Pathways Knowlegdes

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Pathway DOIs Note
pyridoxal 5'-phosphate salvage I

Accession ID: BioCyc:CAULO_PLPSAL-PWY		 -
pyridoxal 5'-phosphate salvage I

Accession ID: BioCyc:AURANTIMONAS_PLPSAL-PWY		 -
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage

Accession ID: BioCyc:PCHR_PWY0-845		 -
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage

Accession ID: BioCyc:ECOL413997_PWY0-845		 -
pyridoxal 5'-phosphate salvage I

Accession ID: BioCyc:ECOL413997_PLPSAL-PWY		 -
pyridoxal 5'-phosphate salvage I

Accession ID: BioCyc:BTHE_PLPSAL-PWY		 -
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis (yeast)

Accession ID: BioCyc:META_PWY-7282
  • 10.1002/biof.5520110136
  • 10.1007/s00294-004-0557-x
  • 10.1016/s0021-9258(17)39755-7
  • 10.1016/s0304-4165(89)80014-5
  • 10.1021/ja012708z
  • 10.1021/ja030261j
  • 10.1021/ja302474a
  • 10.1046/j.1365-2958.1999.01412.x
  • 10.1074/jbc.m112.397240
  • 10.1099/mic.0.26194-0
  • 10.1111/j.1567-1364.2007.00333.x
  • 10.1128/jb.177.7.1817-1823.1995
  • 10.1248/bpb.23.108
  • 10.1371/journal.pgen.0030134
  • 10.2478/s11658-007-0055-5
  • 10.3177/jnsv.54.7
 Coquille S, Roux C, Fitzpatrick TB, Thore S. The last piece in the vitamin B1 biosynthesis puzzle: structural and functional insight into yeast 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase. J Biol Chem. 2012 Dec 07;287(50):42333–43. PMID: 23048037; PMCID: PMC3516776.; Lai RY, Huang S, Fenwick MK, Hazra A, Zhang Y, Rajashankar K, Philmus B, Kinsland C, Sanders JM, Ealick SE, Begley TP. Thiamin pyrimidine biosynthesis in Candida albicans : a remarkable reaction between histidine and pyridoxal phosphate. J Am Chem Soc. 2012 Jun 06;134(22):9157–9. PMID: 22568620; PMCID: PMC3415583.; Onozuka M, Konno H, Kawasaki Y, Akaji K, Nosaka K. Involvement of thiaminase II encoded by the THI20 gene in thiamin salvage of Saccharomyces cerevisiae. FEMS Yeast Res. 2008 Mar;8(2):266–75. doi: 10.1111/j.1567-1364.2007.00333.x. PMID: 18028398.; Ishida S, Tazuya-Murayama K, Kijima Y, Yamada K. The direct precursor of the pyrimidine moiety of thiamin is not urocanic acid but histidine in Saccharomyces cerevisiae. J Nutr Sci Vitaminol (Tokyo). 2008 Feb;54(1):7–10. doi: 10.3177/jnsv.54.7. PMID: 18388401.; Kowalska E, Kozik A. The genes and enzymes involved in the biosynthesis of thiamin and thiamin diphosphate in yeasts. Cellular & Molecular Biology Letters. 2008 Apr 10;13(2):271–82. doi: 10.2478/s11658-007-0055-5.; Kanellis P, Gagliardi M, Banath JP, Szilard RK, Nakada S, Galicia S, Sweeney FD, Cabelof DC, Olive PL, Durocher D. A Screen for Suppressors of Gross Chromosomal Rearrangements Identifies a Conserved Role for PLP in Preventing DNA Lesions. PLoS Genet. 2007 Aug 10;3(8):e134. doi: 10.1371/journal.pgen.0030134.; Kawasaki Y, Onozuka M, Mizote T, Nosaka K. Biosynthesis of hydroxymethylpyrimidine pyrophosphate in Saccharomyces cerevisiae. Curr Genet. 2005 Mar;47(3):156–62. doi: 10.1007/s00294-004-0557-x. PMID: 15614489.; Zeidler J, Sayer BG, Spenser ID. Biosynthesis of vitamin B1 in yeast. Derivation of the pyrimidine unit from pyridoxine and histidine. Intermediacy of urocanic acid. J Am Chem Soc. 2003 Oct 29;125(43):13094–105. doi: 10.1021/ja030261j. PMID: 14570482.; Wightman R, Meacock PA. The THI5 gene family of Saccharomyces cerevisiae: distribution of homologues among the hemiascomycetes and functional redundancy in the aerobic biosynthesis of thiamin from pyridoxine. Microbiology (Reading). 2003 Jun;149(Pt 6):1447–60. doi: 10.1099/mic.0.26194-0. PMID: 12777485.; Zeidler J, Ullah N, Gupta RN, Pauloski RM, Sayer BG, Spenser ID. 2‘-Hydroxypyridoxol, a Biosynthetic Precursor of Vitamins B6 and B1 in Yeast. J. Am. Chem. Soc. 2002 Apr 06;124(17):4542–3. doi: 10.1021/ja012708z.; Tanaka K, Tazuya K, Yamada K, Kumaoka H. Biosynthesis of thiamin under anaerobic conditions in Saccharomyces cerevisiae. Biofactors. 2000;11(1-2):121–2. doi: 10.1002/biof.5520110136. PMID: 10705981.; TANAKA K, TAZUYA K, YAMADA K, KUMAOKA H. Biosynthesis of Thiamin under Anaerobic Conditions in Saccharomyces cerevisiae. Biological & Pharmaceutical Bulletin. 2000;23(1):108–11. doi: 10.1248/bpb.23.108.; Llorente B, Fairhead C, Dujon B. Genetic redundancy and gene fusion in the genome of the baker's yeast Saccharomyces cerevisiae : functional characterization of a three-member gene family involved in the thiamine biosynthetic pathway. Molecular Microbiology. 1999 Jun;32(6):1140–52. doi: 10.1046/j.1365-2958.1999.01412.x.; Tazuya K, Azumi C, Yamada K, Kumaoka H. Pyrimidine moiety of thiamin is biosynthesized from pyridoxine and histidine in Saccharomyces cerevisiae. Biochem Mol Biol Int. 1995 Jul;36(4):883–8. PMID: 8528151.; Loubbardi A, Marcireau C, Karst F, Guilloton M. Sterol uptake induced by an impairment of pyridoxal phosphate synthesis in Saccharomyces cerevisiae: cloning and sequencing of the PDX3 gene encoding pyridoxine (pyridoxamine) phosphate oxidase. J Bacteriol. 1995 Apr;177(7):1817–23. doi: 10.1128/jb.177.7.1817-1823.1995.; Tazuya K, Yamada K, Kumaoka H. Incorporation of histidine into the pyrimidine moiety of thiamin in Saccharomyces cerevisiae. Biochimica et Biophysica Acta (BBA) - General Subjects. 1989 Jan;990(1):73–9. doi: 10.1016/s0304-4165(89)80014-5.; Guirard BM, Snell EE. Physical and kinetic properties of a pyridoxal reductase purified from bakers' yeast. Biofactors. 1988 Jul;1(2):187–92. PMID: 3076441.; Tazuya K, Morisaki M, Yamada K, Kumaoka H. Participation of histidine in biosynthesis of the pyrimidine moiety of thiamin in Saccharomyces cerevisiae. Biochem Int. 1988 May;16(5):955–62. PMID: 3048267.; Mäntsälä P, Zalkin H. Glutamine nucleotide sequence of Saccharomyces cerevisiae ADE4 encoding phosphoribosylpyrophosphate amidotransferase. Journal of Biological Chemistry. 1984 Jul;259(13):8478–84. doi: 10.1016/s0021-9258(17)39755-7.
tetrapyrrole biosynthesis II (from glycine)

