Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
dTDP-N-acetylthomosamine biosynthesis

Accession ID: BioCyc:META_PWY-7315
  • 10.1016/s0021-9258(18)77373-0
  • 10.1128/jb.00306-06
  • 10.1128/jb.180.22.5875-5884.1998
 Hung MN, Rangarajan E, Munger C, Nadeau G, Sulea T, Matte A. Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthesis. J Bacteriol. 2006 Aug;188(15):5606–17. PMID: 16855251; PMCID: PMC1540030.; Danese PN, Oliver GR, Barr K, Bowman GD, Rick PD, Silhavy TJ. Accumulation of the Enterobacterial Common Antigen Lipid II Biosynthetic Intermediate Stimulates degP Transcription in Escherichia coli. J Bacteriol. 1998 Nov 15;180(22):5875–84. doi: 10.1128/jb.180.22.5875-5884.1998.; Meier-Dieter U, Starman R, Barr K, Mayer H, Rick PD. Biosynthesis of enterobacterial common antigen in Escherichia coli. Biochemical characterization of Tn10 insertion mutants defective in enterobacterial common antigen synthesis. Journal of Biological Chemistry. 1990 Aug;265(23):13490–7. doi: 10.1016/s0021-9258(18)77373-0.
purine deoxyribonucleosides degradation I

Accession ID: BioCyc:META_PWY-7179		 -
inosine 5'-phosphate degradation

Accession ID: BioCyc:META_PWY-5695
  • 10.1016/s0163-7258(00)00097-8
  • 10.1046/j.1432-1033.2002.03097.x
  • 10.1128/jb.182.19.5332-5341.2000
 Stoychev G, Kierdaszuk B, Shugar D. Xanthosine and xanthine. Substrate properties with purine nucleoside phosphorylases, and relevance to other enzyme systems. Eur J Biochem. 2002 Aug;269(16):4048–57. doi: 10.1046/j.1432-1033.2002.03097.x. PMID: 12180982.; Bzowska A, Kulikowska E, Shugar D. Purine nucleoside phosphorylases: properties, functions, and clinical aspects. Pharmacol Ther. 2000 Dec;88(3):349–425. doi: 10.1016/s0163-7258(00)00097-8. PMID: 11337031.; Xi H, Schneider BL, Reitzer L. Purine Catabolism in Escherichia coli and Function of Xanthine Dehydrogenase in Purine Salvage. J Bacteriol. 2000 Oct;182(19):5332–41. doi: 10.1128/jb.182.19.5332-5341.2000.
L-asparagine degradation III (mammalian)

Accession ID: BioCyc:META_ASPARAGINE-DEG1-PWY-1
  • 10.1021/bi300870g
  • 10.1038/nsb1295-1102
 Nomme J, Su Y, Konrad M, Lavie A. Structures of Apo and Product-Bound Human l-Asparaginase: Insights into the Mechanism of Autoproteolysis and Substrate Hydrolysis. Biochemistry. 2012 Aug 14;51(34):6816–26. doi: 10.1021/bi300870g.; Oinonen C, Tikkanen R, Rouvinen J, Peltonen L. Three-dimensional structure of human lysosomal aspartylglucosaminidase. Nature Structural & Molecular Biology. 1995 Dec 01;2(12):1102–8. doi: 10.1038/nsb1295-1102.
L-asparagine degradation II

Accession ID: BioCyc:META_PWY-4002
  • 10.1016/0003-9861(83)90594-5
 Ireland RJ, Joy KW. Purification and properties of an asparagine aminotransferase from Pisum sativum leaves. Archives of Biochemistry and Biophysics. 1983 May;223(1):291–6. doi: 10.1016/0003-9861(83)90594-5.
5-hydroxybenzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP

Accession ID: BioCyc:META_PWY-7969
  • 10.1073/pnas.1509132112
  • 10.1111/j.1432-1033.1988.tb14303.x
 Hazra AB, Han AW, Mehta AP, Mok KC, Osadchiy V, Begley TP, Taga ME. Anaerobic biosynthesis of the lower ligand of vitamin B 12. Proc. Natl. Acad. Sci. U.S.A. 2015 Aug 05;112(34):10792–7. doi: 10.1073/pnas.1509132112.; KRÄUTLER B, KOHLER HE, STUPPERICH E. 5'-Methylbenzimidazolyl-cobamides are the corrinoids from some sulfate-reducing and sulfur-metabolizing bacteria. European Journal of Biochemistry. 1988 Sep;176(2):461–9. doi: 10.1111/j.1432-1033.1988.tb14303.x.
estradiol biosynthesis II

