chembox verifiedrevid 450937939 Name small D small Ribulose ImageFileL1 D Ribulose.svg ImageSizeL1 88px ImageFileR1 Ribulose.svg ImageSizeR1 150px IUPACName 3R,4R 1,3,4,5 Tetrahydroxypentan 2 one OtherNames small D small erythro 2 Pentulose br Adonose br Arabinulose br Araboketose br Ribosone Section1 Chembox Identifiers CASNo 488 84 6 CASOther D br 2042027 5 L br 5556 48 9 DL PubChem 151261 SMILES D C C H C H C O CO O O O br L OCC C H O C H O CO O Section2 Chembox Properties C 5 H 10 O 5 Appearance Density MeltingPt BoilingPt Solubility Section3 Chembox Hazards MainHazards FlashPt Autoignition Ribulose is a ketopentose &mdash a monosaccharide containing five carbon atom s, and including a ketone functional group . It has chemical formula carbon sub 5 sub hydrogen sub 10 sub oxygen sub 5 sub . Two enantiomers are possible, small D small ribulose small D small erythro pentulose and small L small ribulose small L small erythro pentulose . small D small Ribulose is the diastereomer of small D small xylulose . Ribulose sugars are composed in the pentose phosphate pathway . They are important in the formation of many bioactive substances. For example, small D small ribulose is an intermediate in the fungal pathway for small D small arabitol production. Also, as the 1,5 bisphosphate, small D small ribulose combines with carbon dioxide at the start of the photosynthesis process in green plants carbon dioxide trap . A synthetic form of ribulose known as sucroribulose is found in many brands of artificial sweeteners. See also Arabinose Deoxyribose Lyxose Ribose Xylose Xylulose Carbohydrates Category Ketopentoses bg ca Ribulosa de Ribulose es Ribulosa fa fr Ribulose gl Ribulosa it Ribulosio hu Ribul z ja pl Rybuloza pt Ribulose ru sr sh Ribuloza tr Ribuloz zh ... more details
chembox Verifiedfields changed verifiedrevid 464382238 ImageFile Ribulose 5 phosphate.svg ImageSize IUPACName OtherNames Section1 Chembox Identifiers InChI 1 C5H11O8P c6 1 3 7 5 9 4 8 2 13 14 10,11 12 h4 6,8 9H,1 2H2, H2,10,11,12 p 2 t4 ,5 m1 s1 InChIKey FNZLKVNUWIIPSJ DAZPBWGKBO StdInChI Ref stdinchicite correct chemspider StdInChI 1S C5H11O8P c6 1 3 7 5 9 4 8 2 13 14 10,11 12 h4 6,8 9H,1 2H2, H2,10,11,12 p 2 t4 ,5 m1 s1 StdInChIKey Ref stdinchicite correct chemspider StdInChIKey FNZLKVNUWIIPSJ UHNVWZDZSA L CASNo Ref cascite changed ?? CASNo 4151 19 3 PubChem 439184 ChemSpiderID Ref chemspidercite correct chemspider ChemSpiderID 20015724 ChEBI Ref ebicite correct EBI ChEBI 58121 SMILES O P O O OC C H O C H O C O CO MeSHName ribulose 5 phosphate Section2 Chembox Properties Formula C sub 5 sub H sub 11 sub O sub 8 sub P MolarMass 230.11 g mol Appearance Density MeltingPt BoilingPt Section3 Chembox Hazards Solubility MainHazards FlashPt Autoignition Ribulose 5 phosphate is one of the end products of the pentose phosphate pathway . It is also an intermediate in the Calvin cycle . It is formed by phosphogluconate dehydrogenase , and it can be acted upon by phosphopentose isomerase and phosphopentose epimerase . See also RibuloseRibulose 1,5 bisphosphate Pentose phosphate pathway intermediates Category Organophosphates Category Monosaccharide derivatives biochem stub ca Ribulosa 5 fosfat de Ribulose 5 phosphat es Ribulosa 5 fosfato fr Ribulose 5 phosphate gl Ribulosa 5 fosfato ja 5 pl Rybulozo 5 fosforan fi Ribuloosi 5 fosfaatti zh 5 ... more details
