ENTRY map04966 Pathway NAME Collecting duct acid secretion DESCRIPTION One of the important roles of the collecting duct segment of the kidney nephron is acid secretion. As daily food intake loads acid into the body, urinary acid excretion is essential, and urine pH can drop as low as 4.5. The alpha-intercalated cell of collecting duct is the main responsible for hydrogen secretion into the urine. The carbon dioxide, which is generated in the cells and enters from the blood, is changed to carbonic acid. This carbonic acid is divided into hydrogen ion and bicarbonate ion. Intracellular CA II catalyses the formation of these ions. The hydrogen ion is secreted into the lumen by the luminal H(+)-ATPase. The bicarbonate ion is transported to the blood side by the anion exchanger type 1. Hydrogen ion in the lumen is trapped by urinary buffers. These include ammonium and phosphate. CLASS Organismal Systems; Excretory system PATHWAY_MAP map04966 Collecting duct acid secretion REFERENCE PMID:16352913 AUTHORS Wagner CA, Kovacikova J, Stehberger PA, Winter C, Benabbas C, Mohebbi N TITLE Renal acid-base transport: old and new players. JOURNAL Nephron Physiol 103:p1-6 (2006) DOI:10.1159/000090217 REFERENCE PMID:19277700 AUTHORS Wagner CA, Devuyst O, Bourgeois S, Mohebbi N TITLE Regulated acid-base transport in the collecting duct. JOURNAL Pflugers Arch 458:137-56 (2009) DOI:10.1007/s00424-009-0657-z REFERENCE PMID:19948674 AUTHORS Koeppen BM TITLE The kidney and acid-base regulation. JOURNAL Adv Physiol Educ 33:275-81 (2009) DOI:10.1152/advan.00054.2009 REFERENCE PMID:9550618 AUTHORS Hayashi M TITLE Physiology and pathophysiology of acid-base homeostasis in the kidney. JOURNAL Intern Med 37:221-5 (1998) DOI:10.2169/internalmedicine.37.221 REFERENCE PMID:17557941 AUTHORS Fry AC, Karet FE TITLE Inherited renal acidoses. JOURNAL Physiology (Bethesda) 22:202-11 (2007) DOI:10.1152/physiol.00044.2006 REFERENCE PMID:19721811 AUTHORS Pereira PC, Miranda DM, Oliveira EA, Silva AC TITLE Molecular pathophysiology of renal tubular acidosis. JOURNAL Curr Genomics 10:51-9 (2009) DOI:10.2174/138920209787581262 REFERENCE PMID:11045400 AUTHORS Rodriguez-Soriano J TITLE New insights into the pathogenesis of renal tubular acidosis--from functional to molecular studies. JOURNAL Pediatr Nephrol 14:1121-36 (2000) DOI:10.1007/s004670000407 REFERENCE PMID:11826292 AUTHORS Alper SL TITLE Genetic diseases of acid-base transporters. JOURNAL Annu Rev Physiol 64:899-923 (2002) DOI:10.1146/annurev.physiol.64.092801.141759 REL_PATHWAY map04530 Tight junction KO_PATHWAY ko04966 /// ENTRY map03460 Pathway NAME Fanconi anemia pathway DESCRIPTION The Fanconi anemia pathway is required for the efficient repair of damaged DNA, especially interstrand cross-links (ICLs). DNA ICL is directly recognized by FANCM and associated proteins, that recruit the FA core complex. The FA core complex monoubiquitinates FANCD2 and FANCI. The monoubiquitinated FANCD2/FANCI becomes an active form and interacts with a series of DNA repair proteins and facilitates downstream repair pathways. Fanconi anemia is caused by mutations in one of at least 13 FA genes and is characterized by congenital growth abnormalities, bone marrow failure and cancer predisposition. CLASS Genetic Information Processing; Replication and repair PATHWAY_MAP map03460 Fanconi anemia pathway DBLINKS GO: 0043240 REFERENCE PMID:18047734 AUTHORS Jacquemont C, Taniguchi T TITLE The Fanconi anemia pathway and ubiquitin. JOURNAL BMC Biochem 8 Suppl 1:S10 (2007) DOI:10.1186/1471-2091-8-S1-S10 REFERENCE PMID:19805513 AUTHORS Bhagwat N, Olsen AL, Wang AT, Hanada K, Stuckert P, Kanaar R, D'Andrea A, Niedernhofer LJ, McHugh PJ TITLE XPF-ERCC1 participates in the Fanconi anemia pathway of cross-link repair. JOURNAL Mol Cell Biol 29:6427-37 (2009) DOI:10.1128/MCB.00086-09 REFERENCE PMID:21701511 AUTHORS Deans AJ, West SC TITLE DNA interstrand crosslink repair and cancer. JOURNAL Nat Rev Cancer 11:467-80 (2011) DOI:10.1038/nrc3088 REFERENCE PMID:20064461 AUTHORS Deans AJ, West SC TITLE FANCM connects the genome instability disorders Bloom's Syndrome and Fanconi Anemia. JOURNAL Mol Cell 36:943-53 (2009) DOI:10.1016/j.molcel.2009.12.006 REFERENCE PMID:20039786 AUTHORS Muniandy PA, Liu J, Majumdar A, Liu ST, Seidman MM TITLE DNA interstrand crosslink repair in mammalian cells: step by step. JOURNAL Crit Rev Biochem Mol Biol 45:23-49 (2010) DOI:10.3109/10409230903501819 REFERENCE PMID:18518821 AUTHORS Ciccia A, McDonald N, West SC TITLE Structural and functional relationships of the XPF/MUS81 family of