Accession ID: BioCyc:META_PWY-7306
  • 10.1016/s0021-9258(20)79736-x
 Thompson EA, Siiteri PK. The Involvement of Human Placental Microsomal Cytochrome P-450 in Aromatization. Journal of Biological Chemistry. 1974 Sep;249(17):5373–8. doi: 10.1016/s0021-9258(20)79736-x.
punicate biosynthesis

Accession ID: BioCyc:META_PWY-5374
  • 10.1046/j.1432-1033.2002.03184.x
  • 10.1074/jbc.m210748200
 Iwabuchi M, Kohno-Murase J, Imamura J. Delta 12-oleate desaturase-related enzymes associated with formation of conjugated trans-delta 11, cis-delta 13 double bonds. J Biol Chem. 2003 Feb 14;278(7):4603–10. doi: 10.1074/jbc.m210748200. PMID: 12464604.; Hornung E, Pernstich C, Feussner I. Formation of conjugated ?11?13-double bonds by ?12-linoleic acid (1,4)-acyl-lipid-desaturase in pomegranate seeds. European Journal of Biochemistry. 2002 Sep 18;269(19):4852–9. doi: 10.1046/j.1432-1033.2002.03184.x.
α-eleostearate biosynthesis

Accession ID: BioCyc:META_PWY-5375
  • 10.1104/pp.102.010835
 Dyer JM, Chapital DC, Kuan JC, Mullen RT, Turner C, McKeon TA, Pepperman AB. Molecular analysis of a bifunctional fatty acid conjugase/desaturase from tung. Implications for the evolution of plant fatty acid diversity. Plant Physiol. 2002 Dec;130(4):2027–38. PMID: 12481086; PMCID: PMC166714.
dimorphecolate biosynthesis

Accession ID: BioCyc:META_PWY-5368
  • 10.1074/jbc.m314329200
 Cahoon EB, Kinney AJ. Dimorphecolic acid is synthesized by the coordinate activities of two divergent Delta12-oleic acid desaturases. J Biol Chem. 2004 Mar 26;279(13):12495–502. doi: 10.1074/jbc.m314329200. PMID: 14718523.
estradiol biosynthesis I (via estrone)

Accession ID: BioCyc:META_PWY66-380
  • 10.1016/s0021-9258(20)79736-x
 Thompson EA, Siiteri PK. The Involvement of Human Placental Microsomal Cytochrome P-450 in Aromatization. Journal of Biological Chemistry. 1974 Sep;249(17):5373–8. doi: 10.1016/s0021-9258(20)79736-x.
cyanate degradation

Accession ID: BioCyc:META_CYANCAT-PWY
  • 10.1016/s0003-9861(02)00243-6
  • 10.1016/s0021-9258(19)75797-4
  • 10.1104/pp.105.2.707
  • 10.1371/journal.pone.0018300
 Qian D, Jiang L, Lu L, Wei C, Li Y. Biochemical and Structural Properties of Cyanases from Arabidopsis thaliana and Oryza sativa. PLoS ONE. 2011 Mar 31;6(3):e18300. doi: 10.1371/journal.pone.0018300.; Rowlett RS, Tu C, McKay MM, Preiss JR, Loomis RJ, Hicks KA, Marchione RJ, Strong JA, Donovan GS, Chamberlin JE. Kinetic characterization of wild-type and proton transfer-impaired variants of beta-carbonic anhydrase from Arabidopsis thaliana. Arch Biochem Biophys. 2002 Aug 15;404(2):197–209. doi: 10.1016/s0003-9861(02)00243-6. PMID: 12147257.; Fett JP, Coleman JR. Characterization and expression of two cDNAs encoding carbonic anhydrase in Arabidopsis thaliana. Plant Physiol. 1994 Jun;105(2):707–13. PMID: 7520589; PMCID: PMC159412.; Murakami H, Sly WS. Purification and characterization of human salivary carbonic anhydrase. Journal of Biological Chemistry. 1987 Jan;262(3):1382–8. doi: 10.1016/s0021-9258(19)75797-4.
ellagic acid degradation to urolithins