enzyme Name ribulose phosphate 3 epimerase EC number 5.1.3.1 CAS number 9024 20 8 IUBMB EC number 5 1 3 1 GO code 0004750 image width caption Pfam box Symbol Ribul P 3 epim Name Ribulose phosphate 3 epimerase family image width caption Pfam PF00834 InterPro IPR000056 SMART Prosite PDOC00833 SCOP 1rpx TCDB OPM family OPM protein PDB PDB3 1tqj B 6 208 PDB3 1rpx A 58 260 PDB3 1h1z A 8 208 PDB3 1h1y B 8 208 PDB3 1tqx A 7 208 In enzymology , a ribulose phosphate 3 epimerase EC number 5.1.3.1 also known as pentose 5 phosphate 3 epimerase or PPE is the enzyme that converts D ribulose 5 phosphate into D xylulose 5 phosphate in Calvin cycle Calvin s reductive pentose phosphate cycle . D ribulose 5 phosphate math rightleftharpoons math D xylulose 5 phosphate Hence, this enzyme has one substrate biochemistry substrate , D ribulose 5 phosphate , and one product chemistry product , D xylulose 5 phosphate . This enzyme belongs to the family of isomerase s, specifically those racemase s and epimerase s acting on carbohydrate s and derivatives. In Alcaligenes eutrophus two copies of the gene coding for PPE are known ref name PUB00002204 cite journal author Bowien B, Kusian B, Yoo JG, Bednarski R title The Calvin cycle enzyme pentose 5 phosphate 3 epimeras e is encoded within the cfx operons of the chemoautotroph Alcaligenes eutrophus journal J. Bacteriol. volume 174 issue 22 pages 7337 7344 year 1992 pmid 1429456 pmc 207429 ref , one is chromosomally encoded Uniprot P40117 , the other one is on a plasmid Uniprot Q04539 . PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure. The systematic name of this enzyme class is D ribulose 5 phosphate 3 epimerase . Other names ... 3 epimerase , xylulose phosphate 3 epimerase , phosphoketopentose epimerase , ribulose 5 phosphate 3 epimerase , D ribulose phosphate 3 epimerase , D ribulose 5 phosphate epimerase , D ribulose ... more details
enzyme Name ribulose bisphosphate carboxylase lysine N methyltransferase EC number 2.1.1.127 CAS number 139171 98 5 IUBMB EC number 2 1 1 127 GO code 0030785 image width caption In enzymology , a ribulose bisphosphate carboxylase lysine N methyltransferase EC number 2.1.1.127 is an enzyme that catalysis catalyzes the chemical reaction S adenosyl L methionine ribulose 1,5 bisphosphate carboxylase lysine math rightleftharpoons math S adenosyl L homocysteine ribulose 1,5 bisphosphate carboxylase N sub 6 sub methyl L lysine Thus, the two substrate biochemistry substrates of this enzyme are S Adenosyl methionine S adenosyl methionine and ribulose 1,5 bisphosphate carboxylase lysine , whereas its two product chemistry products are S adenosylhomocysteine and ribulose 1,5 bisphosphate carboxylase N6 methyl L lysine . This enzyme belongs to the family of transferase s, specifically those transferring one carbon group methyltransferases. The systematic name of this enzyme class is S adenosyl L methionine 3 phospho D glycerate carboxy lyase dimerizing lysine N6 methyltransferase . Other names in common use include rubisco methyltransferase , ribulose bisphosphate carboxylase oxygenase N methyltransferase , ribulose 1,5 bisphosphate carboxylase oxygenase large subunit , epsilonN methyltransferase , S adenosyl L methionine 3 phospho D glycerate carboxy lyase , and dimerizing lysine 6 N methyltransferase . Structural studies As of late 2007, 7 tertiary structure structures have been solved for this class of enzymes, with Protein Data Bank PDB accession codes PDB link 1MLV , PDB link 1OZV , PDB link 1P0Y , PDB link 2H21 , PDB link 2H23 , PDB link 2H2E , and PDB link 2H2J . References reflist 1 cite journal author Wang P, Royer M, Houtz RL date 1995 title Affinity purification of ribulose ... author Ying Z, Janney N, Houtz RL date 1996 title Organization and characterization of the ribulose ... Ribulose Bisphosphate Carboxylase Lysine N Methyltransferase Category EC 2.1.1 Category Enzymes ... more details
Merge Ribulose phosphate 3 epimerase date November 2010 Phosphopentose epimerase is an enzyme which intraconverts ribulose 5 phosphate and xylulose 5 phosphate . It plays a role in the Calvin cycle and the pentose phosphate pathway . External links http www.ncbi.nlm.nih.gov books bv.fcgi?rid stryer.figgrp.2802 Diagram at nlm.nih.gov http cmgm.stanford.edu biochem200 OVERHEADS PPP.html Diagram at stanford.edu Pentose phosphate pathway Category Enzymes biochem stub ... more details