proteins. JOURNAL Annu Rev Biochem 77:259-87 (2008) DOI:10.1146/annurev.biochem.77.070306.102408 REL_PATHWAY map03430 Mismatch repair map03440 Homologous recombination KO_PATHWAY ko03460 /// ENTRY map00440 Pathway NAME Phosphonate and phosphinate metabolism DESCRIPTION Natural products containing carbon-phosphorous bonds, so-called C-P compounds, are derivatives of phosphonate and phosphinate with substitution of alkyl group for hydrogen of phosphorus-hydrogen bonds. C-P compounds have been found in many organisms, but only protists and bacteria, mostly Actinobacteria, have biosynthetic capacity. A common reaction in the biosynthetic pathway is C-P bond forming reaction from phosphoenolpyruvate (PEP) to phosphonopyruvate (PnPy) catalyzed by PEP phosphomutase. 2-Aminoethylphosphonate (AEP) is the most abundant C-P compound in the natural world. AEP derivatives include phosphonoprotein, phosphonoglycan, and phosphonolipid. Other known C-P compounds are bioactive substances used in medicine (antibiotics) and agriculture (herbicide) such as fosfomycin, FR-33289, rhizocticin, and bialaphos. CLASS Metabolism; Metabolism of other amino acids PATHWAY_MAP map00440 Phosphonate and phosphinate metabolism DBLINKS GO: 0019634 REFERENCE PMID:19489722 AUTHORS Metcalf WW, van der Donk WA TITLE Biosynthesis of phosphonic and phosphinic acid natural products. JOURNAL Annu Rev Biochem 78:65-94 (2009) DOI:10.1146/annurev.biochem.78.091707.100215 REFERENCE PMID:19053721 AUTHORS Xiao Y, Lee K, Liu P TITLE Syntheses of the P-methylase substrates of the bialaphos biosynthetic pathway. JOURNAL Org Lett 10:5521-4 (2008) DOI:10.1021/ol802269x REFERENCE PMID:17168571 AUTHORS van der Donk WA TITLE Rings, radicals, and regeneration: the early years of a bioorganic laboratory. JOURNAL J Org Chem 71:9561-71 (2006) DOI:10.1021/jo0614240 REFERENCE PMID:15616300 AUTHORS Blodgett JA, Zhang JK, Metcalf WW TITLE Molecular cloning, sequence analysis, and heterologous expression of the phosphinothricin tripeptide biosynthetic gene cluster from Streptomyces viridochromogenes DSM 40736. JOURNAL Antimicrob Agents Chemother 49:230-40 (2005) DOI:10.1128/AAC.49.1.230-240.2005 REFERENCE PMID:15574905 AUTHORS Schwartz D, Berger S, Heinzelmann E, Muschko K, Welzel K, Wohlleben W TITLE Biosynthetic gene cluster of the herbicide phosphinothricin tripeptide from Streptomyces viridochromogenes Tu494. JOURNAL Appl Environ Microbiol 70:7093-102 (2004) DOI:10.1128/AEM.70.12.7093-7102.2004 REL_PATHWAY map00010 Glycolysis / Gluconeogenesis map00030 Pentose phosphate pathway map00260 Glycine, serine and threonine metabolism KO_PATHWAY ko00440 /// ENTRY map04064 Pathway NAME NF-kappa B signaling pathway DESCRIPTION Nuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are several pathways leading to NF-kappa B-activation. The canonical pathway is induced by tumour necrosis factor-alpha (TNF-alpha), interleukin-1 (IL-1) or byproducts of bacterial and viral infections. This pathway relies on IKK- mediated IkappaB-alpha phosphorylation on Ser32 and 36, leading to its degradation, which allows the p50/p65 NF-kappa B dimer to enter the nucleus and activate gene transcription. Atypical pathways are IKK-independent and rely on phosphorylation of IkappaB-alpha on Tyr42 or on Ser residues in IkappaB-alpha PEST domain. The non-canonical pathway is triggered by particular members of the TNFR superfamily, such as lymphotoxin-beta (LT-beta) or BAFF. It involves NIK and IKK-alpha-mediated p100 phosphorylation and processing to p52, resulting in nuclear translocation of p52/RelB heterodimers. CLASS Environmental Information Processing; Signal transduction PATHWAY_MAP map04064 NF-kappa B signaling pathway REFERENCE PMID:21772278 AUTHORS Oeckinghaus A, Hayden MS, Ghosh S TITLE Crosstalk in NF-kappaB signaling pathways. JOURNAL Nat Immunol 12:695-708 (2011) DOI:10.1038/ni.2065 REFERENCE PMID:19203223 AUTHORS Gloire G, Piette J TITLE Redox regulation of nuclear post-translational modifications during NF-kappaB activation. JOURNAL Antioxid Redox Signal 11:2209-22 (2009) DOI:10.1089/ARS.2009.2463 REFERENCE PMID:17183360 AUTHORS Perkins ND TITLE Integrating cell-signalling pathways with NF-kappaB and IKK function. JOURNAL Nat Rev Mol Cell Biol 8:49-62 (2007) DOI:10.1038/nrm2083 REFERENCE PMID:16264088 AUTHORS Lindstrom TM, Bennett PR TITLE The role of nuclear factor kappa B in human labour. JOURNAL Reproduction 130:569-81 (2005) DOI:10.1530/rep.1.00197 REFERENCE PMID:22017430 AUTHORS Razani B, Reichardt AD, Cheng G TITLE Non-canonical NF-kappaB signaling activation