Accession ID: BioCyc:META_PWY-5189
  • 10.1016/j.abb.2008.02.015
 Heinemann IU, Jahn M, Jahn D. The biochemistry of heme biosynthesis. Archives of Biochemistry and Biophysics. 2008 Jun;474(2):238–51. doi: 10.1016/j.abb.2008.02.015.
pyridoxal 5'-phosphate salvage pathway

Accession ID: BioCyc:YEAST_PLPSAL-PWY
  • 10.1093/molbev/msi011
  • 10.1371/journal.pgen.0030134
 Kanellis P, Gagliardi M, Banath JP, Szilard RK, Nakada S, Galicia S, Sweeney FD, Cabelof DC, Olive PL, Durocher D. A Screen for Suppressors of Gross Chromosomal Rearrangements Identifies a Conserved Role for PLP in Preventing DNA Lesions. PLoS Genet. 2007 Aug 10;3(8):e134. doi: 10.1371/journal.pgen.0030134.; 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.
vitamin B6 degradation

Accession ID: BioCyc:VCHO_PWY-5499		 -
pyridoxal 5'-phosphate salvage I

Accession ID: BioCyc:SHIGELLA_PLPSAL-PWY		 -
pyridoxamine anabolism

Accession ID: BioCyc:PLASMO_PYRIDOXAMINEANABOLISM		 -
pyridoxal 5'-phosphate salvage I

Accession ID: BioCyc:MTBCDC1551_PLPSAL-PWY		 -
pyridoxal 5'-phosphate salvage I

Accession ID: BioCyc:ECOL199310_PLPSAL-PWY		 -
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage

Accession ID: BioCyc:CAULO_PWY0-845		 -
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage

Accession ID: BioCyc:AGRO_PWY0-845		 -
pyridoxal 5'-phosphate salvage I

Accession ID: BioCyc:SCO_PLPSAL-PWY		 -
pyridoxal 5'-phosphate salvage I

Accession ID: BioCyc:BSUB_PLPSAL-PWY
  • 10.1016/j.biotechadv.2016.11.004
 Rosenberg J, Ischebeck T, Commichau FM. Vitamin B6 metabolism in microbes and approaches for fermentative production. Biotechnol Adv. 2017 Jan;35(1):31–40. doi: 10.1016/j.biotechadv.2016.11.004. PMID: 27890703.
pyridoxal 5'-phosphate salvage pathway

Accession ID: BioCyc:PCHR_PLPSAL-PWY		 -
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage

Accession ID: BioCyc:MOB3B_PWY0-845		 -