Revision as of 16:20, 9 January 2012 editBeetstra (talk | contribs)Edit filter managers, Administrators172,031 edits Saving copy of the {{chembox}} taken from revid 469631534 of page Ribose_5-phosphate for the Chem/Drugbox validation project (updated: 'StdInChI', 'CASNo'). |
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{{Short description|Chemical compound}} |
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{{ambox | text = This page contains a copy of the infobox ({{tl|chembox}}) taken from revid of page ] with values updated to verified values.}} |
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{{Distinguish|Riboflavin-5'-phosphate}} |
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{{chembox |
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| verifiedrevid = 464382183 |
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| verifiedrevid = 470456083 |
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| ImageFile = Ribose 5-phosphate.png |
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| ImageFile = Ribose 5-phosphate.png |
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| ImageSize = |
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| ImageSize = |
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| IUPACName = (2,3,4-Trihydroxy-5-oxo-pentoxy)phosphonic acid |
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| IUPACName = 5-''O''-Phosphono-<small>D</small>-ribose |
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| OtherNames = |
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| OtherNames = Ribose 5-phosphate |
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| Section1 = {{Chembox Identifiers |
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|Section1={{Chembox Identifiers |
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| CASNo_Ref = {{cascite|correct|CAS}} |
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| InChI = 1/C5H9O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/p-2/t3-,4+,5-/m0/s1 |
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| CASNo = 4300-28-1 |
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| InChIKey = PPQRONHOSHZGFQ-QRUISDQRBJ |
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| UNII_Ref = {{fdacite|correct|FDA}} |
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| UNII = 4B2428FLTO |
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| PubChem = 77982 |
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| ChemSpiderID_Ref = {{chemspidercite|changed|chemspider}} |
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| ChemSpiderID = 70368 |
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| SMILES = C((((C=O)O)O)O)OP(=O)(O)O |
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| InChI = 1/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4+,5-/m0/s1 |
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| InChIKey = PPQRONHOSHZGFQ-LMVFSUKVBC |
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| StdInChI_Ref = {{stdinchicite|changed|chemspider}} |
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| StdInChI_Ref = {{stdinchicite|changed|chemspider}} |
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| StdInChI = 1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/p-2/t3-,4+,5-/m0/s1 |
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| StdInChI = 1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4+,5-/m0/s1 |
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| StdInChIKey_Ref = {{stdinchicite|correct|chemspider}} |
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| StdInChIKey_Ref = {{stdinchicite|changed|chemspider}} |
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| StdInChIKey = PPQRONHOSHZGFQ-LMVFSUKVSA-L |
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| StdInChIKey = PPQRONHOSHZGFQ-LMVFSUKVSA-N |
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| CASNo_Ref = {{cascite|changed|??}} |
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| ChEBI_Ref = {{ebicite|correct|EBI}} |
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| CASNo = <!-- blanked - oldvalue: 3615-55-2 --> |
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| PubChem = 230 |
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| ChemSpiderID_Ref = {{chemspidercite|correct|chemspider}} |
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| ChemSpiderID=19971025 |
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| ChEBI = 58273 |
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| ChEBI = 58273 |
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| MeSHName = ribose-5-phosphate |
