Pathways Knowlegdes

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Pathway DOIs Note
inositol pyrophosphates biosynthesis

Accession ID: BioCyc:HUMAN_PWY-6369
  • 10.1074/jbc.275.17.12730
 Caffrey JJ, Safrany ST, Yang X, Shears SB. Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases. An expanding Nudt family. J Biol Chem. 2000 Apr 28;275(17):12730–6. doi: 10.1074/jbc.275.17.12730. PMID: 10777568.
D-myo-inositol (1,4,5,6)-tetrakisphosphate biosynthesis

Accession ID: BioCyc:HUMAN_PWY-6366
  • 10.1016/j.bbrc.2005.10.201
 Chang S, Majerus PW. Inositol polyphosphate multikinase regulates inositol 1,4,5,6-tetrakisphosphate. Biochemical and Biophysical Research Communications. 2006 Jan;339(1):209–16. doi: 10.1016/j.bbrc.2005.10.201.
1D-myo-inositol hexakisphosphate biosynthesis III (Spirodela polyrrhiza)

Accession ID: BioCyc:META_PWY-4661
  • 10.1016/s0031-9422(03)00446-1
  • 10.1038/346580a0
  • 10.1042/bj3140215
  • 10.1042/bj3140227
  • 10.1073/pnas.0504172102
 Stevenson-Paulik J, Bastidas RJ, Chiou S, Frye RA, York JD. Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases. Proc. Natl. Acad. Sci. U.S.A. 2005 Aug 17;102(35):12612–7. doi: 10.1073/pnas.0504172102.; Raboy V. myo-Inositol-1,2,3,4,5,6-hexakisphosphate. Phytochemistry. 2003 Nov;64(6):1033–43. doi: 10.1016/s0031-9422(03)00446-1. PMID: 14568069.; Brearley CA, Hanke DE. Inositol phosphates in the duckweed Spirodela polyrhiza L. Biochem J. 1996 Feb 15;314 ( Pt 1)():215–25. PMID: 8660286; PMCID: PMC1217028.; Brearley CA, Hanke DE. Metabolic evidence for the order of addition of individual phosphate esters in the myo-inositol moiety of inositol hexakisphosphate in the duckweed Spirodela polyrhiza L. Biochem J. 1996 Feb 15;314 ( Pt 1)():227–33. PMID: 8660287; PMCID: PMC1217029.; Stephens LR, Irvine RF. Stepwise phosphorylation of myo-inositol leading to myo-inositol hexakisphosphate in Dictyostelium. Nature. 1990 Aug 09;346(6284):580–3. doi: 10.1038/346580a0. PMID: 2198472.
lipid-dependent phytate biosynthesis II (via Ins(1,3,4)P3)

Accession ID: BioCyc:ARA_PWY-4562
  • 10.1073/pnas.0504172102
 Stevenson-Paulik J, Bastidas RJ, Chiou S, Frye RA, York JD. Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases. Proc. Natl. Acad. Sci. U.S.A. 2005 Aug 17;102(35):12612–7. doi: 10.1073/pnas.0504172102.
lipid-dependent phytate biosynthesis I (via Ins(1,4,5)P3)

Accession ID: BioCyc:ARA_PWY-4541
  • 10.1073/pnas.0504172102
 Stevenson-Paulik J, Bastidas RJ, Chiou S, Frye RA, York JD. Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases. Proc. Natl. Acad. Sci. U.S.A. 2005 Aug 17;102(35):12612–7. doi: 10.1073/pnas.0504172102.
D-myo-inositol (3,4,5,6)-tetrakisphosphate biosynthesis

Accession ID: BioCyc:HUMAN_PWY-6365		 -
1D-myo-inositol hexakisphosphate biosynthesis V (from Ins(1,3,4)P3)

Accession ID: BioCyc:META_PWY-6554
  • 10.1016/s0031-9422(03)00446-1
 Raboy V. myo-Inositol-1,2,3,4,5,6-hexakisphosphate. Phytochemistry. 2003 Nov;64(6):1033–43. doi: 10.1016/s0031-9422(03)00446-1. PMID: 14568069.
1D-myo-inositol hexakisphosphate biosynthesis II (mammalian)

