Pathways Knowlegdes
Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit
| Pathway | DOIs | Note |
|---|---|---|
| nitrate reduction IX (dissimilatory) Accession ID: BioCyc:META_PWY0-1581 |
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Garland PB, Downie JA, Haddock BA. Proton translocation and the respiratory nitrate reductase of Escherichia coli. Biochem J. 1975 Dec;152(3):547–59. PMID: 5996; PMCID: PMC1172508.; Miki K, Lin EC. Electron transport chain from glycerol 3-phosphate to nitrate in Escherichia coli. J Bacteriol. 1975 Dec;124(3):1288–94. doi: 10.1128/jb.124.3.1288-1294.1975. |
| superpathway of b heme biosynthesis from glycine Accession ID: BioCyc:META_PWY-5920 |
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Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD. Computational prediction of human metabolic pathways from the complete human genome. Genome Biology. 2004 Dec 22;6(1):r2. doi: 10.1186/gb-2004-6-1-r2.; Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB. Computational Analysis of Plasmodium falciparum Metabolism: Organizing Genomic Information to Facilitate Drug Discovery. Genome Res. 2004 Apr 12;14(5):917–24. doi: 10.1101/gr.2050304.; Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 01;32(Database issue):D311–4. PMID: 14681421; PMCID: PMC308767.; Frankenberg N, Moser J, Jahn D. Bacterial heme biosynthesis and its biotechnological application. Applied Microbiology and Biotechnology. 2003 Dec 01;63(2):115–27. doi: 10.1007/s00253-003-1432-2.; Panek H, O'Brian MR. A whole genome view of prokaryotic haem biosynthesis. Microbiology (Reading). 2002 Aug;148(Pt 8):2273–82. doi: 10.1099/00221287-148-8-2273. PMID: 12177321. |
| camalexin biosynthesis Accession ID: BioCyc:META_CAMALEXIN-SYN |
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Glawischnig E. The role of cytochrome P450 enzymes in the biosynthesis of camalexin. Biochem Soc Trans. 2006 Dec;34(Pt 6):1206–8. doi: 10.1042/bst0341206. PMID: 17073786.; Schuhegger R, Nafisi M, Mansourova M, Petersen BL, Olsen CE, Svatos A, Halkier BA, Glawischnig E. CYP71B15 (PAD3) catalyzes the final step in camalexin biosynthesis. Plant Physiol. 2006 Aug;141(4):1248–54. PMID: 16766671; PMCID: PMC1533948.; Glawischnig E, Hansen BG, Olsen CE, Halkier BA. Camalexin is synthesized from indole-3-acetaldoxime, a key branching point between primary and secondary metabolism in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2004 May 17;101(21):8245–50. doi: 10.1073/pnas.0305876101.; Naur P, Hansen CH, Bak S, Hansen BG, Jensen NB, Nielsen HL, Halkier BA. CYP79B1 from Sinapis alba converts tryptophan to indole-3-acetaldoxime. Archives of Biochemistry and Biophysics. 2003 Jan;409(1):235–41. doi: 10.1016/s0003-9861(02)00567-2.; Zhao Y, Hull AK, Gupta NR, Goss KA, Alonso J, Ecker JR, Normanly J, Chory J, Celenza JL. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes Dev. 2002 Dec 01;16(23):3100–12. PMID: 12464638; PMCID: PMC187496.; Mikkelsen MD, Hansen CH, Wittstock U, Halkier BA. Cytochrome P450 CYP79B2 from Arabidopsis Catalyzes the Conversion of Tryptophan to Indole-3-acetaldoxime, a Precursor of Indole Glucosinolates and Indole-3-acetic Acid. Journal of Biological Chemistry. 2000 Oct;275(43):33712–7. doi: 10.1074/jbc.m001667200.; Hull AK, Vij R, Celenza JL. Arabidopsis cytochrome P450s that catalyze the first step of tryptophan-dependent indole-3-acetic acid biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 2000 Feb 18;97(5):2379–84. doi: 10.1073/pnas.040569997.; Zook M, Hammerschmidt R. Origin of the thiazole ring of camalexin, a phytoalexin from Arabidopsis thaliana. Plant Physiol. 1997 Feb;113(2):463–8. PMID: 9046593; PMCID: PMC158161. |
| L-tryptophan degradation V (side chain pathway) Accession ID: BioCyc:META_PWY-3162 |