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| SMILES = P()(=O)OC(O)(O)(O)C=O |
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| MeSHName = ribose-5-phosphate |
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| Section2 = {{Chembox Properties |
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|Section2={{Chembox Properties |
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| Formula = C<sub>5</sub>H<sub>9</sub>O<sub>8</sub>P |
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| Formula = C<sub>5</sub>H<sub>11</sub>O<sub>8</sub>P |
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| MolarMass = 230.110 |
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| MolarMass = 230.110 |
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| Section3 = {{Chembox Hazards |
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'''Ribose 5-phosphate''' ('''R5P''') is both a product and an intermediate of the ]. The last step of the ] in the pentose phosphate pathway is the production of ]. Depending on the body's state, ribulose 5-phosphate can reversibly ] to ribose 5-phosphate. Ribulose 5-phosphate can alternatively undergo a series of isomerizations as well as transaldolations and transketolations that result in the production of other pentose phosphates as well as ] and ] (both intermediates in ]). |
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The enzyme ] converts ribose-5-phosphate into ]. |
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== Structure == |
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] |
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R5P consists of a five-carbon ], ], and a ] group at the five-position carbon. It can exist in open chain form or in ] form. The furanose form is most commonly referred to as ribose 5-phosphoric acid.<ref>{{cite journal | vauthors = Levene PA, Stiller ET | date = February 1934 | title = The Synthesis of Ribose-5-Phosphoric Acid | url = http://www.jbc.org/content/104/2/299 | journal = Journal of Biological Chemistry | volume = 104 | issue = 2 | pages = 299–306 | doi = 10.1016/S0021-9258(18)75766-9 | doi-access = free }}</ref> |
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== Biosynthesis == |
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The formation of R5P is highly dependent on the cell growth and the need for ] (]), R5P, and ATP (]). Formation of each molecule is controlled by the flow of ] in two different metabolic pathways: the pentose phosphate pathway and glycolysis. The relationship between the two pathways can be examined through different metabolic situations.<ref name="Berg_2015">{{cite book | title = Biochemistry | edition = 7th | last1 = Berg | first1 = Jeremy M. | first2 = John L. | last2 = Tymoczko | first3 = Lubert | last3 = Stryer | name-list-style = vanc |publisher=W.H. Freeman|year=2015|isbn=978-1-4292-7635-1|pages=589–613}}</ref> |
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=== Pentose phosphate pathway === |
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] |
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R5P is produced in the ] in all organisms.<ref name="Berg_2015" /> The pentose phosphate pathway (PPP) is a metabolic pathway that runs parallel to glycolysis. It is a crucial source for NADPH generation for reductive biosynthesis<ref>{{cite journal | vauthors = Kruger NJ, von Schaewen A | title = The oxidative pentose phosphate pathway: structure and organisation | journal = Current Opinion in Plant Biology | volume = 6 | issue = 3 | pages = 236–46 | date = June 2003 | pmid = 12753973 | doi = 10.1016/s1369-5266(03)00039-6 }}</ref> (e.g. ]) and ] sugars. The pathway consists of two phases: an oxidative phase that generates NADPH and a non-oxidative phase that involves the interconversion of sugars. In the oxidative phase of PPP, two molecules of ] are reduced to NADPH through the conversion of G6P to ] (Ru5P). In the non-oxidative of PPP, Ru5P can be converted to R5P through ] ].<ref>{{cite journal | vauthors = Zhang R, Andersson CE, Savchenko A, Skarina T, Evdokimova E, Beasley S, Arrowsmith CH, Edwards AM, Joachimiak A, Mowbray SL | title = Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle | journal = Structure | volume = 11 | issue = 1 | pages = 31–42 | date = January 2003 | pmid = 12517338| pmc = 2792023 | doi = 10.1016/s0969-2126(02)00933-4 }}</ref> |
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When demand for NADPH and R5P is balanced, G6P forms one Ru5P molecule through the PPP, generating two NADPH molecules and one R5P molecule.<ref name="Berg_2015" /> |