Accession ID: BioCyc:META_PWY-6362
  • 10.1016/s0021-9258(19)47192-5
  • 10.1074/jbc.m411528200
 Verbsky JW, Chang S, Wilson MP, Mochizuki Y, Majerus PW. The Pathway for the Production of Inositol Hexakisphosphate in Human Cells. Journal of Biological Chemistry. 2005 Jan;280(3):1911–20. doi: 10.1074/jbc.m411528200.; Shears SB. The pathway of myo-inositol 1,3,4-trisphosphate phosphorylation in liver. Identification of myo-inositol 1,3,4-trisphosphate 6-kinase, myo-inositol 1,3,4-trisphosphate 5-kinase, and myo-inositol 1,3,4,6-tetrakisphosphate 5-kinase. J Biol Chem. 1989 Nov 25;264(33):19879–86. PMID: 2584198.
superpathway of inositol phosphate compounds

Accession ID: BioCyc:META_PWY-6371
  • 10.1006/scdb.1997.0220
  • 10.1016/j.bbalip.2007.01.015
  • 10.1016/s0960-9822(01)00501-2
  • 10.1073/pnas.0509740102
  • 10.1074/jbc.m805686200
  • 10.1093/emboj/cdf522
 Lin H, Fridy PC, Ribeiro AA, Choi JH, Barma DK, Vogel G, Falck JR, Shears SB, York JD, Mayr GW. Structural Analysis and Detection of Biological Inositol Pyrophosphates Reveal That the Family of VIP/Diphosphoinositol Pentakisphosphate Kinases Are 1/3-Kinases. Journal of Biological Chemistry. 2009 Jan;284(3):1863–72. doi: 10.1074/jbc.m805686200.; Strahl T, Thorner J. Synthesis and function of membrane phosphoinositides in budding yeast, Saccharomyces cerevisiae. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2007 Mar;1771(3):353–404. doi: 10.1016/j.bbalip.2007.01.015.; Ungewickell A, Hugge C, Kisseleva M, Chang SC, Zou J, Feng Y, Galyov EE, Wilson M, Majerus PW. The identification and characterization of two phosphatidylinositol-4,5-bisphosphate 4-phosphatases. Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18854–9. PMID: 16365287; PMCID: PMC1323219.; Niebuhr K, Giuriato S, Pedron T, Philpott DJ, Gaits F, Sable J, Sheetz MP, Parsot C, Sansonetti PJ, Payrastre B. Conversion of PtdIns(4,5)P(2) into PtdIns(5)P by the S.flexneri effector IpgD reorganizes host cell morphology. EMBO J. 2002 Oct 01;21(19):5069–78. PMID: 12356723; PMCID: PMC129044.; Walker DM, Urbé S, Dove SK, Tenza D, Raposo G, Clague MJ. Characterization of MTMR3. an inositol lipid 3-phosphatase with novel substrate specificity. Curr Biol. 2001 Oct 16;11(20):1600–5. doi: 10.1016/s0960-9822(01)00501-2. PMID: 11676921.; Zhang X, Majerus PW. Phosphatidylinositol signalling reactions. Seminars in Cell & Developmental Biology. 1998 Apr;9(2):153–60. doi: 10.1006/scdb.1997.0220.
D-myo-inositol (1,4,5,6)-tetrakisphosphate biosynthesis

Accession ID: BioCyc:META_PWY-6366
  • 10.1016/j.bbrc.2005.10.201
 Chang S, Majerus PW. Inositol polyphosphate multikinase regulates inositol 1,4,5,6-tetrakisphosphate. Biochemical and Biophysical Research Communications. 2006 Jan;339(1):209–16. doi: 10.1016/j.bbrc.2005.10.201.
inositol phosphate biosynthesis

Accession ID: BioCyc:YEAST_PWY3O-402
  • 10.1007/s00018-005-5446-z
  • 10.1016/j.bbalip.2006.04.014
  • 10.1074/jbc.m202206200
  • 10.1126/science.1139099
 Mulugu S, Bai W, Fridy PC, Bastidas RJ, Otto JC, Dollins DE, Haystead TA, Ribeiro AA, York JD. A conserved family of enzymes that phosphorylate inositol hexakisphosphate. Science. 2007 Apr 06;316(5821):106–9. doi: 10.1126/science.1139099. PMID: 17412958.; York JD. Regulation of nuclear processes by inositol polyphosphates. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2006 May;1761(5-6):552–9. doi: 10.1016/j.bbalip.2006.04.014.; Bennett M, Onnebo SMN, Azevedo C, Saiardi A. Inositol pyrophosphates: metabolism and signaling. Cellular and Molecular Life Sciences. 2006 Jan 25;63(5):552. doi: 10.1007/s00018-005-5446-z.; Dubois E, Scherens B, Vierendeels F, Ho MMW, Messenguy F, Shears SB. In Saccharomyces cerevisiae, the Inositol Polyphosphate Kinase Activity of Kcs1p Is Required for Resistance to Salt Stress, Cell Wall Integrity, and Vacuolar Morphogenesis. Journal of Biological Chemistry. 2002 Jun;277(26):23755–63. doi: 10.1074/jbc.m202206200.
1D-myo-inositol hexakisphosphate biosynthesis V (from Ins(1,3,4)P3)

