Pathways Knowlegdes

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Pathway DOIs Note
sulfite oxidation

Accession ID: BioCyc:HUMAN_PWY-5326
  • 10.1007/s11120-005-5221-x
  • 10.1074/jbc.m108078200
  • 10.1074/jbc.m513054200
  • 10.1093/pcp/pch212
  • 10.1172/jci108499
 Hänsch R, Lang C, Riebeseel E, Lindigkeit R, Gessler A, Rennenberg H, Mendel RR. Plant sulfite oxidase as novel producer of H2O2: combination of enzyme catalysis with a subsequent non-enzymatic reaction step. J Biol Chem. 2006 Mar 10;281(10):6884–8. doi: 10.1074/jbc.m513054200. PMID: 16407262.; Hänsch R, Mendel RR. Sulfite oxidation in plant peroxisomes. Photosynth Res. 2005 Dec;86(3):337–43. doi: 10.1007/s11120-005-5221-x. PMID: 16307306.; Nowak K, Luniak N, Witt C, Wüstefeld Y, Wachter A, Mendel RR, Hänsch R. Peroxisomal localization of sulfite oxidase separates it from chloroplast-based sulfur assimilation. Plant Cell Physiol. 2004 Dec;45(12):1889–94. doi: 10.1093/pcp/pch212. PMID: 15653809.; Eilers T, Schwarz G, Brinkmann H, Witt C, Richter T, Nieder J, Koch B, Hille R, Hänsch R, Mendel RR. Identification and biochemical characterization of Arabidopsis thaliana sulfite oxidase. A new player in plant sulfur metabolism. J Biol Chem. 2001 Dec 14;276(50):46989–94. doi: 10.1074/jbc.m108078200. PMID: 11598126.; Johnson JL, Rajagopalan KV. Purification and properties of sulfite oxidase from human liver. J Clin Invest. 1976 Sep;58(3):543–50. PMID: 956383; PMCID: PMC333211.
superpathway of methionine degradation

Accession ID: BioCyc:HUMAN_PWY-5328		 -
sulfide oxidation IV (metazoa)

Accession ID: BioCyc:HUMAN_PWY-7927		 -
purine nucleotides degradation I (plants)

Accession ID: BioCyc:META_PWY-5044
  • 10.1074/jbc.m312929200
  • 10.1104/pp.115.4.1307
 Hesberg C, Hänsch R, Mendel RR, Bittner F. Tandem orientation of duplicated xanthine dehydrogenase genes from Arabidopsis thaliana: differential gene expression and enzyme activities. J Biol Chem. 2004 Apr 02;279(14):13547–54. doi: 10.1074/jbc.m312929200. PMID: 14726515.; Capote-Maínez N, Sánchez F. Characterization of the common bean uricase II and its expression in organs other than nodules. Plant Physiol. 1997 Dec;115(4):1307–17. PMID: 9414545; PMCID: PMC158596.
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.
superpathway of nicotinate degradation

Accession ID: BioCyc:META_PWY-5062		 -
guanosine nucleotides degradation I

Accession ID: BioCyc:META_PWY-6607
  • 10.1074/jbc.m312929200
 Hesberg C, Hänsch R, Mendel RR, Bittner F. Tandem orientation of duplicated xanthine dehydrogenase genes from Arabidopsis thaliana: differential gene expression and enzyme activities. J Biol Chem. 2004 Apr 02;279(14):13547–54. doi: 10.1074/jbc.m312929200. PMID: 14726515.
superpathway of sulfide oxidation (Starkeya novella)

Accession ID: BioCyc:META_PWY-5335
  • 10.1074/jbc.275.18.13202
  • 10.1099/mic.0.26212-0
 Rohwerder T, Sand W. The sulfane sulfur of persulfides is the actual substrate of the sulfur-oxidizing enzymes from Acidithiobacillus and Acidiphilium spp. Microbiology (Reading). 2003 Jul;149(Pt 7):1699–710. doi: 10.1099/mic.0.26212-0. PMID: 12855721.; Kappler U, Bennett B, Rethmeier J, Schwarz G, Deutzmann R, McEwan AG, Dahl C. Sulfite:Cytochrome c oxidoreductase from Thiobacillus novellus. Purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family. J Biol Chem. 2000 May 05;275(18):13202–12. doi: 10.1074/jbc.275.18.13202. PMID: 10788424.
superpathway of heme biosynthesis from uroporphyrinogen-III