and regulation: principles and perspectives. JOURNAL Immunol Rev 244:44-54 (2011) DOI:10.1111/j.1600-065X.2011.01059.x REFERENCE PMID:21173796 AUTHORS Sun SC TITLE Non-canonical NF-kappaB signaling pathway. JOURNAL Cell Res 21:71-85 (2011) DOI:10.1038/cr.2010.177 REFERENCE PMID:17431096 AUTHORS Neumann M, Naumann M TITLE Beyond IkappaBs: alternative regulation of NF-kappaB activity. JOURNAL FASEB J 21:2642-54 (2007) DOI:10.1096/fj.06-7615rev REFERENCE PMID:22119011 AUTHORS Verhelst K, Carpentier I, Beyaert R TITLE Regulation of TNF-induced NF-kappaB activation by different cytoplasmic ubiquitination events. JOURNAL Cytokine Growth Factor Rev 22:277-86 (2011) DOI:10.1016/j.cytogfr.2011.11.002 REFERENCE PMID:22017435 AUTHORS Rickert RC, Jellusova J, Miletic AV TITLE Signaling by the tumor necrosis factor receptor superfamily in B-cell biology and disease. JOURNAL Immunol Rev 244:115-33 (2011) DOI:10.1111/j.1600-065X.2011.01067.x REFERENCE PMID:21232019 AUTHORS Naude PJ, den Boer JA, Luiten PG, Eisel UL TITLE Tumor necrosis factor receptor cross-talk. JOURNAL FEBS J 278:888-98 (2011) DOI:10.1111/j.1742-4658.2011.08017.x REFERENCE PMID:16984817 AUTHORS Grivennikov SI, Kuprash DV, Liu ZG, Nedospasov SA TITLE Intracellular signals and events activated by cytokines of the tumor necrosis factor superfamily: From simple paradigms to complex mechanisms. JOURNAL Int Rev Cytol 252:129-61 (2006) DOI:10.1016/S0074-7696(06)52002-9 REFERENCE PMID:16356770 AUTHORS Wada T, Nakashima T, Hiroshi N, Penninger JM TITLE RANKL-RANK signaling in osteoclastogenesis and bone disease. JOURNAL Trends Mol Med 12:17-25 (2006) DOI:10.1016/j.molmed.2005.11.007 REFERENCE PMID:17098202 AUTHORS Schulze-Luehrmann J, Ghosh S TITLE Antigen-receptor signaling to nuclear factor kappa B. JOURNAL Immunity 25:701-15 (2006) DOI:10.1016/j.immuni.2006.10.010 REFERENCE PMID:15134788 AUTHORS Weil R, Israel A TITLE T-cell-receptor- and B-cell-receptor-mediated activation of NF-kappaB in lymphocytes. JOURNAL Curr Opin Immunol 16:374-81 (2004) DOI:10.1016/j.coi.2004.03.003 REFERENCE PMID:15905862 AUTHORS Siebenlist U, Brown K, Claudio E TITLE Control of lymphocyte development by nuclear factor-kappaB. JOURNAL Nat Rev Immunol 5:435-45 (2005) DOI:10.1038/nri1629 REFERENCE PMID:14657271 AUTHORS Lucas PC, McAllister-Lucas LM, Nunez G TITLE NF-kappaB signaling in lymphocytes: a new cast of characters. JOURNAL J Cell Sci 117:31-9 (2004) DOI:10.1242/jcs.00904 REFERENCE PMID:19726767 AUTHORS Khan WN TITLE B cell receptor and BAFF receptor signaling regulation of B cell homeostasis. JOURNAL J Immunol 183:3561-7 (2009) DOI:10.4049/jimmunol.0800933 REFERENCE PMID:19302050 AUTHORS Vallabhapurapu S, Karin M TITLE Regulation and function of NF-kappaB transcription factors in the immune system. JOURNAL Annu Rev Immunol 27:693-733 (2009) DOI:10.1146/annurev.immunol.021908.132641 REFERENCE PMID:17047224 AUTHORS Hacker H, Karin M TITLE Regulation and function of IKK and IKK-related kinases. JOURNAL Sci STKE 2006:re13 (2006) DOI:10.1126/stke.3572006re13 REFERENCE PMID:21872579 AUTHORS Sabatel H, Pirlot C, Piette J, Habraken Y TITLE Importance of PIKKs in NF-kappaB activation by genotoxic stress. JOURNAL Biochem Pharmacol 82:1371-83 (2011) DOI:10.1016/j.bcp.2011.07.105 REFERENCE PMID:21187855 AUTHORS Miyamoto S TITLE Nuclear initiated NF-kappaB signaling: NEMO and ATM take center stage. JOURNAL Cell Res 21:116-30 (2011) DOI:10.1038/cr.2010.179 REFERENCE PMID:18832076 AUTHORS Brzoska K, Szumiel I TITLE Signalling loops and linear pathways: NF-kappaB activation in response to genotoxic stress. JOURNAL Mutagenesis 24:1-8 (2009) DOI:10.1093/mutage/gen056 REFERENCE PMID:17607554 AUTHORS Wu ZH, Miyamoto S TITLE Many faces of NF-kappaB signaling induced by genotoxic stress. JOURNAL J Mol Med (Berl) 85:1187-202 (2007) DOI:10.1007/s00109-007-0227-9 REFERENCE PMID:22390971 AUTHORS Maelfait J, Beyaert R TITLE Emerging role of ubiquitination in antiviral RIG-I signaling. JOURNAL Microbiol Mol Biol Rev 76:33-45 (2012) DOI:10.1128/MMBR.05012-11 REFERENCE PMID:18613837 AUTHORS Ware CF TITLE Targeting lymphocyte activation through the lymphotoxin and LIGHT pathways. JOURNAL Immunol Rev 223:186-201 (2008) DOI:10.1111/j.1600-065X.2008.00629.x REFERENCE PMID:15546385 AUTHORS Schneider K, Potter KG, Ware CF TITLE Lymphotoxin and LIGHT signaling pathways and target genes. JOURNAL Immunol Rev 202:49-66 (2004) DOI:10.1111/j.0105-2896.2004.00206.x REFERENCE PMID:22152226 AUTHORS Remouchamps C, Boutaffala L, Ganeff C, Dejardin E TITLE Biology and signal transduction pathways of the