enzyme Name D ribulokinase EC number 2.7.1.47 CAS number 9026 40 8 IUBMB EC number 2 7 1 47 GO code 0019150 image width caption In enzymology , a D ribulokinase EC number 2.7.1.47 is an enzyme that catalysis catalyzes the chemical reaction ATP D ribulose math rightleftharpoons math ADP D ribulose 5 phosphate Thus, the two substrate biochemistry substrates of this enzyme are adenosine triphosphate ATP and D ribulose , whereas its two product chemistry products are adenosine diphosphate ADP and D ribulose 5 phosphate . This enzyme belongs to the family of transferase s, specifically those transferring phosphorus containing groups phosphotransferase s with an alcohol group as acceptor. The systematic name of this enzyme class is ATP D ribulose 5 phosphotransferase . This enzyme is also called D ribulokinase phosphorylating . This enzyme participates in pentose and glucuronate interconversions . References reflist 1 cite journal author FROMM HJ date 1959 title D Ribulokinase from Aerobacter aerogenes journal J. Biol. Chem. volume 234 pages 3097&ndash 101 pmid 13825363 enzyme stub Category EC 2.7.1 Category Enzymes of unknown structure ... more details
enzyme Name ribulokinase EC number 2.7.1.16 CAS number 9030 57 3 IUBMB EC number 2 7 1 16 GO code 0008741 image width caption In enzymology , a ribulokinase EC number 2.7.1.16 is an enzyme that catalysis catalyzes the chemical reaction ATP L or D ribulose math rightleftharpoons math ADP L or D ribulose 5 phosphate The 3 substrate biochemistry substrates of this enzyme are adenosine triphosphate ATP , L ribulose , and D ribulose , whereas its 3 product chemistry products are adenosine diphosphate ADP , L ribulose 5 phosphate , and D ribulose 5 phosphate . This enzyme belongs to the family of transferase s, specifically those transferring phosphorus containing groups phosphotransferase s with an alcohol group as acceptor. The systematic name of this enzyme class is ATP L or D ribulose 5 phosphotransferase . Other names in common use include ribulokinase phosphorylating , and L ribulokinase . This enzyme participates in pentose and glucuronate interconversions . References reflist 1 cite journal author BURMA DP, HORECKER BL date 1958 title Pentose fermentation by Lactobacillus plantarum. III. Ribulokinase journal J. Biol. Chem. volume 231 pages 1039&ndash 51 pmid 13539035 issue 2 cite journal author Lee N, Bendet I date 1967 title Crystalline L ribulokinase from Escherichia coli journal J. Biol. Chem. volume 242 pages 2043&ndash 50 pmid 5336963 issue 9 cite journal author Simpson FJ, Wolin MJ and Wood WA date 1958 title Degradation of L arabinose by Aerobacter aerogenes. I. A pathway involving phosphorylated intermediates journal J. Biol. Chem. volume 230 pages 457&ndash 472 pmid 13502414 issue 1 enzyme stub Category EC 2.7.1 Category Enzymes of unknown structure ... more details
DISPLAYTITLE C sub 5 sub H sub 11 sub O sub 8 sub P The molecular formula C sub 5 sub H sub 11 sub O sub 8 sub P may refer to Ribulose 5 phosphate Ribose 5 phosphate MolFormDisambig fr C5H11O8P sr C5H11O8P ... more details
enzyme Name L arabinitol 2 dehydrogenase EC number 1.1.1.13 CAS number 9028 20 0 IUBMB EC number 1 1 1 13 GO code 0047002 image width caption In enzymology , a L arabinitol 2 dehydrogenase EC number 1.1.1.13 is an enzyme that catalysis catalyzes the chemical reaction L arabinitol NAD sup sup math rightleftharpoons math L ribulose NADH H sup sup Thus, the two substrate biochemistry substrates of this enzyme are L arabinitol and nicotinamide adenine dinucleotide NAD sup sup , whereas its 3 product chemistry products are L ribulose , nicotinamide adenine dinucleotide NADH , and hydrogen ion H sup sup . This enzyme belongs to the family of oxidoreductase s, specifically those acting on the CH OH group of donor with NAD or NADP as acceptor. The systematic name of this enzyme class is L arabinitol NAD 2 oxidoreductase L ribulose forming . Other names in common use include L arabinitol dehydrogenase ribulose forming , and L arabinitol ribulose forming dehydrogenase . This enzyme participates in pentose and glucuronate interconversions . References reflist 1 cite journal author CHIANG C, KNIGHT SG date 1961 title L Arabinose metabolism by cell free extracts of Penicillium chrysogenum journal Biochim. Biophys. Acta. volume 46 pages 271&ndash 8 pmid 13692999 doi 10.1016 0006 3002 61 90750 8 issue 2 1.1.1 enzyme stub Category EC 1.1.1 Category NADH dependent enzymes Category Enzymes of unknown structure it L arabinitolo 2 deidrogenasi ja L 2 ... more details