Accession ID: BioCyc:HPY_PWY0-1415		 -
methanol oxidation to carbon dioxide

Accession ID: BioCyc:CORYNE_PWY-7616		 -
adenosine nucleotides degradation I

Accession ID: BioCyc:META_PWY-6596
  • 10.1074/jbc.m312929200
  • 10.1104/pp.115.4.1307
 Hesberg C, Hänsch R, Mendel RR, Bittner F. Tandem orientation of duplicated xanthine dehydrogenase genes from Arabidopsis thaliana: differential gene expression and enzyme activities. J Biol Chem. 2004 Apr 02;279(14):13547–54. doi: 10.1074/jbc.m312929200. PMID: 14726515.; Capote-Maínez N, Sánchez F. Characterization of the common bean uricase II and its expression in organs other than nodules. Plant Physiol. 1997 Dec;115(4):1307–17. PMID: 9414545; PMCID: PMC158596.
nicotinate degradation II

Accession ID: BioCyc:META_PWY-5033
  • 10.1016/s0021-9258(20)82232-7
  • 10.1128/mmbr.60.3.483-498.1996
 Kaiser JP, Feng Y, Bollag JM. Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions. Microbiol Rev. 1996 Sep;60(3):483–98. doi: 10.1128/mr.60.3.483-498.1996.; Ensign JC, Rittenberg SC. The Pathway of Nicotinic Acid Oxidation by a Bacillus Species. Journal of Biological Chemistry. 1964 Jul;239(7):2285–91. doi: 10.1016/s0021-9258(20)82232-7.
superpathway of purines degradation in plants

Accession ID: BioCyc:META_P165-PWY
  • 10.1006/abio.1994.1515
  • 10.1016/0304-4165(92)90074-5
 Pineda M, Piedras P, Cárdenas J. A continuous spectrophotometric assay for ureidoglycolase activity with lactate dehydrogenase or glyoxylate reductase as coupling enzyme. Anal Biochem. 1994 Nov 01;222(2):450–5. doi: 10.1006/abio.1994.1515. PMID: 7864371.; Pérez-Vecinte R, Alamillo JM, Cárdenas J, Pineda M. Purification and substrate inactivation of xanthine dehydrogenase from Chlamydomonasreinhardtii. Biochimica et Biophysica Acta (BBA) - General Subjects. 1992 Sep;1117(2):159–66. doi: 10.1016/0304-4165(92)90074-5.
L-tryptophan biosynthesis

Accession ID: BioCyc:HPY_TRPSYN-PWY		 -
indole-3-acetate biosynthesis VI (bacteria)

Accession ID: BioCyc:META_TRPIAACAT-PWY
  • 10.1016/s0021-9258(19)49609-9
  • 10.1128/aem.62.11.4121-4128.1996
 Brandl MT, Lindow SE. Cloning and characterization of a locus encoding an indolepyruvate decarboxylase involved in indole-3-acetic acid synthesis in Erwinia herbicola. Appl Environ Microbiol. 1996 Nov;62(11):4121–8. doi: 10.1128/aem.62.11.4121-4128.1996.; Koga J, Adachi T, Hidaka H. Purification and characterization of indolepyruvate decarboxylase. A novel enzyme for indole-3-acetic acid biosynthesis in Enterobacter cloacae. Journal of Biological Chemistry. 1992 Aug;267(22):15823–8. doi: 10.1016/s0021-9258(19)49609-9.
ureide biosynthesis

Accession ID: BioCyc:META_URSIN-PWY
  • 10.1016/s0163-7258(00)00097-8
  • 10.1046/j.1432-1033.2002.03097.x
 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.
heme biosynthesis from uroporphyrinogen-III II

Accession ID: BioCyc:HPY_HEMESYN2-PWY		 -
phenylacetate degradation II (anaerobic)

Accession ID: BioCyc:META_PWY-1341
  • 10.1007/s002030050604
  • 10.1046/j.1432-1327.1999.00399.x
 Rhee S, Fuchs G. Phenylacetyl-CoA:acceptor oxidoreductase, a membrane-bound molybdenum–iron–sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. European Journal of Biochemistry. 1999 Jun;262(2):507–15. doi: 10.1046/j.1432-1327.1999.00399.x.; Schneider S, Fuchs G. Phenylacetyl-CoA:acceptor oxidoreductase, a new alpha-oxidizing enzyme that produces phenylglyoxylate. Assay, membrane localization, and differential production in Thauera aromatica. Arch Microbiol. 1998 Jun;169(6):509–16. doi: 10.1007/s002030050604. PMID: 9575237.
sulfite oxidation I

Accession ID: BioCyc:META_PWY-5276
  • 10.1074/jbc.275.18.13202
 Kappler U, Bennett B, Rethmeier J, Schwarz G, Deutzmann R, McEwan AG, Dahl C. Sulfite:Cytochrome c oxidoreductase from Thiobacillus novellus. Purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family. J Biol Chem. 2000 May 05;275(18):13202–12. doi: 10.1074/jbc.275.18.13202. PMID: 10788424.
3-methylquinoline degradation

Accession ID: BioCyc:META_PWY-721		 -