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Narumiya S, Takai K, Tokuyama T, Noda Y, Ushiro H, Hayaishi O. A new metabolic pathway of tryptophan initiated by tryptophan side chain oxidase. Journal of Biological Chemistry. 1979 Aug;254(15):7007–15. doi: 10.1016/s0021-9258(18)50276-3.; Roberts J, Rosenfeld HJ. Isolation, crystallization, and properties of indolyl-3-alkane alpha-hydroxylase. A novel tryptophan-metabolizing enzyme. Journal of Biological Chemistry. 1977 Apr;252(8):2640–7. doi: 10.1016/s0021-9258(17)40506-0.; Takai K, Ushiro H, Noda Y, Narumiya S, Tokuyama T. Crystalline hemoprotein from Pseudomonas that catalyzes oxidation of side chain of tryptophan and other indole derivatives. Journal of Biological Chemistry. 1977 Apr;252(8):2648–56. doi: 10.1016/s0021-9258(17)40507-2. |
| superpathway of sulfate assimilation and cysteine biosynthesis Accession ID: BioCyc:META_SULFATE-CYS-PWY |
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| nitrite oxidation Accession ID: BioCyc:META_P282-PWY |
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Ehrich S, Behrens D, Lebedeva E, Ludwig W, Bock E. A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Archives of Microbiology. 1995 Jul 19;164(1):16–23. doi: 10.1007/s002030050230.; Yamanaka T, Fukumori Y. The nitrite oxidizing system of Nitrobacter winogradskyi. FEMS Microbiol Rev. 1988 Dec;4(4):259–70. doi: 10.1016/0378-1097(88)90246-7. PMID: 2856189.; Aleem MI, Hoch GE, Varner JE. Water as the source of oxidant and reductant in bacterial chemosynthesis. Proc Natl Acad Sci U S A. 1965 Sep;54(3):869–73. PMID: 5217465; PMCID: PMC219757. |
| D-glucarate degradation I Accession ID: BioCyc:META_GLUCARDEG-PWY |
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| superpathway of aromatic compound degradation via 2-hydroxypentadienoate Accession ID: BioCyc:META_PWY-6954 |
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Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Kasai D, Fujinami T, Abe T, Mase K, Katayama Y, Fukuda M, Masai E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J Bacteriol. 2009 Nov;191(21):6758–68. PMID: 19717587; PMCID: PMC2795304.; Takenaka S, Sato T, Koshiya J, Murakami S, Aoki K. Gene cloning and characterization of a deaminase from the 4-amino-3-hydroxybenzoate-assimilating Bordetella sp. strain 10d. FEMS Microbiol Lett. 2009 Sep;298(1):93–8. doi: 10.1111/j.1574-6968.2009.01699.x. PMID: 19594622.; Harwood CS, Parales RE. The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol. 1996;50():553–90. doi: 10.1146/annurev.micro.50.1.553. PMID: 8905091.; Kukor JJ, Olsen RH. Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1. J Bacteriol. 1991 Aug;173(15):4587–94. doi: 10.1128/jb.173.15.4587-4594.1991.; Menn FM, Zylstra GJ, Gibson DT. Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1. Gene. 1991 Jul 31;104(1):91–4. doi: 10.1016/0378-1119(91)90470-v. PMID: 1916282.; Kishore G, Sugumaran M, Vaidyanathan CS. Metabolism of DL-(+/-)-phenylalanine by Aspergillus niger. J Bacteriol. 1976 Oct;128(1):182–91. doi: 10.1128/jb.128.1.182-191.1976.; Wheelis ML, Stanier RY. The genetic control of dissimilatory pathways in Pseudomonas putida. Genetics. 1970 Oct;66(2):245–66. PMID: 5525301; PMCID: PMC1212492. |
| dhurrin degradation Accession ID: BioCyc:META_PWY-5976 |
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Cicek M, Esen A. Structure and expression of a dhurrinase (beta-glucosidase) from sorghum. Plant Physiol. 1998 Apr;116(4):1469–78. PMID: 9536065; PMCID: PMC35055. |
| linustatin bioactivation Accession ID: BioCyc:META_PWY-7091 |
