Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| 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. |
| vitamin B6 degradation Accession ID: BioCyc:META_PWY-5499 |
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Yokochi N, Nishimura S, Yoshikane Y, Ohnishi K, Yagi T. Identification of a new tetrameric pyridoxal 4-dehydrogenase as the second enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing symbiotic bacterium, Mesorhizobium loti. Archives of Biochemistry and Biophysics. 2006 Aug;452(1):1–8. doi: 10.1016/j.abb.2006.06.002.; Burg RW, Rodwell VW, Snell EE. Bacterial Oxidation of Vitamin B6. Journal of Biological Chemistry. 1960 Apr;235(4):1164–9. doi: 10.1016/s0021-9258(18)69498-0. |
| pyridoxal 5'-phosphate salvage II (plants) Accession ID: BioCyc:META_PWY-7204 |
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Herrero S, González E, Gillikin JW, Vélëz H, Daub ME. Identification and characterization of a pyridoxal reductase involved in the vitamin B6 salvage pathway in Arabidopsis. Plant Mol Biol. 2011 May;76(1-2):157–69. doi: 10.1007/s11103-011-9777-x. PMID: 21533842.; Havaux M, Ksas B, Szewczyk A, Rumeau D, Franck F, Caffarri S, Triantaphylidès C. Vitamin B6 deficient plants display increased sensitivity to high light and photo-oxidative stress. BMC Plant Biol. 2009 Nov 10;9():130. PMID: 19903353; PMCID: PMC2777905.; Mooney S, Leuendorf JE, Hendrickson C, Hellmann H. Vitamin B6: a long known compound of surprising complexity. Molecules. 2009 Jan 12;14(1):329–51. PMID: 19145213; PMCID: PMC6253932.; Fitzpatrick TB, Amrhein N, Kappes B, Macheroux P, Tews I, Raschle T. Two independent routes of de novo vitamin B6 biosynthesis: not that different after all. Biochem J. 2007 Oct 01;407(1):1–13. doi: 10.1042/bj20070765. PMID: 17822383.; Roje S. Vitamin B biosynthesis in plants. Phytochemistry. 2007 Jul;68(14):1904–21. doi: 10.1016/j.phytochem.2007.03.038. PMID: 17512961.; Sang Y, Barbosa JM, Wu H, Locy RD, Singh NK: Identification of a pyridoxine (pyridoxamine) 5'-phosphate oxidase from Arabidopsis thaliana. FEBS Lett. 2007 Feb 6;581(3):344-8. doi: 10.1016/j.febslet.2006.12.028. Epub 2007 Jan 3.; Titiz O, Tambasco-Studart M, Warzych E, Apel K, Amrhein N, Laloi C, Fitzpatrick TB. PDX1 is essential for vitamin B6 biosynthesis, development and stress tolerance in Arabidopsis. Plant J. 2006 Dec;48(6):933–46. doi: 10.1111/j.1365-313x.2006.02928.x. PMID: 17227548.; Tanaka T, Tateno Y, Gojobori T. Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes. Mol Biol Evol. 2005 Feb;22(2):243–50. doi: 10.1093/molbev/msi011. PMID: 15483325.; Wang H, Liu D, Liu C, Zhang A. The pyridoxal kinase gene TaPdxK from wheat complements vitamin B6 synthesis-defective Escherichia coli. J Plant Physiol. 2004 Sep;161(9):1053–60. doi: 10.1016/j.jplph.2004.05.012. PMID: 15499907.; Tsang EWT, Hu Z, Chang Q, McGregor DI, Keller WA. Expression of a Brassic napus glutamate 1-semialdehyde aminotransferase in Escherichia coli and characterization of the recombinant protein. Protein Expression and Purification. 2003 Jun;29(2):193–201. doi: 10.1016/s1046-5928(03)00010-x.; Lum HK, Kwok F, Lo SC. Cloning and characterization of Arabidopsis thaliana pyridoxal kinase. Planta. 2002 Sep;215(5):870–9. doi: 10.1007/s00425-002-0799-0. PMID: 12244454.; Breitinger U, Clausen T, Ehlert S, Huber R, Laber B, Schmidt F, Pohl E, Messerschmidt A. The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity. Plant Physiol. 2001 Jun;126(2):631–42. PMID: 11402193; PMCID: PMC111155.; Thomazeau K, Curien G, Dumas R, Biou V. Crystal structure of threonine synthase from Arabidopsis thaliana. Protein Science. 