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=== Glycolysis === |
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When more R5P is needed than NADPH, R5P can be formed through ] intermediates. Glucose 6-phosphate is converted to ] and ] during ]. ] and ] convert two molecules of F6P and one molecule of G3P to three molecules of R5P.<ref name="Berg_2015" /> During rapid cell growth, higher quantities of R5P and NADPH are needed for nucleotide and fatty acid synthesis, respectively. Glycolytic intermediates can be diverted toward the non-oxidative phase of PPP by the expression of the gene for ] isozyme, PKM. PKM creates a bottleneck in the glycolytic pathway, allowing intermediates to be utilized by the PPP to synthesize NADPH and R5P. This process is further enabled by ] inhibition by ], the PKM substrate.<ref name="Berg_2015" /> |
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== Function == |
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R5P and its derivatives serve as precursors to many biomolecules, including ], ], ATP, ], ] (]), and ].<ref>{{cite book |last1=Coleman|first1=James P.|last2=Smith|first2=C. Jeffrey | name-list-style = vanc | pages = 1–6 | doi = 10.1016/b978-008055232-3.60227-2 |title = X ''Pharm'': The Comprehensive Pharmacology Reference|year = 2007|isbn = 9780080552323}}</ref> |
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=== Nucleotide biosynthesis === |
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]s serve as the building blocks for nucleic acids, DNA and RNA.<ref>{{cite book | chapter-url = http://goldbook.iupac.org/N04255.html | publisher = International Union of Pure and Applied Chemistry | doi = 10.1351/goldbook.n04255 | title = IUPAC Compendium of Chemical Terminology | year = 2009 | isbn = 978-0-9678550-9-7 | chapter = Nucleotides }}</ref> They are composed of a nitrogenous base, a pentose sugar, and at least one phosphate group. Nucleotides contain either a ] or a ] nitrogenous base. All intermediates in purine biosynthesis are constructed on a R5P "scaffold".<ref>{{cite book | title = Textbook of Veterinary Physiological Chemistry | edition = Third | date = 2015 | chapter = Purine Biosynthesis | last = Engelking | first = Larry R. | name-list-style = vanc | pages = 88–92 | doi = 10.1016/b978-0-12-391909-0.50015-3 | isbn = 978-0-12-391909-0 }}</ref> R5P also serves as an important precursor to pyrimidine ribonucleotide synthesis. |
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During nucleotide biosynthesis, R5P undergoes activation by ] (PRPS1) to form ] (PRPP). Formation of PRPP is essential for both the ] and for the ].<ref name="Pelley_2011">{{cite book | title = Elsevier's Integrated Review Biochemistry | edition = 2nd | date = 2011 | chapter = Purine, Pyrimidine, and Single-Carbon Metabolism | last = Pelley | first = John W. | name-list-style = vanc | pages = 119–124 | doi = 10.1016/b978-0-323-07446-9.00014-3 | isbn = 9780323074469 }}</ref> The de novo synthesis pathway begins with the activation of R5P to PRPP, which is later catalyzed to become ], a nucleotide precursor. During the purine salvage pathway,<ref>{{cite book | title = Textbook of Veterinary Physiological Chemistry | edition = Third | date = 2015 | chapter = Chapter 31 {{mdash}} Carbohydrate Metabolism in Erythrocytes | last = Engelking | first = Larry R. | name-list-style = vanc | pages = 190–194 | doi = 10.1016/b978-0-12-391909-0.50031-1 | isbn = 978-0-12-391909-0 }}</ref> phosphoribosyltransferases add PRPP to bases.<ref>{{Cite book | title=Phosphoribosyltransferase Mechanisms and Roles in Nucleic Acid Metabolism|journal=Progress in Nucleic Acid Research and Molecular Biology|volume=78|last1=Schramm|first1=Vern L|last2=Grubmeyer|first2=Charles | name-list-style = vanc |year=2004|isbn=9780125400787|pages=261–304|doi=10.1016/s0079-6603(04)78007-1|pmid=15210333}}</ref> |
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PRPP also plays an important role in pyrimidine ribonucleotide synthesis. During the fifth step of pyrimidine nucleotide synthesis, PRPP covalently links to ] at the one-position carbon on the ribose unit. The reaction is catalyzed by ] (PRPP transferase), yielding ] (OMP).<ref name="Pelley_2011" /> |
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=== Histidine biosynthesis === |