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Zagrobelny M, Møller BL. Cyanogenic glucosides in the biological warfare between plants and insects: the Burnet moth-Birdsfoot trefoil model system. Phytochemistry. 2011 Sep;72(13):1585–92. doi: 10.1016/j.phytochem.2011.02.023. PMID: 21429539.; Kongsawadworakul P, Viboonjun U, Romruensukharom P, Chantuma P, Ruderman S, Chrestin H. The leaf, inner bark and latex cyanide potential of Hevea brasiliensis: evidence for involvement of cyanogenic glucosides in rubber yield. Phytochemistry. 2009 Apr;70(6):730–9. doi: 10.1016/j.phytochem.2009.03.020. PMID: 19409582.; Piotrowski M. Primary or secondary? Versatile nitrilases in plant metabolism. Phytochemistry. 2008 Nov;69(15):2655–67. doi: 10.1016/j.phytochem.2008.08.020. PMID: 18842274.; Zagrobelny M, Bak S, Rasmussen AV, Jørgensen B, Naumann CM, Lindberg Møller B. Cyanogenic glucosides and plant-insect interactions. Phytochemistry. 2004 Feb;65(3):293–306. doi: 10.1016/j.phytochem.2003.10.016. PMID: 14751300.; Vetter J. Plant cyanogenic glycosides. Toxicon. 2000 Jan;38(1):11–36. doi: 10.1016/s0041-0101(99)00128-2. PMID: 10669009.; Jones DA. Why are so many food plants cyanogenic? Phytochemistry. 1998 Jan;47(2):155–62. doi: 10.1016/s0031-9422(97)00425-1. PMID: 9431670.; Hasslacher M, Kratky C, Griengl H, Schwab H, Kohlwein SD. Hydroxynitrile lyase from Hevea brasiliensis: Molecular characterization and mechanism of enzyme catalysis. Proteins. 1997 Mar;27(3):438–49. doi: 10.1002/(sici)1097-0134(199703)27:3<438::aid-prot11>3.3.co;2-r.; Hasslacher M, Schall M, Hayn M, Griengl H, Kohlwein SD, Schwab H. Molecular cloning of the full-length cDNA of (S)-hydroxynitrile lyase from Hevea brasiliensis. Functional expression in Escherichia coli and Saccharomyces cerevisiae and identification of an active site residue. J Biol Chem. 1996 Mar 08;271(10):5884–91. doi: 10.1074/jbc.271.10.5884. PMID: 8621461.; Selmar D, Lieberei R, Biehl B. Mobilization and utilization of cyanogenic glycosides: the linustatin pathway. Plant Physiol. 1988 Mar;86(3):711–6. PMID: 16665975; PMCID: PMC1054557.; Selmar D, Lieberei R, Biehl B, Voigt J. Hevea Linamarase-A Nonspecific beta-Glycosidase. Plant Physiol. 1987 Mar;83(3):557–63. PMID: 16665288; PMCID: PMC1056404.; Fan TW-, Conn EE. Isolation and characterization of two cyanogenic ß-glucosidases from flax seeds. Archives of Biochemistry and Biophysics. 1985 Dec;243(2):361–73. doi: 10.1016/0003-9861(85)90513-2. |
| lotaustralin degradation Accession ID: BioCyc:META_PWY-6002 |
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Morant AV, Bjarnholt N, Kragh ME, Kjaergaard CH, Jørgensen K, Paquette SM, Piotrowski M, Imberty A, Olsen CE, Møller BL, Bak S. The beta-glucosidases responsible for bioactivation of hydroxynitrile glucosides in Lotus japonicus. Plant Physiol. 2008 Jul;147(3):1072–91. PMID: 18467457; PMCID: PMC2442532. |
| purine nucleobases degradation II (anaerobic) Accession ID: BioCyc:META_PWY-5497 |
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Vogels GD, Van der Drift C. Degradation of purines and pyrimidines by microorganisms. Bacteriol Rev. 1976 Jun;40(2):403–68. doi: 10.1128/br.40.2.403-468.1976. |
| L-tryptophan degradation VI (via tryptamine) Accession ID: BioCyc:META_PWY-3181 |
- | Büki KG, Vinh DQ, Horváth I. Partial purification and some properties of tryptophan decarboxylase from a Bacillus strain. Acta Microbiol Hung. 1985;32(1):65–73. PMID: 4036551. |
| ammonia oxidation I (aerobic) Accession ID: BioCyc:META_AMMOXID-PWY |
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Hollocher TC, Tate ME, Nicholas DJ. Oxidation of ammonia by Nitrosomonas europaea. Definite 18O-tracer evidence that hydroxylamine formation involves a monooxygenase. Journal of Biological Chemistry. 1981 Nov;256(21):10834–6. doi: 10.1016/s0021-9258(19)68518-2. |
| fatty acid α-oxidation I Accession ID: BioCyc:META_PWY-2501 |