enzyme Name phosphoribulokinase EC number 2.7.1.19 CAS number 9030 60 8 IUBMB EC number 2 7 1 19 GO code 0008974 image width caption In enzymology , a phosphoribulokinase EC number 2.7.1.19 is an enzyme that catalysis catalyzes the chemical reaction ATP D ribulose 5 phosphate math rightleftharpoons math ADP D ribulose 1,5 bisphosphate Thus, the two substrate biochemistry substrates of this enzyme are adenosine triphosphate ATP and D ribulose 5 phosphate , whereas its two product chemistry products are adenosine diphosphate ADP and D ribulose 1,5 bisphosphate . This enzyme belongs to the family of transferase s, specifically those transferring phosphorus containing groups phosphotransferase s with an alcohol group as acceptor. The systematic name of this enzyme class is ATP D ribulose 5 phosphate 1 phosphotransferase . Other names in common use include phosphopentokinase , ribulose 5 phosphate kinase , phosphopentokinase , phosphoribulokinase phosphorylating , 5 phosphoribulose kinase , ribulose phosphate kinase , PKK , PRuK , and PRK . This enzyme participates in carbon fixation . Structural studies As of late 2007, only one tertiary structure structure has been solved for this class of enzymes, with the Protein Data Bank PDB accession code PDB link 1A7J . References reflist 1 cite journal author HURWITZ J, WEISSBACH A, HORECKER BL, SMYRNIOTIS PZ date 1956 title Spinach phosphoribulokinase journal J. Biol. Chem. volume 218 pages 769&ndash 83 pmid 13295229 issue 2 cite journal author JAKOBY WB, BRUMMOND DO, OCHOA S date 1956 title Formation of 3 phosphoglyceric acid by carbon dioxide fixation with spinach leaf enzymes journal J. Biol. Chem. volume 218 pages 811&ndash 22 pmid 13295232 issue 2 enzyme stub Category EC 2.7.1 Category Enzymes of known structure ... more details
DISPLAYTITLE C sub 5 sub H sub 10 sub O sub 5 sub The molecular formula C sub 5 sub H sub 10 sub O sub 5 sub molar mass 150.13 g mol, exact mass 150.052823 may refer to Apiose Aldopentose s Arabinose Lyxose Ribose Xylose Ketopentose s Ribulose Xylulose MolFormDisambig fr C5H10O5 it C5H10O5 sr C5H10O5 ... more details
enzyme Name D arabinitol 2 dehydrogenase EC number 1.1.1.250 CAS number 336883 93 3 IUBMB EC number 1 1 1 250 GO code 0047038 image width caption In enzymology , a D arabinitol 2 dehydrogenase EC number 1.1.1.250 is an enzyme that catalysis catalyzes the chemical reaction D arabinitol NAD sup sup math rightleftharpoons math D ribulose NADH H sup sup Thus, the two substrate biochemistry substrates of this enzyme are D arabinitol and nicotinamide adenine dinucleotide NAD sup sup , whereas its 3 product chemistry products are D ribulose , nicotinamide adenine dinucleotide NADH , and hydrogen ion H sup sup . This enzyme belongs to the family of oxidoreductase s, specifically those acting on the CH OH group of donor with NAD or NADP as acceptor. The systematic name of this enzyme class is D arabinitol NAD 2 oxidoreductase D ribulose forming . This enzyme is also called D arabinitol 2 dehydrogenase ribulose forming . References reflist 1 cite journal author Wong B, Murray JS, Castellanos M, Croen KD date 1993 title D arabitol metabolism in Candida albicans studies of the biosynthetic pathway and the gene that encodes NAD dependent D arabitol dehydrogenase journal J. Bacteriol. volume 175 pages 6314&ndash 20 pmid 8407803 issue 19 pmc 206728 cite journal author Quong MW, Miyada CG, Switchenko AC, Goodman TC date 1993 title Identification, purification, and characterization of a D arabinitol specific dehydrogenase from Candida tropicalis journal Biochem. Biophys. Res. Commun. volume 196 pages 1323&ndash 9 pmid 8250887 doi 10.1006 bbrc.1993.2397 issue 3 1.1.1 enzyme stub Category EC 1.1.1 Category NADH dependent enzymes Category Enzymes of unknown structure it D arabinitolo 2 deidrogenasi ja D 2 ... more details
