essential genes. J Bacteriol. 1987 Jun;169(6):2398–404. doi: 10.1128/jb.169.6.2398-2404.1987.; Kutty RK, Devi NA, Veeraswamy M, Ramesh S, Rao PV. Degradation of (+/-)-synephrine by Arthrobacter synephrinum. Oxidation of 3,4-dihydroxyphenylacetate to 2-hydroxy-5-carboxymethyl-muconate semialdehyde. Biochem J. 1977 Oct 01;167(1):163–70. PMID: 588248; PMCID: PMC1183633. |
| L-lysine degradation XI (mammalian) Accession ID: BioCyc:META_LYSINE-DEG1-PWY |
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Broquist HP. Lysine-pipecolic acid metabolic relationships in microbes and mammals. Annu Rev Nutr. 1991;11():435–48. doi: 10.1146/annurev.nu.11.070191.002251. PMID: 1909881. |
| 4-deoxy-L-threo-hex-4-enopyranuronate degradation Accession ID: BioCyc:META_PWY-6507 |
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Blot N, Berrier C, Hugouvieux-Cotte-Pattat N, Ghazi A, Condemine G. The Oligogalacturonate-specific Porin KdgM of Erwinia chrysanthemi Belongs to a New Porin Family. Journal of Biological Chemistry. 2002 Mar;277(10):7936–44. doi: 10.1074/jbc.m109193200.; Hugouvieux-Cotte-Pattat N, Condemine G, Nasser W, Reverchon S. Regulation of pectinolysis in Erwinia chrysanthemi. Annu Rev Microbiol. 1996;50():213–57. doi: 10.1146/annurev.micro.50.1.213. PMID: 8905080. |