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Hamberg M, Sanz A, Rodriguez MJ, Calvo AP, Castresana C. Activation of the fatty acid alpha-dioxygenase pathway during bacterial infection of tobacco leaves. Formation of oxylipins protecting against cell death. J Biol Chem. 2003 Dec 19;278(51):51796–805. doi: 10.1074/jbc.m310514200. PMID: 14522973.; Hamberg M, Ponce de León I, Sanz A, Castresana C. Fatty acid alpha-dioxygenases. Prostaglandins Other Lipid Mediat. 2002 Aug;68-69():363–74. doi: 10.1016/s0090-6980(02)00040-0. PMID: 12432929.; De León IP, Sanz A, Hamberg M, Castresana C. Involvement of the Arabidopsis alpha-DOX1 fatty acid dioxygenase in protection against oxidative stress and cell death. Plant J. 2002 Jan;29(1):61–2. doi: 10.1046/j.1365-313x.2002.01195.x. PMID: 12060227.; Saffert A, Hartmann-Schreier J, Schön A, Schreier P. A dual function alpha-dioxygenase-peroxidase and NAD(+) oxidoreductase active enzyme from germinating pea rationalizing alpha-oxidation of fatty acids in plants. Plant Physiol. 2000 Aug;123(4):1545–52. PMID: 10938370; PMCID: PMC59111.; Hamberg M, Sanz A, Castresana C. alpha-oxidation of fatty acids in higher plants. Identification of a pathogen-inducible oxygenase (piox) as an alpha-dioxygenase and biosynthesis of 2-hydroperoxylinolenic acid. J Biol Chem. 1999 Aug 27;274(35):24503–13. doi: 10.1074/jbc.274.35.24503. PMID: 10455113. |
| L-histidine degradation II Accession ID: BioCyc:META_PWY-5028 |
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Yu Y, Liang YH, Brostromer E, Quan JM, Panjikar S, Dong YH, Su XD. A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis. J Biol Chem. 2006 Dec 01;281(48):36929–36. doi: 10.1074/jbc.m607703200. PMID: 16990261.; Tabor H, Mehler AH. ISOLATION OF N-FORMYL-l-GLUTAMIC ACID AS AN INTERMEDIATE IN THE ENZYMATIC DEGRADATION OF l-HISTIDINE. Journal of Biological Chemistry. 1954 Oct;210(2):559–68. doi: 10.1016/s0021-9258(18)65382-7. |
| L-histidine degradation VI Accession ID: BioCyc:META_HISHP-PWY |
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Yu Y, Liang YH, Brostromer E, Quan JM, Panjikar S, Dong YH, Su XD. A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis. J Biol Chem. 2006 Dec 01;281(48):36929–36. doi: 10.1074/jbc.m607703200. PMID: 16990261.; HASSALL H, GREENBERG DM. Studies on the enzymic decomposition of urocanic acid. V. The formation of 4-oxoglutaramic acid, a nonenzymic oxidation product of 4(5)-imidazolone-5(4)-propionic acid. J Biol Chem. 1963 Apr;238():1423–31. PMID: 13960897.; BROWN DD, KIES MW. The mammalian metabolism of L-histidine. I. The enzymatic formation of L-hydantion-5-propionic acid. J Biol Chem. 1959 Dec;234():3182–7. PMID: 13804906. |
| nitrogen fixation I (ferredoxin) Accession ID: BioCyc:META_N2FIX-PWY |
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Eady RR, Smith BE, Cook KA, Postgate JR. Nitrogenase of Klebsiella pneumoniae. Purification and properties of the component proteins. Biochem J. 1972 Jul;128(3):655–75. PMID: 4344006; PMCID: PMC1173817.; Vandecasteele J, Burris RH. Purification and Properties of the Constituents of the Nitrogenase Complex from Clostridium pasteurianum. J Bacteriol. 1970 Mar;101(3):794–801. doi: 10.1128/jb.101.3.794-801.1970. |
| ascorbate glutathione cycle Accession ID: BioCyc:META_PWY-2261 |