Lymphotoxin-alphabeta/LTbetaR system. JOURNAL Cytokine Growth Factor Rev 22:301-10 (2011) DOI:10.1016/j.cytogfr.2011.11.007 REFERENCE PMID:21135871 AUTHORS Liu S, Chen ZJ TITLE Expanding role of ubiquitination in NF-kappaB signaling. JOURNAL Cell Res 21:6-21 (2011) DOI:10.1038/cr.2010.170 REFERENCE PMID:19489733 AUTHORS Skaug B, Jiang X, Chen ZJ TITLE The role of ubiquitin in NF-kappaB regulatory pathways. JOURNAL Annu Rev Biochem 78:769-96 (2009) DOI:10.1146/annurev.biochem.78.070907.102750 REFERENCE PMID:20300215 AUTHORS Wertz IE, Dixit VM TITLE Signaling to NF-kappaB: regulation by ubiquitination. JOURNAL Cold Spring Harb Perspect Biol 2:a003350 (2010) DOI:10.1101/cshperspect.a003350 REFERENCE PMID:11875461 AUTHORS Karin M, Lin A TITLE NF-kappaB at the crossroads of life and death. JOURNAL Nat Immunol 3:221-7 (2002) DOI:10.1038/ni0302-221 REFERENCE PMID:12654254 AUTHORS Lin A, Karin M TITLE NF-kappaB in cancer: a marked target. JOURNAL Semin Cancer Biol 13:107-14 (2003) DOI:10.1016/S1044-579X(02)00128-1 REFERENCE PMID:16251197 AUTHORS Morlon A, Munnich A, Smahi A TITLE TAB2, TRAF6 and TAK1 are involved in NF-kappaB activation induced by the TNF-receptor, Edar and its adaptator Edaradd. JOURNAL Hum Mol Genet 14:3751-7 (2005) DOI:10.1093/hmg/ddi405 REFERENCE PMID:24070496 AUTHORS Sadier A, Viriot L, Pantalacci S, Laudet V TITLE The ectodysplasin pathway: from diseases to adaptations. JOURNAL Trends Genet 30:24-31 (2014) DOI:10.1016/j.tig.2013.08.006 REFERENCE PMID:26260321 AUTHORS Verhelst K, Gardam S, Borghi A, Kreike M, Carpentier I, Beyaert R TITLE XEDAR activates the non-canonical NF-kappaB pathway. JOURNAL Biochem Biophys Res Commun 465:275-80 (2015) DOI:10.1016/j.bbrc.2015.08.019 REFERENCE PMID:27508514 AUTHORS McDaniel DK, Eden K, Ringel VM, Allen IC TITLE Emerging Roles for Noncanonical NF-kappaB Signaling in the Modulation of Inflammatory Bowel Disease Pathobiology. JOURNAL Inflamm Bowel Dis 22:2265-79 (2016) DOI:10.1097/MIB.0000000000000858 REFERENCE PMID:12787560 AUTHORS Mikkola ML, Thesleff I TITLE Ectodysplasin signaling in development. JOURNAL Cytokine Growth Factor Rev 14:211-24 (2003) DOI:10.1016/S1359-6101(03)00020-0 REFERENCE PMID:26646590 AUTHORS Hu Y, Ge W, Wang X, Sutendra G, Zhao K, Dedeic Z, Slee EA, Baer C, Lu X TITLE Caspase cleavage of iASPP potentiates its ability to inhibit p53 and NF-kappaB. JOURNAL Oncotarget 6:42478-90 (2015) DOI:10.18632/oncotarget.6478 REL_PATHWAY map03050 Proteasome map04020 Calcium signaling pathway map04060 Cytokine-cytokine receptor interaction map04120 Ubiquitin mediated proteolysis map04210 Apoptosis map04380 Osteoclast differentiation map04620 Toll-like receptor signaling pathway map04622 RIG-I-like receptor signaling pathway map04660 T cell receptor signaling pathway map04662 B cell receptor signaling pathway KO_PATHWAY ko04064 /// ENTRY map04066 Pathway NAME HIF-1 signaling pathway DESCRIPTION Hypoxia-inducible factor 1 (HIF-1) is a transcription factor that functions as a master regulator of oxygen homeostasis. It consists of two subunits: an inducibly-expressed HIF-1alpha subunit and a constitutively-expressed HIF-1beta subunit. Under normoxia, HIF-1 alpha undergoes hydroxylation at specific prolyl residues which leads to an immediate ubiquitination and subsequent proteasomal degradation of the subunit. In contrast, under hypoxia, HIF-1 alpha subunit becomes stable and interacts with coactivators such as p300/CBP to modulate its transcriptional activity. Eventually, HIF-1 acts as a master regulator of numerous hypoxia-inducible genes under hypoxic conditions. The target genes of HIF-1 encode proteins that increase O2 delivery and mediate adaptive responses to O2 deprivation. Despite its name, HIF-1 is induced not only in response to reduced oxygen availability but also by other stimulants, such as nitric oxide, or various growth factors. CLASS Environmental Information Processing; Signal transduction PATHWAY_MAP map04066 HIF-1 signaling pathway REFERENCE PMID:20836033 AUTHORS Semenza GL TITLE Oxygen homeostasis. JOURNAL Wiley Interdiscip Rev Syst Biol Med 2:336-61 (2010) DOI:10.1002/wsbm.69 REFERENCE PMID:17955264 AUTHORS Mole DR, Ratcliffe PJ TITLE Cellular oxygen sensing in health and disease. JOURNAL Pediatr Nephrol 23:681-94 (2008) DOI:10.1007/s00467-007-0632-x REFERENCE PMID:18498744 AUTHORS Kaelin WG Jr, Ratcliffe PJ TITLE Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. JOURNAL Mol Cell 30:393-402 (2008) DOI:10.1016/j.molcel.2008.04.009 REFERENCE PMID:22205687 AUTHORS Palazon A, Aragones J, Morales-Kastresana A, de