Accession ID: BioCyc:META_PWY-7951
  • 10.3389/fmicb.2017.01521
 Selma MV, Beltrán D, Luna MC, Romo-Vaquero M, García-Villalba R, Mira A, Espín JC, Tomás-Barberán FA. Isolation of Human Intestinal Bacteria Capable of Producing the Bioactive Metabolite Isourolithin A from Ellagic Acid. Front Microbiol. 2017;8():1521. PMID: 28824607; PMCID: PMC5545574.
dTDP-D-olivose, dTDP-D-oliose and dTDP-D-mycarose biosynthesis

Accession ID: BioCyc:META_PWY-6973
  • 10.1002/cbic.201100540
  • 10.1021/ja0771383
  • 10.1099/00221287-148-4-1091
  • 10.1128/aem.71.5.2539-2547.2005
 Wang G, Kharel MK, Pahari P, Rohr J. Investigating Mithramycin Deoxysugar Biosynthesis: Enzymatic Total Synthesis of TDP-D-Olivose. ChemBioChem. 2011 Sep 29;12(17):2568–71. doi: 10.1002/cbic.201100540.; Hong L, Zhao Z, Melançon CE, Zhang H, Liu H. In Vitro Characterization of the Enzymes Involved in TDP-d-Forosamine Biosynthesis in the Spinosyn Pathway of Saccharopolyspora spinosa. J. Am. Chem. Soc. 2008 Mar 18;130(14):4954–67. doi: 10.1021/ja0771383.; Peiru´ S, Menzella HG, Rodri´guez E, Carney J, Gramajo H. Production of the Potent Antibacterial Polyketide Erythromycin C in Escherichia coli. Appl Environ Microbiol. 2005 May;71(5):2539–47. doi: 10.1128/aem.71.5.2539-2547.2005.; Wang L, White RL, Vining LC. Biosynthesis of the dideoxysugar component of jadomycin B: genes in the jad cluster of Streptomyces venezuelae ISP5230 for l-digitoxose assembly and transfer to the angucycline aglycone The GenBank accession number for the sequence reported in this paper is AY026363. 2002 Apr 01;148(4):1091–103. doi: 10.1099/00221287-148-4-1091.
L-carnitine degradation III

Accession ID: BioCyc:META_PWY-3641
  • 10.1016/s0378-1097(96)00412-0
 Kleber HP. Bacterial carnitine metabolism. FEMS Microbiol Lett. 1997 Feb 01;147(1):1–9. doi: 10.1111/j.1574-6968.1997.tb10212.x. PMID: 9037756.
farnesylcysteine salvage pathway

Accession ID: BioCyc:META_PWY-6577
  • 10.1006/abbi.1998.0611
  • 10.1006/bbrc.1997.7145
  • 10.1073/pnas.96.23.13080
  • 10.1093/mp/ssp091
  • 10.1111/j.1365-313x.2007.03091.x
  • 10.1146/annurev.bi.65.070196.001325
 Huizinga DH, Denton R, Koehler KG, Tomasello A, Wood L, Sen SE, Crowell DN. Farnesylcysteine lyase is involved in negative regulation of abscisic acid signaling in Arabidopsis. Mol Plant. 2010 Jan;3(1):143–55. PMID: 19969520; PMCID: PMC2807925.; Crowell DN, Huizinga DH, Deem AK, Trobaugh C, Denton R, Sen SE. Arabidopsis thaliana plants possess a specific farnesylcysteine lyase that is involved in detoxification and recycling of farnesylcysteine. The Plant Journal. 2007 Apr 08;50(5):839–47. doi: 10.1111/j.1365-313x.2007.03091.x.; Thai L, Rush JS, Maul JE, Devarenne T, Rodgers DL, Chappell J, Waechter CJ. Farnesol is utilized for isoprenoid biosynthesis in plant cells via farnesyl pyrophosphate formed by successive monophosphorylation reactions. Proc. Natl. Acad. Sci. U.S.A. 1999 Nov 09;96(23):13080–5. doi: 10.1073/pnas.96.23.13080.; Bentinger M, Grünler J, Peterson E, Swiezewska E, Dallner G. Phosphorylation of Farnesol in Rat Liver Microsomes: Properties of Farnesol Kinase and Farnesyl Phosphate Kinase. Archives of Biochemistry and Biophysics. 1998 May;353(2):191–8. doi: 10.1006/abbi.1998.0611.; Crick DC, Andres DA, Waechter CJ. Novel Salvage Pathway Utilizing Farnesol and Geranylgeraniol for Protein Isoprenylation. Biochemical and Biophysical Research Communications. 1997 Aug;237(3):483–7. doi: 10.1006/bbrc.1997.7145.; Zhang FL, Casey PJ. Protein prenylation: molecular mechanisms and functional consequences. Annu Rev Biochem. 1996;65():241–69. doi: 10.1146/annurev.bi.65.070196.001325. PMID: 8811180.
D-galactose detoxification