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Macdonald IK, Badyal SK, Ghamsari L, Moody PCE, Raven EL. Interaction of Ascorbate Peroxidase with Substrates: A Mechanistic and Structural Analysis. Biochemistry. 2006 Jun 01;45(25):7808–17. doi: 10.1021/bi0606849.; Sharp KH, Moody PC, Brown KA, Raven EL. Crystal structure of the ascorbate peroxidase-salicylhydroxamic acid complex. Biochemistry. 2004 Jul 13;43(27):8644–51. doi: 10.1021/bi049343q. PMID: 15236572.; Chew O, Whelan J, Millar AH. Molecular Definition of the Ascorbate-Glutathione Cycle in Arabidopsis Mitochondria Reveals Dual Targeting of Antioxidant Defenses in Plants. Journal of Biological Chemistry. 2003 Nov;278(47):46869–77. doi: 10.1074/jbc.m307525200.; Shigeoka S, Ishikawa T, Tamoi M, Miyagawa Y, Takeda T, Yabuta Y, Yoshimura K. Regulation and function of ascorbate peroxidase isoenzymes. 2002 May 15;53(372):1305–19. doi: 10.1093/jxb/53.372.1305.; Noctor G, Foyer CH. ASCORBATE AND GLUTATHIONE: Keeping Active Oxygen Under Control. Annu Rev Plant Physiol Plant Mol Biol. 1998 Jun;49():249–79. doi: 10.1146/annurev.arplant.49.1.249. PMID: 15012235.; Jimenez A, Hernandez JA, Del Rio LA, Sevilla F. Evidence for the Presence of the Ascorbate-Glutathione Cycle in Mitochondria and Peroxisomes of Pea Leaves. Plant Physiol. 1997 May;114(1):275–84. PMID: 12223704; PMCID: PMC158303.; Patterson WR, Poulos TL. Crystal structure of recombinant pea cytosolic ascorbate peroxidase. Biochemistry. 1995 Apr 04;34(13):4331–41. doi: 10.1021/bi00013a023. PMID: 7703247.; Shigeoka S, Nakano Y, Kitaoka S. Purification and some properties of l-ascorbic acid-specific peroxidase in Euglena gracilis z. Archives of Biochemistry and Biophysics. 1980 Apr;201(1):121–7. doi: 10.1016/0003-9861(80)90495-6.; Shigeoka S, Nakano Y, Kitaoka S. Metabolism of hydrogen peroxide in Euglena gracilis Z by L-ascorbic acid peroxidase. Biochem J. 1980 Jan 15;186(1):377–80. PMID: 6768357; PMCID: PMC1161541. |
| superpathway of hydrolyzable tannin biosynthesis Accession ID: BioCyc:META_PWY-5478 |
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Niemetz R, Gross GG. Enzymology of gallotannin and ellagitannin biosynthesis. Phytochemistry. 2005 Sep;66(17):2001–11. doi: 10.1016/j.phytochem.2005.01.009. PMID: 16153405.; Niemetz R, Gross GG. Ellagitannin biosynthesis: laccase-catalyzed dimerization of tellimagrandin II to cornusiin E in Tellima grandiflora. Phytochemistry. 2003 Dec;64(7):1197–201. doi: 10.1016/j.phytochem.2003.08.013. PMID: 14599517.; Beecher GR. Overview of Dietary Flavonoids: Nomenclature, Occurrence and Intake. The Journal of Nutrition. 2003 Oct;133(10):3248S–3254S. doi: 10.1093/jn/133.10.3248s.; Niemetz R, Gross GG. Oxidation of pentagalloylglucose to the ellagitannin, tellimagrandin II, by a phenol oxidase from Tellima grandiflora leaves. Phytochemistry. 2003 Feb;62(3):301–6. doi: 10.1016/s0031-9422(02)00557-5. PMID: 12620341.; Fröhlich B, Niemetz R, Gross GG. Gallotannin biosynthesis: two new galloyltransferases from Rhus typhina leaves preferentially acylating hexa- and heptagalloylglucoses. Planta. 2002 Nov;216(1):168–72. doi: 10.1007/s00425-002-0877-3. PMID: 12430027.; Niemetz R, Gross GG. Gallotannin biosynthesis: beta-glucogallin: hexagalloyl 3-O-galloyltransferase from Rhus typhina leaves. Phytochemistry. 2001 Nov;58(5):657–61. doi: 10.1016/s0031-9422(01)00300-4. PMID: 11672728.; Haslam E. Natural polyphenols (vegetable tannins) as drugs: possible modes of action. J Nat Prod. 1996 Feb;59(2):205–15. doi: 10.1021/np960040+. PMID: 8991956.; Haslam E, Cai Y. Plant polyphenols (vegetable tannins): gallic acid metabolism. Nat Prod Rep. 1994 Jan;11(1):41–66. doi: 10.1039/np9941100041. PMID: 15206456.; Hofmann AS, Gross GG. Biosynthesis of gallotannins: Formation of polygalloylglucoses by enzymatic acylation of 1,2,3,4,6-penta-O-galloylglucose. Archives of Biochemistry and Biophysics. 1990 Dec;283(2):530–2. doi: 10.1016/0003-9861(90)90678-r.; Cammann J, Denzel K, Schilling G, Gross GG. Biosynthesis of gallotannins: beta-glucogallin-dependent formation of 1,2,3,4,6-pentagalloylglucose by enzymatic galloylation of 1,2,3,6-tetragalloylglucose. Arch Biochem Biophys. 1989 Aug 15;273(1):58–63. doi: 10.1016/0003-9861(89)90161-6. PMID: 2757399. |