Landazuri MO, Melero I TITLE Molecular pathways: hypoxia response in immune cells fighting or promoting cancer. JOURNAL Clin Cancer Res 18:1207-13 (2012) DOI:10.1158/1078-0432.CCR-11-1591 REFERENCE PMID:20965423 AUTHORS Majmundar AJ, Wong WJ, Simon MC TITLE Hypoxia-inducible factors and the response to hypoxic stress. JOURNAL Mol Cell 40:294-309 (2010) DOI:10.1016/j.molcel.2010.09.022 REFERENCE PMID:22562152 AUTHORS Greer SN, Metcalf JL, Wang Y, Ohh M TITLE The updated biology of hypoxia-inducible factor. JOURNAL EMBO J 31:2448-60 (2012) DOI:10.1038/emboj.2012.125 REFERENCE PMID:15448722 AUTHORS Zagorska A, Dulak J TITLE HIF-1: the knowns and unknowns of hypoxia sensing. JOURNAL Acta Biochim Pol 51:563-85 (2004) REFERENCE PMID:19364912 AUTHORS Semenza GL TITLE Regulation of oxygen homeostasis by hypoxia-inducible factor 1. JOURNAL Physiology (Bethesda) 24:97-106 (2009) DOI:10.1152/physiol.00045.2008 REFERENCE PMID:16234508 AUTHORS Wenger RH, Stiehl DP, Camenisch G TITLE Integration of oxygen signaling at the consensus HRE. JOURNAL Sci STKE 2005:re12 (2005) DOI:10.1126/stke.3062005re12 REFERENCE PMID:15031665 AUTHORS Lee JW, Bae SH, Jeong JW, Kim SH, Kim KW TITLE Hypoxia-inducible factor (HIF-1)alpha: its protein stability and biological functions. JOURNAL Exp Mol Med 36:1-12 (2004) DOI:10.1038/emm.2004.1 REFERENCE PMID:18259201 AUTHORS Weidemann A, Johnson RS TITLE Biology of HIF-1alpha. JOURNAL Cell Death Differ 15:621-7 (2008) DOI:10.1038/cdd.2008.12 REFERENCE PMID:11902584 AUTHORS Harris AL TITLE Hypoxia--a key regulatory factor in tumour growth. JOURNAL Nat Rev Cancer 2:38-47 (2002) DOI:10.1038/nrc704 REFERENCE PMID:19147540 AUTHORS Knaup KX, Jozefowski K, Schmidt R, Bernhardt WM, Weidemann A, Juergensen JS, Warnecke C, Eckardt KU, Wiesener MS TITLE Mutual regulation of hypoxia-inducible factor and mammalian target of rapamycin as a function of oxygen availability. JOURNAL Mol Cancer Res 7:88-98 (2009) DOI:10.1158/1541-7786.MCR-08-0288 REFERENCE PMID:18505681 AUTHORS Kaluz S, Kaluzova M, Stanbridge EJ TITLE Regulation of gene expression by hypoxia: integration of the HIF-transduced hypoxic signal at the hypoxia-responsive element. JOURNAL Clin Chim Acta 395:6-13 (2008) DOI:10.1016/j.cca.2008.05.002 REFERENCE PMID:20679415 AUTHORS Cadenas S, Aragones J, Landazuri MO TITLE Mitochondrial reprogramming through cardiac oxygen sensors in ischaemic heart disease. JOURNAL Cardiovasc Res 88:219-28 (2010) DOI:10.1093/cvr/cvq256 REFERENCE PMID:19861159 AUTHORS Berchner-Pfannschmidt U, Tug S, Kirsch M, Fandrey J TITLE Oxygen-sensing under the influence of nitric oxide. JOURNAL Cell Signal 22:349-56 (2010) DOI:10.1016/j.cellsig.2009.10.004 REL_PATHWAY map00020 Citrate cycle (TCA cycle) map04010 MAPK signaling pathway map04020 Calcium signaling pathway map04120 Ubiquitin mediated proteolysis map04150 mTOR signaling pathway map04151 PI3K-Akt signaling pathway map04370 VEGF signaling pathway KO_PATHWAY ko04066 /// ENTRY map07048 Drug Pathway NAME Antimigraines PATHWAY_MAP map07048 Antimigraines COMPOUND D00109 Aspirin (JP18/USP) D00118 Naproxen (JP18/USP/INN) D00126 Ibuprofen (JP18/USP/INN) D00217 Acetaminophen (JP18/USP) D00235 Atenolol (JP18/USP/INN) D00270 Chlorpromazine (USP/INN) D00304 Divalproex sodium (USP) D00399 Valproic acid (USP) D00415 Zolmitriptan (JAN/USP/INN) D00432 Nadolol (JP18/USP/INN) D00451 Sumatriptan (JAN/USP/INN) D00479 Prochlorperazine maleate (JP18/USP) D00483 Propranolol hydrochloride (JP18/USP) D00493 Prochlorperazine (JAN/USP/INN) D00601 Metoprolol tartrate (JP18/USP) D00619 Verapamil hydrochloride (JP18/USP) D00635 Metoprolol succinate (USP) D00674 Naratriptan hydrochloride (JAN/USP) D00675 Rizatriptan benzoate (JAN/USP) D00676 Sumatriptan succinate (JAN/USP) D00679 Ergotamine tartrate (JP18/USP) D00681 Methysergide maleate (USP) D00710 Valproate sodium (USAN) D00726 Metoclopramide (JP18/INN) D00789 Chlorpromazine hydrochloride (JP18/USP) D00809 Amitriptyline hydrochloride (JP18/USP) D00816 Nortriptyline hydrochloride (JP18/USP/INN) D00970 Naproxen sodium (USP) D01122 Ibuprofen piconol (JP18/USAN) D01303 Flunarizine hydrochloride (JAN/USAN) D01462 Lisuride maleate (JAN) D01902 Fonazine mesylate (USAN) D01973 Eletriptan hydrobromide (JAN/USAN) D02022 Prochlorperazine mesilate (JAN) D02211 Dihydroergotamine mesylate (USP) D02213 Metoclopramide hydrochloride (JAN) D02356 Verapamil (USAN/INN) D02357 Methysergide (USAN/INN) D02358 Metoprolol (USAN/INN) D02609 Prochlorperazine edisylate (USP) D02633 Lomerizine hydrochloride (JAN) D02824 Almotriptan (USAN) D02825 Almotriptan