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Histidine is an essential amino acid that is not synthesized de novo in humans. Like nucleotides, biosynthesis of histidine is initiated by the conversion of R5P to PRPP. The step of histidine biosynthesis is the condensation of ATP and PRPP by ], the rate determining enzyme. Histidine biosynthesis is carefully regulated by feedback inhibition/<ref>{{cite journal | vauthors = Ingle RA | title = Histidine biosynthesis | journal = The Arabidopsis Book | volume = 9 | pages = e0141 | date = January 2011 | pmid = 22303266 | doi = 10.1199/tab.0141 | pmc = 3266711 }}</ref> |
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=== Other functions === |
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R5P can be converted to ], which binds and activates the ] ion channel. The reaction is catalyzed by ]<ref>{{cite journal | vauthors = Evans WR, San Pietro A | title = Phosphorolysis of adenosine diphosphoribose | journal = Archives of Biochemistry and Biophysics | volume = 113 | issue = 1 | pages = 236–44 | date = January 1966 | pmid = 4287446 | doi = 10.1016/0003-9861(66)90178-0 }}</ref> |
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== Disease relevance == |
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Diseases have been linked to R5P imbalances in cells. Cancers and tumors show upregulated production of R5P correlated to increased RNA and DNA synthesis.<ref name="Berg_2015" /> ], the rarest disease in the world,<ref>{{cite journal | vauthors = Wamelink MM, Grüning NM, Jansen EE, Bluemlein K, Lehrach H, Jakobs C, Ralser M | title = The difference between rare and exceptionally rare: molecular characterization of ribose 5-phosphate isomerase deficiency | journal = Journal of Molecular Medicine | volume = 88 | issue = 9 | pages = 931–9 | date = September 2010 | pmid = 20499043 | doi = 10.1007/s00109-010-0634-1 | hdl = 1871/34686 | url = https://research.vumc.nl/en/publications/5b80fa40-596c-4de8-acf2-5374a1d878a0 }}</ref><ref>{{cite journal | vauthors = Huck JH, Verhoeven NM, Struys EA, Salomons GS, Jakobs C, van der Knaap MS | title = Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy | journal = American Journal of Human Genetics | volume = 74 | issue = 4 | pages = 745–51 | date = April 2004 | pmid = 14988808 | pmc = 1181951 | doi = 10.1086/383204 }}</ref> is also linked to an imbalance of R5P. Although the molecular pathology of the disease is poorly understood, hypotheses included decreased RNA synthesis. |
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Another disease linked to R5P is ].<ref>{{cite book | title = Gout & Other Crystal Arthropathies | chapter = Purine Metabolism in the Pathogenesis of Hyperuricemia and Inborn Errors of Purine Metabolism Associated With Disease|last1=Jiménez|first1=Rosa Torres|last2=Puig|first2=Juan García | name-list-style = vanc |pages=36–50|doi=10.1016/b978-1-4377-2864-4.10003-x | date = 2012 | isbn = 978-1-4377-2864-4 }}</ref> Higher levels of G6P lead to a buildup of glycolytic intermediates, that are diverted to R5P production. R5P converts to PRPP, which forces an overproduction of purines, leading to ] build up.<ref name="Pelley_2011" /> |
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Accumulation of PRPP is found in ].<ref>{{cite book | title = Genetic Diseases of the Kidney | chapter = Primary Metabolic and Renal Hyperuricemia | last1 = Ichida | first1 = Kimiyoshi | last2 = Hosoyamada | first2 = Makoto | last3 = Hosoya | first3 = Tatsuo | last4 = Endou | first4 = Hitoshi | name-list-style = vanc |pages=651–660 | date = 2009 |doi=10.1016/b978-0-12-449851-8.00038-3 | isbn = 978-0-12-449851-8 }}</ref> The build up is caused by a deficiency of the ] ] (HGPRT), which leads to decreased nucleotide synthesis and an increase of uric acid production. |
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Superactivity in ], the enzyme that catalyzes the R5P to PRPP, has also been linked to gout, as well as neurodevelopmental impairment and sensorineural deafness.<ref>{{cite book | title = Movement Disorders in Childhood | chapter = Inherited Metabolic Disorders Associated with Extrapyramidal Symptoms|last1=Singer|first1=Harvey S.|last2=Mink|first2=Jonathan W.|last3=Gilbert|first3=Donald L.|last4=Jankovic|first4=Joseph | name-list-style = vanc |pages=164–204|doi=10.1016/B978-0-7506-9852-8.00015-1 | date = 2010 | isbn = 978-0-7506-9852-8 }}</ref> |
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== References == |
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{{reflist|32em}} |
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{{Pentose phosphate pathway intermediates}} |
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{{Nucleotide metabolism intermediates}} |
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