enzyme Name arabinose 5 phosphate isomerase EC number 5.3.1.13 CAS number 9023 86 3 IUBMB EC number 5 3 1 13 GO code 0019146 image width caption In enzymology , an arabinose 5 phosphate isomerase EC number 5.3.1.13 is an enzyme that catalysis catalyzes the chemical reaction D arabinose 5 phosphate math rightleftharpoons math D ribulose 5 phosphate Hence, this enzyme has one substrate biochemistry substrate , D arabinose 5 phosphate , and one product chemistry product , D ribulose 5 phosphate . This enzyme belongs to the family of isomerase s, specifically those intramolecular oxidoreductases interconverting aldoses and ketoses. The systematic name of this enzyme class is D arabinose 5 phosphate aldose ketose isomerase . Other names in common use include arabinose phosphate isomerase , phosphoarabinoisomerase , and D arabinose 5 phosphate ketol isomerase . References reflist 1 cite journal author Volk WA date 1960 title Purification and properties of phosphoarabinoisomerase from Propionibacterium pentosaceum journal J. Biol. Chem. volume 235 pages 1550&ndash 1553 isomerase stub Category EC 5.3.1 Category Enzymes of unknown structure ... more details
enzyme Name L ribulose phosphate 4 epimerase EC number 5.1.3.4 CAS number 9024 19 5 IUBMB EC number 5 1 3 4 GO code 0008742 image Ribulose Epimerase Pymol.jpg width caption In enzymology , a L ribulose ... of Ribulose 5 phosphate and Xylulose 5 phosphate in the oxidative phase of the Pentose phosphate pathway ... Sensitive, L Ribulose 5 phosphate 4 Epimerase Deficient Mutants of Escherichia coli journal Journal ... 84 1 137 accessdate 17 May 2011 ref L ribulose 5 phosphate math rightleftharpoons math D xylulose ... Yu first Luo coauthors Jomy Samuel, Steven Mosimann, Jeffrey Lee title The Structure of Ribulose ... 10.1021 bi0112513 pmid 11732895 ref The systematic name of this enzyme class is L ribulose 5 phosphate 4 epimerase . Other names in common use include phosphoribulose isomerase , ribulose phosphate 4 epimerase , L ribulose phosphate 4 epimerase , L ribulose 5 phosphate 4 epimerase , AraD , and L Ru5P ... metabolism . Enzyme Mechanism gallery File Epimerase Mechanism.jpg Mechanism of Ribulose 5 Phosphate 4 Epimerase in active site File Aldol.jpg Aldol and dehydration mechanims gallery Ribulose 5 phosphate 4 epimerase catalyzes the epimerization of Ribulose 5 phosphate to Xylulose 5 phosphate by aldol ... WW title 13C and deuterium isotope effects suggest an aldol cleavage mechanism for L ribulose ... similarity with Ribulose 5 Phosphate 4 Epimerase. Second, the analysis of carbon 13 sup 13 sup ... gallery File Ribulose Epimerase Pymol.jpg Homo tetrameric structure of L Ru5P File Epimerase monomer.jpg L Ru5P monomer File Ribulose 5 Phosphate 4 Epimerase Active site.gif L Ru5p active site ... of recombinant ribulose 5 phosphate 4 epimerase from Escherichia coli journal Protein Science .... Biological Function Ribulose 5 phosphate 4 epimerase is found on the well studied L arabinose operon . This operon consists of eight genes araA araH with the gene for Ribulose 5 phosphate 4 epimerase ... AraF Uptake AraG Uptake AraH Uptake Evolution L Ribulose 5 phosphate 4 epimerase and L fuculose 1 phosphate ... more details