malate (USP) D03014 Avitriptan fumarate (USAN) D04264 Frovatriptan succinate (USAN) D04490 Ibuprofen aluminum (USAN) D05008 Metoclopramide hydrochloride (USP) D05011 Metoprolol fumarate (USP) D05181 Aspirin aluminum (JP18) D05740 Rizatriptan sulfate (USAN) D06606 Ibuprofen lysine (USAN) D07296 Flumedroxone (INN) D07448 Amitriptyline (INN) D07579 Aspirin calcium salt D07581 Aspirin magnesium salt D07582 Aspirin sodium D07837 Dihydroergotamine (INN) D07838 Dihydroergotamine tartrate D07854 Dimetotiazine (INN) D07887 Eletriptan (INN) D07906 Ergotamine (INN) D07971 Flunarizine (INN) D07997 Frovatriptan (INN) D08058 Ibuprofen arginine salt D08059 Ibuprofen sodium D08132 Lisuride (INN) D08255 Naratriptan (INN) D08288 Nortriptyline (INN) D08443 Propranolol (INN) D08485 Rizatriptan (INN) REFERENCE AUTHORS Societas Neurologica Japonica (ed). TITLE [Treatment of chronic headache guideline 2002, II Migraine.] (In Japanese) JOURNAL /// ENTRY map00363 Pathway NAME Bisphenol degradation CLASS Metabolism; Xenobiotics biodegradation and metabolism PATHWAY_MAP map00363 Bisphenol degradation DBLINKS UMBBD: tbp2 bpa hap bpf REFERENCE PMID:15635150 AUTHORS Kitamura S, Suzuki T, Sanoh S, Kohta R, Jinno N, Sugihara K, Yoshihara S, Fujimoto N, Watanabe H, Ohta S. TITLE Comparative study of the endocrine-disrupting activity of bisphenol A and 19 related compounds. JOURNAL Toxicol Sci 84:249-59 (2005) DOI:10.1093/toxsci/kfi074 REFERENCE PMID:9607780 AUTHORS Steinmetz R, Mitchner NA, Grant A, Allen DL, Bigsby RM, Ben-Jonathan N. TITLE The xenoestrogen bisphenol A induces growth, differentiation, and c-fos gene expression in the female reproductive tract. JOURNAL Endocrinology 139:2741-7 (1998) DOI:10.1210/endo.139.6.6027 REFERENCE PMID:11259533 AUTHORS Elsby R, Maggs JL, Ashby J, Park BK. TITLE Comparison of the modulatory effects of human and rat liver microsomal metabolism on the estrogenicity of bisphenol A: implications for extrapolation to humans. JOURNAL J Pharmacol Exp Ther 297:103-13 (2001) REFERENCE PMID:10831413 AUTHORS Ronen Z, Abeliovich A. TITLE Anaerobic-aerobic process for microbial degradation of tetrabromobisphenol A. JOURNAL Appl Environ Microbiol 66:2372-7 (2000) DOI:10.1128/AEM.66.6.2372-2377.2000 REFERENCE PMID:14559264 AUTHORS Eriksson J, Rahm S, Green N, Bergman A, Jakobsson E. TITLE Photochemical transformations of tetrabromobisphenol A and related phenols in water. JOURNAL Chemosphere 54:117-26 (2004) DOI:10.1016/S0045-6535(03)00704-5 REFERENCE PMID:12242676 AUTHORS Ike M, Chen MY, Jin CS, Fujita M. TITLE Acute toxicity, mutagenicity, and estrogenicity of biodegradation products of bisphenol-A. JOURNAL Environ Toxicol 17:457-61 (2002) DOI:10.1002/tox.10079 REFERENCE PMID:8031091 AUTHORS Jones KH, Trudgill PW, Hopper DJ TITLE 4-Ethylphenol metabolism by Aspergillus fumigatus. JOURNAL Appl Environ Microbiol 60:1978-83 (1994) DOI:10.1128/AEM.60.6.1978-1983.1994 REFERENCE PMID:18024680 AUTHORS Inoue D, Hara S, Kashihara M, Murai Y, Danzl E, Sei K, Tsunoi S, Fujita M, Ike M TITLE Degradation of Bis(4-Hydroxyphenyl)methane (bisphenol F) by Sphingobium yanoikuyae strain FM-2 isolated from river water. JOURNAL Appl Environ Microbiol 74:352-8 (2008) DOI:10.1128/AEM.01708-07 REL_PATHWAY map00361 Chlorocyclohexane and chlorobenzene degradation map00362 Benzoate degradation KO_PATHWAY ko00363 /// ENTRY map00362 Pathway NAME Benzoate degradation CLASS Metabolism; Xenobiotics biodegradation and metabolism PATHWAY_MAP map00362 Benzoate degradation MODULE M00540 Benzoate degradation, cyclohexanecarboxylic acid =>pimeloyl-CoA [PATH:map00362] M00541 Benzoyl-CoA degradation, benzoyl-CoA => 3-hydroxypimeloyl-CoA [PATH:map00362] M00547 Benzene/toluene degradation, benzene => catechol / toluene => 3-methylcatechol [PATH:map00362] M00548 Benzene degradation, benzene => catechol [PATH:map00362] M00551 Benzoate degradation, benzoate => catechol / methylbenzoate => methylcatechol [PATH:map00362] M00568 Catechol ortho-cleavage, catechol => 3-oxoadipate [PATH:map00362] M00569 Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA [PATH:map00362] DBLINKS UMBBD: benz2 benz abs GO: 0043639 REFERENCE PMID:19258534 AUTHORS Carmona M, Zamarro MT, Blazquez B, Durante-Rodriguez G, Juarez JF, Valderrama JA, Barragan MJ, Garcia JL, Diaz E TITLE Anaerobic catabolism of aromatic compounds: a genetic and genomic view. JOURNAL Microbiol Mol Biol Rev 73:71-133 (2009) DOI:10.1128/MMBR.00021-08 REFERENCE PMID:12486039 AUTHORS Hara H, Masai E, Miyauchi K, Katayama Y, Fukuda M. TITLE Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6. JOURNAL