2001 Mar;10(3):638–48. doi: 10.1110/ps.44301.; Tamura K, Nishiura H, Mori J, Imai H. Cloning and characterization of a cDNA encoding serine palmitoyltransferase in Arabidopsis thaliana. Biochem. Soc. Trans. 2000 Dec 01;28(6):745. doi: 10.1042/0300-5127:0280745.; Bilski P, Li MY, Ehrenshaft M, Daub ME, Chignell CF. Vitamin B6 (pyridoxine) and its derivatives are efficient singlet oxygen quenchers and potential fungal antioxidants. Photochem Photobiol. 2000 Feb;71(2):129–34. doi: 10.1562/0031-8655(2000)071<0129:sipvbp>2.0.co;2. PMID: 10687384.; Zhou H, Wang HW, Zhu K, Sui SF, Xu P, Yang SF, Li N. The multiple roles of conserved arginine 286 of 1-aminocyclopropane-1-carboxylate synthase. Coenzyme binding, substrate binding, and beyond. Plant Physiol. 1999 Nov;121(3):913–9. PMID: 10557240; PMCID: PMC59454.; Ravanel S, Droux M, Douce R. Methionine biosynthesis in higher plants. I. Purification and characterization of cystathionine gamma-synthase from spinach chloroplasts. Arch Biochem Biophys. 1995 Jan 10;316(1):572–84. doi: 10.1006/abbi.1995.1077. PMID: 7840669.; Tsuge H, Kuroda Y, Iwamoto A, Ohashi K. Partial purification and property of pyridoxine (pyridoxamine)-5'-phosphate oxidase isozymes from wheat seedlings. Archives of Biochemistry and Biophysics. 1982 Sep;217(2):479–84. doi: 10.1016/0003-9861(82)90527-6.; Takagi M, Shimomura S, Fukui T. Function of the phosphate group of pyridoxal 5'-phosphate in the glycogen phosphorylase reaction. Journal of Biological Chemistry. 1981 Jan;256(2):728–30. doi: 10.1016/s0021-9258(19)70035-0. |
| pyridoxal 5'-phosphate salvage I Accession ID: BioCyc:META_PLPSAL-PWY |
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Yang Y, Tsui HT, Man T, Winkler ME. Identification and Function of the pdxY Gene, Which Encodes a Novel Pyridoxal Kinase Involved in the Salvage Pathway of Pyridoxal 5'-Phosphate Biosynthesis in Escherichia coli K-12. J Bacteriol. 1998 Apr;180(7):1814–21. doi: 10.1128/jb.180.7.1814-1821.1998.; Yang Y, Zhao G, Winkler ME. Identification of the pdxK gene that encodes pyridoxine (vitamin B6) kinase in Escherichia coli K-12. FEMS Microbiol Lett. 1996 Jul 15;141(1):89–95. doi: 10.1111/j.1574-6968.1996.tb08368.x. PMID: 8764513.; YAMADA R, TSUJI T, NOSE Y. Uptake and utilization of vitamin B6 and its phosphate esters by Escherichia coli. Journal of Nutritional Science and Vitaminology, J Nutr Sci Vitaminol. 1977;23(1):7–17. doi: 10.3177/jnsv.23.7. |
| superpathway of pyridoxal 5'-phosphate biosynthesis and salvage Accession ID: BioCyc:ECOL199310_PWY0-845 |
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| pyridoxal 5'-phosphate salvage pathway Accession ID: BioCyc:MOUSE_PLPSAL-PWY |
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| pyridoxal 5'-phosphate salvage pathway Accession ID: BioCyc:SMAN_PLPSAL-PWY |
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| pyridoxal 5'-phosphate salvage I Accession ID: BioCyc:ECOL316407_PLPSAL-PWY |
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| vitamin B6 degradation Accession ID: BioCyc:MOB3B_PWY-5499 |
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| superpathway of pyridoxal 5'-phosphate biosynthesis and salvage Accession ID: BioCyc:CLOSSAC_PWY0-845 |
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| pyridoxal 5'-phosphate salvage pathway Accession ID: BioCyc:CLOSSAC_PLPSAL-PWY |
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| pyridoxal 5'-phosphate salvage I Accession ID: BioCyc:LACTORHA_PLPSAL-PWY |
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| superpathway of bacteriochlorophyll a biosynthesis Accession ID: BioCyc:META_PWY-5529 |