enzyme Name arabinose isomerase EC number 5.3.1.3 CAS number 9023 81 8 IUBMB EC number 5 3 1 3 GO code 0008790 image width caption In enzymology , an arabinose isomerase EC number 5.3.1.3 is an enzyme that catalysis catalyzes the chemical reaction D arabinose math rightleftharpoons math D ribulose Hence, this enzyme has one substrate biochemistry substrate , D arabinose , and one product chemistry product , D ribulose . This enzyme belongs to the family of isomerase s, specifically those intramolecular oxidoreductases interconverting aldoses and ketoses. The systematic name of this enzyme class is D arabinose aldose ketose isomerase . Other names in common use include D arabinose L fucose isomerase , D arabinose isomerase , L fucose isomerase , and D arabinose ketol isomerase . Structural studies As of late 2007, only one tertiary structure structure has been solved for this class of enzymes, with the Protein Data Bank PDB accession code PDB link 1FUI . References reflist 1 cite journal author Cohen SS date 1953 title Studies on D ribulose and its enzymatic conversion to D arabinose journal J. Biol. Chem. volume 201 issue 1 pages 71&ndash 84 pmid 13044776 cite journal author Green M and Cohen SS date 1956 title Enzymatic conversion of L fucose to L fuculose journal J. Biol. Chem. volume 219 issue 2 pages 557&ndash 568 pmid 13319278 isomerase stub Category EC 5.3.1 Category Enzymes of known structure ... more details
enzyme Name methylthioribulose 1 phosphate dehydratase EC number 4.2.1.109 CAS number IUBMB EC number 4 2 1 109 GO code 0043809 image width caption Orphan date February 2009 In enzymology , a methylthioribulose 1 phosphate dehydratase EC number 4.2.1.109 is an enzyme that catalysis catalyzes the chemical reaction S methyl 5 thio D ribulose 1 phosphate math rightleftharpoons math 5 methylthio 2,3 dioxopentyl phosphate H sub 2 sub O Hence, this enzyme has one substrate biochemistry substrate , S methyl 5 thio D ribulose 1 phosphate , and two product chemistry products , 5 methylthio 2,3 dioxopentyl phosphate and water H sub 2 sub O . This enzyme belongs to the family of lyase s, specifically the hydro lyases, which cleave carbon oxygen bonds. The systematic name of this enzyme class is S methyl 5 thio D ribulose 1 phosphate 4 hydro lyase 5 methylthio 2,3 dioxopentyl phosphate forming . Other names in common use include 1 PMT ribulose dehydratase , and S methyl 5 thio D ribulose 1 phosphate hydro lyase . This enzyme participates in methionine metabolism . References reflist 1 cite journal author Furfine ES, Abeles RH year 1988 title Intermediates in the conversion of 5 S methylthioadenosine to methionine in Klebsiella pneumoniae journal J. Biol. Chem. volume 263 pages 9598&ndash 606 pmid 2838472 issue 20 cite journal author Wray JW, Abeles RH year 1995 title The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases journal J. Biol. Chem. volume 270 pages 3147&ndash 53 pmid 7852397 issue 7 doi 10.1074 jbc.270.7.3147 Category EC 4.2.1 Category Enzymes of unknown structure 4.2 enzyme stub ... more details
Unreferenced stub type bacteria auto yes date December 2009 Taxobox image Methylococcus capsulatus.png image caption Methylococcus capsulatus regnum Bacteria phylum Proteobacteria classis Gamma Proteobacteria ordo Methylococcales familia Methylococcaceae subdivision ranks Genera subdivision Methylomonas br Methylobacter br Methylococcus br Methylomicrobium br Methylosphaera br Methylocaldum The Methylococcaceae are a family of bacterium bacteria that obtain their carbon and energy from methane , called methanotroph s. They comprise the type I methanotrophs, in contrast to the Methylocystaceae or type II methanotrophs. They belong among the gamma subdivision of the Proteobacteria , and are typically given their own Order biology order . The Methylococcaceae have internal membranes in the form of flattened discs, perpendicular to the cell wall . Methane is oxidized to give formaldehyde , which is fixed by a process called the RuMP cycle. Here formaldehyde is combined with sugar ribulose , producing hexulose . This, in turn, is broken down to produce glyceraldehyde , which is used to produce new ribulose and other organic compounds. Catabolism does not involve a complete citric acid cycle . Category Proteobacteria Proteobacteria stub ca Metilococc cia de Methylococcaceae mk pt Methylococcaceae ... more details