Accession ID: BioCyc:ARA_PWY-6554
  • 10.1016/s0031-9422(03)00446-1
 Raboy V. myo-Inositol-1,2,3,4,5,6-hexakisphosphate. Phytochemistry. 2003 Nov;64(6):1033–43. doi: 10.1016/s0031-9422(03)00446-1. PMID: 14568069.
inositol pyrophosphates biosynthesis

Accession ID: BioCyc:ARA_PWY-6369		 -
superpathway of lipid-dependent phytate biosynthesis

Accession ID: BioCyc:ARA_PWY-4765		 -
1D-myo-inositol hexakisphosphate biosynthesis V (from Ins(1,3,4)P3)

Accession ID: BioCyc:HUMAN_PWY-6554		 -
1D-myo-inositol hexakisphosphate biosynthesis II (mammalian)

Accession ID: BioCyc:HUMAN_PWY-6362
  • 10.1016/s0021-9258(19)47192-5
  • 10.1074/jbc.m411528200
 Verbsky JW, Chang S, Wilson MP, Mochizuki Y, Majerus PW. The Pathway for the Production of Inositol Hexakisphosphate in Human Cells. Journal of Biological Chemistry. 2005 Jan;280(3):1911–20. doi: 10.1074/jbc.m411528200.; Shears SB. The pathway of myo-inositol 1,3,4-trisphosphate phosphorylation in liver. Identification of myo-inositol 1,3,4-trisphosphate 6-kinase, myo-inositol 1,3,4-trisphosphate 5-kinase, and myo-inositol 1,3,4,6-tetrakisphosphate 5-kinase. J Biol Chem. 1989 Nov 25;264(33):19879–86. PMID: 2584198.
1D-myo-inositol hexakisphosphate biosynthesis I (from Ins(1,4,5)P3)

Accession ID: BioCyc:META_PWY-6361
  • 10.1016/s0065-2571(00)00025-x
  • 10.1126/science.285.5424.96
 York JD, Guo S, Odom AR, Spiegelberg BD, Stolz LE. An expanded view of inositol signaling. Advances in Enzyme Regulation. 2001 May;41(1):57–71. doi: 10.1016/s0065-2571(00)00025-x.; York JD, Odom AR, Murphy R, Ives EB, Wente SR. A phospholipase C-dependent inositol polyphosphate kinase pathway required for efficient messenger RNA export. Science. 1999 Jul 02;285(5424):96–100. doi: 10.1126/science.285.5424.96. PMID: 10390371.
1D-myo-inositol hexakisphosphate biosynthesis IV (Dictyostelium)

Accession ID: BioCyc:META_PWY-6372
  • 10.1038/346580a0
 Stephens LR, Irvine RF. Stepwise phosphorylation of myo-inositol leading to myo-inositol hexakisphosphate in Dictyostelium. Nature. 1990 Aug 09;346(6284):580–3. doi: 10.1038/346580a0. PMID: 2198472.
inositol diphosphates biosynthesis

Accession ID: BioCyc:META_PWY-6369
  • 10.1074/jbc.275.17.12730
  • 10.1074/jbc.m805686200
 Lin H, Fridy PC, Ribeiro AA, Choi JH, Barma DK, Vogel G, Falck JR, Shears SB, York JD, Mayr GW. Structural Analysis and Detection of Biological Inositol Pyrophosphates Reveal That the Family of VIP/Diphosphoinositol Pentakisphosphate Kinases Are 1/3-Kinases. Journal of Biological Chemistry. 2009 Jan;284(3):1863–72. doi: 10.1074/jbc.m805686200.; Caffrey JJ, Safrany ST, Yang X, Shears SB. Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases. An expanding Nudt family. J Biol Chem. 2000 Apr 28;275(17):12730–6. doi: 10.1074/jbc.275.17.12730. PMID: 10777568.
inositol pyrophosphates biosynthesis

Accession ID: BioCyc:YEAST_PWY-6369		 -