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Gough SP, Petersen BO, Duus JØ. Anaerobic chlorophyll isocyclic ring formation inRhodobacter capsulatusrequires a cobalamin cofactor. Proc. Natl. Acad. Sci. U.S.A. 2000 Jun 06;97(12):6908–13. doi: 10.1073/pnas.97.12.6908.; Suzuki JY, Bollivar DW, Bauer CE. Genetic analysis of chlorophyll biosynthesis. Annu Rev Genet. 1997;31():61–89. doi: 10.1146/annurev.genet.31.1.61. PMID: 9442890. |
| superpathway of pyridoxal 5'-phosphate biosynthesis and salvage Accession ID: BioCyc:META_PWY0-845 |
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| pyridoxal 5'-phosphate salvage I Accession ID: BioCyc:ARA_PLPSAL-PWY |
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Roje S. Vitamin B biosynthesis in plants. Phytochemistry. 2007 Jul;68(14):1904–21. doi: 10.1016/j.phytochem.2007.03.038. PMID: 17512961.; Sang Y, Barbosa JM, Wu H, Locy RD, Singh NK: Identification of a pyridoxine (pyridoxamine) 5'-phosphate oxidase from Arabidopsis thaliana. FEBS Lett. 2007 Feb 6;581(3):344-8. doi: 10.1016/j.febslet.2006.12.028. Epub 2007 Jan 3.; Tambasco-Studart M, Titiz O, Raschle T, Forster G, Amrhein N, Fitzpatrick TB: Vitamin B6 biosynthesis in higher plants. Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13687-92. doi: 10.1073/pnas.0506228102. Epub 2005 Sep 12.; Tanaka T, Tateno Y, Gojobori T. Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes. Mol Biol Evol. 2005 Feb;22(2):243–50. doi: 10.1093/molbev/msi011. PMID: 15483325.; Lum HK, Kwok F, Lo SC. Cloning and characterization of Arabidopsis thaliana pyridoxal kinase. Planta. 2002 Sep;215(5):870–9. doi: 10.1007/s00425-002-0799-0. PMID: 12244454.; Shi H, Zhu JK. SOS4, a pyridoxal kinase gene, is required for root hair development in Arabidopsis. Plant Physiol. 2002 Jun;129(2):585–93. PMID: 12068103; PMCID: PMC161684.; Shi H, Xiong L, Stevenson B, Lu T, Zhu JK. The Arabidopsis salt overly sensitive 4 mutants uncover a critical role for vitamin B6 in plant salt tolerance. Plant Cell. 2002 Mar;14(3):575–88. PMID: 11910005; PMCID: PMC150580.; Bilski P, Li MY, Ehrenshaft M, Daub ME, Chignell CF. Vitamin B6 (pyridoxine) and its derivatives are efficient singlet oxygen quenchers and potential fungal antioxidants. Photochem Photobiol. 2000 Feb;71(2):129–34. doi: 10.1562/0031-8655(2000)071<0129:sipvbp>2.0.co;2. PMID: 10687384.; McCormick DB, Chen H. Update on Interconversions of Vitamin B-6 with Its Coenzyme. The Journal of Nutrition. 1999 Feb;129(2):325–7. doi: 10.1093/jn/129.2.325.; MEISTER A. On the Transamination of Enzymes. Annals of the New York Academy of Sciences. 1990 May;585(1):13–31. doi: 10.1111/j.1749-6632.1990.tb28038.x.; Tsuge H, Kuroda Y, Iwamoto A, Ohashi K. Partial purification and property of pyridoxine (pyridoxamine)-5'-phosphate oxidase isozymes from wheat seedlings. Archives of Biochemistry and Biophysics. 1982 Sep;217(2):479–84. doi: 10.1016/0003-9861(82)90527-6. |
| pyridoxal 5'-phosphate salvage II (plants) Accession ID: BioCyc:ARA_PWY-7204 |
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| pyridoxamine anabolism Accession ID: BioCyc:TRYPANO_PYRIDOXAMINEANABOLISM |
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| pyridoxal 5'-phosphate salvage pathway Accession ID: BioCyc:PLASMO_PLPSAL-PWY |
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| pyridoxal 5'-phosphate salvage I Accession ID: BioCyc:ECOO157_PLPSAL-PWY |
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| superpathway of pyridoxal 5'-phosphate biosynthesis and salvage Accession ID: BioCyc:ECOO157_PWY0-845 |
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