J Bacteriol 185:41-50 (2003) DOI:10.1128/JB.185.1.41-50.2003 REFERENCE PMID:15277747 AUTHORS Maruyama K, Shibayama T, Ichikawa A, Sakou Y, Yamada S, Sugisaki H. TITLE Cloning and characterization of the genes encoding enzymes for the protocatechuate meta-degradation pathway of Pseudomonas ochraceae NGJ1. JOURNAL Biosci Biotechnol Biochem 68:1434-41 (2004) DOI:10.1271/bbb.68.1434 REFERENCE PMID:10589735 AUTHORS Mampel J, Ruff J, Junker F, Cook AM. TITLE The oxygenase component of the 2-aminobenzenesulfonate dioxygenase system from Alcaligenes sp. strain O-1. JOURNAL Microbiology 145 ( Pt 11):3255-64 (1999) DOI:10.1099/00221287-145-11-3255 REFERENCE PMID:8002948 AUTHORS Junker F, Field JA, Bangerter F, Ramsteiner K, Kohler HP, Joannou CL, Mason JR, Leisinger T, Cook AM. TITLE Oxygenation and spontaneous deamination of 2-aminobenzenesulphonic acid in Alcaligenes sp. strain O-1 with subsequent meta ring cleavage and spontaneous desulphonation to 2-hydroxymuconic acid. JOURNAL Biochem J 300 ( Pt 2):429-36 (1994) DOI:10.1042/bj3000429 REFERENCE PMID:8990279 AUTHORS Harwood CS, Gibson J. TITLE Shedding light on anaerobic benzene ring degradation: a process unique to prokaryotes? JOURNAL J Bacteriol 179:301-9 (1997) DOI:10.1128/JB.179.2.301-309.1997 REFERENCE PMID:17122342 AUTHORS Peters F, Shinoda Y, McInerney MJ, Boll M. TITLE Cyclohexa-1,5-diene-1-carbonyl-coenzyme A (CoA) hydratases of Geobacter metallireducens and Syntrophus aciditrophicus: Evidence for a common benzoyl-CoA degradation pathway in facultative and strict anaerobes. JOURNAL J Bacteriol 189:1055-60 (2007) DOI:10.1128/JB.01467-06 REFERENCE PMID:11053377 AUTHORS Cowles CE, Nichols NN, Harwood CS. TITLE BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida. JOURNAL J Bacteriol 182:6339-46 (2000) DOI:10.1128/JB.182.22.6339-6346.2000 REFERENCE PMID:12514037 AUTHORS Smith MA, Weaver VB, Young DM, Ornston LN. TITLE Genes for chlorogenate and hydroxycinnamate catabolism (hca) are linked to functionally related genes in the dca-pca-qui-pob-hca chromosomal cluster of Acinetobacter sp. strain ADP1. JOURNAL Appl Environ Microbiol 69:524-32 (2003) DOI:10.1128/AEM.69.1.524-532.2003 REFERENCE PMID:18312395 AUTHORS Kuntze K, Shinoda Y, Moutakki H, McInerney MJ, Vogt C, Richnow HH, Boll M TITLE 6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes. JOURNAL Environ Microbiol 10:1547-56 (2008) DOI:10.1111/j.1462-2920.2008.01570.x REFERENCE PMID:10781543 AUTHORS Pelletier DA, Harwood CS TITLE 2-Hydroxycyclohexanecarboxyl coenzyme A dehydrogenase, an enzyme characteristic of the anaerobic benzoate degradation pathway used by Rhodopseudomonas palustris. JOURNAL J Bacteriol 182:2753-60 (2000) DOI:10.1128/JB.182.10.2753-2760.2000 REFERENCE PMID:11282627 AUTHORS Elshahed MS, Bhupathiraju VK, Wofford NQ, Nanny MA, McInerney MJ TITLE Metabolism of benzoate, cyclohex-1-ene carboxylate, and cyclohexane carboxylate by "Syntrophus aciditrophicus" strain SB in syntrophic association with H(2)-using microorganisms. JOURNAL Appl Environ Microbiol 67:1728-38 (2001) DOI:10.1128/AEM.67.4.1728-1738.2001 REFERENCE PMID:21219457 AUTHORS Nogales J, Canales A, Jimenez-Barbero J, Serra B, Pingarron JM, Garcia JL, Diaz E TITLE Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. JOURNAL Mol Microbiol 79:359-74 (2011) DOI:10.1111/j.1365-2958.2010.07448.x REL_PATHWAY map00010 Glycolysis / Gluconeogenesis map00020 Citrate cycle (TCA cycle) map00350 Tyrosine metabolism map00360 Phenylalanine metabolism map00361 Chlorocyclohexane and chlorobenzene degradation map00627 Aminobenzoate degradation map00790 Folate biosynthesis KO_PATHWAY ko00362 /// ENTRY map00361 Pathway NAME Chlorocyclohexane and chlorobenzene degradation CLASS Metabolism; Xenobiotics biodegradation and metabolism PATHWAY_MAP map00361 Chlorocyclohexane and chlorobenzene degradation MODULE M00547 Benzene/toluene degradation, benzene => catechol / toluene => 3-methylcatechol [PATH:map00361] M00548 Benzene degradation, benzene => catechol [PATH:map00361] DBLINKS UMBBD: hch ghch dcz 2,4-d pcp 2,4,5-t tcb REFERENCE PMID:10600501 AUTHORS Xun L, Bohuslavek J, Cai M. TITLE Characterization of 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA) of Sphingomonas chlorophenolica ATCC 39723. JOURNAL Biochem Biophys Res Commun 266:322-5 (1999) DOI:10.1006/bbrc.1999.1805 REFERENCE PMID:1987135 AUTHORS van der Meer JR, van Neerven AR, de Vries EJ, de Vos WM, Zehnder AJ. TITLE Cloning and characterization of plasmid-encoded genes for the degradation of 1,2-dichloro-, 1,4-dichloro-, and 1,2,4-trichlorobenzene