Accession ID: BioCyc:META_PWY-3821
  • 10.1016/j.pbi.2004.03.004
  • 10.1016/s0960-9822(02)01260-5
 Seifert GJ. Nucleotide sugar interconversions and cell wall biosynthesis: how to bring the inside to the outside. Curr Opin Plant Biol. 2004 Jun;7(3):277–84. doi: 10.1016/j.pbi.2004.03.004. PMID: 15134748.; Seifert GJ, Barber C, Wells B, Dolan L, Roberts K. Galactose biosynthesis in Arabidopsis: genetic evidence for substrate channeling from UDP-D-galactose into cell wall polymers. Curr Biol. 2002 Oct 29;12(21):1840–5. doi: 10.1016/s0960-9822(02)01260-5. PMID: 12419184.
4-hydroxy-2-nonenal detoxification

Accession ID: BioCyc:META_PWY-7112
  • 10.1016/j.taap.2012.07.002
  • 10.1093/jnen/62.2.146
 Tsirulnikov K, Abuladze N, Bragin A, Faull K, Cascio D, Damoiseaux R, Schibler MJ, Pushkin A. Inhibition of aminoacylase 3 protects rat brain cortex neuronal cells from the toxicity of 4-hydroxy-2-nonenal mercapturate and 4-hydroxy-2-nonenal. Toxicology and Applied Pharmacology. 2012 Sep;263(3):303–14. doi: 10.1016/j.taap.2012.07.002.; Sidell KR, Montine KS, Picklo MJ, Olsen SJ, Amarnath V, Montine TJ. Mercapturate metabolism of 4-hydroxy-2-nonenal in rat and human cerebrum. J Neuropathol Exp Neurol. 2003 Feb;62(2):146–53. doi: 10.1093/jnen/62.2.146. PMID: 12578224.
nitrite oxidation

Accession ID: BioCyc:META_P282-PWY
  • 10.1007/bf02568729
  • 10.1016/0378-1097(88)90246-7
  • 10.1073/pnas.54.3.869
 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.
glutathione-mediated detoxification II

Accession ID: BioCyc:META_PWY-6842
  • 10.1016/0968-0004(92)90489-v
  • 10.1016/j.febslet.2006.10.050
  • 10.1016/j.phytochem.2009.09.034
  • 10.1074/jbc.m801998200
 Wünschmann J, Krajewski M, Letzel T, Huber EM, Ehrmann A, Grill E, Lendzian KJ. Dissection of glutathione conjugate turnover in yeast. Phytochemistry. 2010 Jan;71(1):54–61. doi: 10.1016/j.phytochem.2009.09.034. PMID: 19897216.; Brazier-Hicks M, Evans KM, Cunningham OD, Hodgson DR, Steel PG, Edwards R. Catabolism of glutathione conjugates in Arabidopsis thaliana. Role in metabolic reactivation of the herbicide safener fenclorim. J Biol Chem. 2008 Jul 25;283(30):21102–12. PMID: 18522943; PMCID: PMC3258958.; Grzam A, Tennstedt P, Clemens S, Hell R, Meyer AJ. Vacuolar sequestration of glutathione S-conjugates outcompetes a possible degradation of the glutathione moiety by phytochelatin synthase. FEBS Lett. 2006 Nov 27;580(27):6384–90. doi: 10.1016/j.febslet.2006.10.050. PMID: 17097087.; Ishikawa T. The ATP-dependent glutathione S-conjugate export pump. Trends Biochem Sci. 1992 Nov;17(11):463–8. doi: 10.1016/0968-0004(92)90489-v. PMID: 1455517.