of Pseudomonas sp. strain P51. JOURNAL J Bacteriol 173:6-15 (1991) DOI:10.1128/jb.173.1.6-15.1991 REFERENCE PMID:10464214 AUTHORS Nagata Y, Futamura A, Miyauchi K, Takagi M. TITLE Two different types of dehalogenases, LinA and LinB, involved in gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 are localized in the periplasmic space without molecular processing. JOURNAL J Bacteriol 181:5409-13 (1999) DOI:10.1128/JB.181.17.5409-5413.1999 REFERENCE PMID:11423959 AUTHORS Nagata Y, Miyauchi K, Takagi M. TITLE Complete analysis of genes and enzymes for gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. JOURNAL J Ind Microbiol Biotechnol 23:380-390 (1999) DOI:10.1038/sj/jim/2900736 REFERENCE PMID:15060023 AUTHORS Dogra C, Raina V, Pal R, Suar M, Lal S, Gartemann KH, Holliger C, van der Meer JR, Lal R. TITLE Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer. JOURNAL J Bacteriol 186:2225-35 (2004) DOI:10.1128/JB.186.8.2225-2235.2004 REFERENCE PMID:12676719 AUTHORS Nagata Y, Prokop Z, Marvanova S, Sykorova J, Monincova M, Tsuda M, Damborsky J. TITLE Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB. JOURNAL Appl Environ Microbiol 69:2349-55 (2003) DOI:10.1128/AEM.69.4.2349-2355.2003 REFERENCE PMID:15489427 AUTHORS Vedler E, Vahter M, Heinaru A. TITLE The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. JOURNAL J Bacteriol 186:7161-74 (2004) DOI:10.1128/JB.186.21.7161-7174.2004 REFERENCE PMID:9148781 AUTHORS Sommer C, Gorisch H. TITLE Enzymology of the degradation of (di)chlorobenzenes by Xanthobacter flavus 14p1. JOURNAL Arch Microbiol 167:384-91 (1997) DOI:10.1007/s002030050459 REFERENCE PMID:12070765 AUTHORS Laemmli CM, Schonenberger R, Suter M, Zehnder AJ, van der Meer JR. TITLE TfdD(II), one of the two chloromuconate cycloisomerases of Ralstonia eutropha JMP134 (pJP4), cannot efficiently convert 2-chloro- cis, cis-muconate to trans-dienelactone to allow growth on 3-chlorobenzoate. JOURNAL Arch Microbiol 178:13-25 (2002) DOI:10.1007/s00203-002-0417-3 REFERENCE PMID:16977465 AUTHORS Wu J, Hong Q, Han P, He J, Li S. TITLE A gene linB2 responsible for the conversion of beta-HCH and 2,3,4,5,6-pentachlorocyclohexanol in Sphingomonas sp. BHC-A. JOURNAL Appl Microbiol Biotechnol 73:1097-105 (2007) DOI:10.1007/s00253-006-0579-z REFERENCE PMID:9758802 AUTHORS Potrawfke T, Timmis KN, Wittich RM TITLE Degradation of 1,2,3,4-tetrachlorobenzene by pseudomonas chlororaphis RW71 JOURNAL Appl Environ Microbiol 64:3798-806 (1998) DOI:10.1128/AEM.64.10.3798-3806.1998 REFERENCE PMID:11208799 AUTHORS Potrawfke T, Armengaud J, Wittich RM TITLE Chlorocatechols substituted at positions 4 and 5 are substrates of the broad-spectrum chlorocatechol 1,2-dioxygenase of Pseudomonas chlororaphis RW71. JOURNAL J Bacteriol 183:997-1011 (2001) DOI:10.1128/JB.183.3.997-1011.2001 REL_PATHWAY map00020 Citrate cycle (TCA cycle) map00362 Benzoate degradation map00630 Glyoxylate and dicarboxylate metabolism KO_PATHWAY ko00361 /// ENTRY C00099 Compound NAME beta-Alanine; 3-Aminopropionic acid; 3-Aminopropanoate FORMULA C3H7NO2 EXACT_MASS 89.0477 MOL_WEIGHT 89.09 REMARK Same as: D07561 REACTION R00489 R00904 R00905 R00906 R00907 R00908 R00909 R00910 R00911 R00912 R00913 R00914 R00915 R00916 R00917 R01164 R01166 R02473 R02474 R02741 R03286 R03288 R03935 R09379 R09648 R10821 PATHWAY map00240 Pyrimidine metabolism map00410 beta-Alanine metabolism map00640 Propanoate metabolism map00770 Pantothenate and CoA biosynthesis map01100 Metabolic pathways map01110 Biosynthesis of secondary metabolites map01240 Biosynthesis of cofactors map04080 Neuroactive ligand-receptor interaction map04974 Protein digestion and absorption MODULE M00046 Pyrimidine degradation, uracil => beta-alanine, thymine => 3-aminoisobutanoate M00119 Pantothenate biosynthesis, valine/L-aspartate => pantothenate M00913 Pantothenate biosynthesis, 2-oxoisovalerate/spermine => pantothenate ENZYME 1.2.1.3 1.2.1.5 1.2.1.19 1.5.1.26 2.6.1.18 2.6.1.19 2.6.1.55 2.6.1.120 2.8.3.- 3.4.13.4 3.4.13.5 3.4.13.18 3.4.13.20 3.5.1.6 3.5.1.21 3.5.1.22 3.5.1.100 3.5.3.17 4.1.1.11 4.1.1.15 6.3.2.1 6.3.2.11 6.3.2.23 6.3.2.36 6.3.2.44 BRITE Compounds with biological roles [BR:br08001] Peptides Amino acids Other amino acids C00099 beta-Alanine Amines Biogenic amines C00099 beta-Alanine DBLINKS CAS: 107-95-9 PubChem: 3399 KNApSAcK: C00001333 PDB-CCD: BAL NIKKAJI: J4.070C ATOM 6 1 C1b C 25.6778 -16.8919 2 C6a C 24.4732 -16.1936 3 C1b C 26.8940 -16.1936 4 O6a O 23.2571 -16.8978 5 O6a O 24.4732 -14.7912 6 N1a N 28.1045 -16.8919 BOND 5 1 1 2 1 2 1 3 1 3 2 4 1 4 2 5 2 5 3 6 1 ///