enzyme Name L ribulose 5 phosphate 3 epimerase EC number 5.1.3.22 CAS number IUBMB EC number 5 1 3 22 GO code image width caption In enzymology , a L ribulose 5 phosphate 3 epimerase EC number 5.1.3.22 is an enzyme that catalysis catalyzes the chemical reaction L ribulose 5 phosphate math rightleftharpoons math L xylulose 5 phosphate Hence, this enzyme has one substrate biochemistry substrate , L ribulose 5 phosphate , and one product chemistry product , L xylulose 5 phosphate . This enzyme belongs to the family of isomerase s, specifically those racemase s and epimerase s acting on carbohydrate s and derivatives. The systematic name of this enzyme class is L ribulose 5 phosphate 3 epimerase . Other names in common use include L xylulose 5 phosphate 3 epimerase , UlaE , and SgaU . This enzyme participates in ascorbate and aldarate metabolism . References reflist 1 cite journal author Yew WS, Gerlt JA date 2002 title Utilization of L ascorbate by Escherichia coli K 12 assignments of functions to products of the yjf sga and yia sgb operons journal J. Bacteriol. volume 184 pages 302&ndash 6 pmid 11741871 doi 10.1128 JB.184.1.302 306.2002 issue 1 pmc 134747 isomerase stub Category EC 5.1.3 Category Enzymes of unknown structure ... more details
enzyme Name ribose isomerase EC number 5.3.1.20 CAS number 57534 76 6 IUBMB EC number 5 3 1 20 GO code 0050261 image width caption In enzymology , a ribose isomerase EC number 5.3.1.20 is an enzyme that catalysis catalyzes the chemical reaction D ribose math rightleftharpoons math D ribulose Hence, this enzyme has one substrate biochemistry substrate , D ribose , and one product chemistry product , D ribulose . This enzyme belongs to the family of isomerase s, specifically those intramolecular oxidoreductase s interconverting aldose s and ketose s. The systematic name of this enzyme class is D ribose aldose ketose isomerase . Other names in common use include D ribose isomerase , and D ribose ketol isomerase . References reflist 1 cite journal author Izumori K, Rees AW, Elbein AD date 1975 title Purification, crystallization, and properties of D ribose isomerase from Mycobacterium smegmatis journal J. Biol. Chem. volume 250 pages 8085&ndash 7 pmid 240851 issue 20 isomerase stub Category EC 5.3.1 Category Enzymes of unknown structure ... more details
The small L small arabinose operon , also called ara operon , has genes encoding enzymes needed for the catabolism of arabinose to xylulose 5 phosphate , an intermediate of the pentose phosphate pathway . It has both positive regulation positive and negative regulation . The operon is found in Escherichia coli . It has been a focus for research in molecular biology for over since 1970, and has been investigated extensively at the Genetics genetic , biochemical , physiological , and biophysical levels. Structure The structural gene is araBAD . The regulator gene is araC . The genes, araBAD and araC , are transcribed in opposite directions. ref cite doi 10.1111 j.1574 6976.2010.00226.x ref The operators are araI and araO sub 2 sub . The operators lie between the AraC . AraI lies between the structural genes and the operator. The araI sub 1 sub and araI sub 2 sub are DNA binding sites that, when occupied by AraC, induce expression. Function Repression The ara operon is regulated by the AraC protein . If arabinose is absent, the dimer AraC protein represses the structural gene by binding to araI sub 1 sub and araO sub 2 sub and the DNA forms a loop. The loop prevents RNA polymerase from binding to the Promoter genetics promoter of the ara operon, thereby blocking Transcription genetics transcription . Activation When arabinose is present, arabinose binds AraC and prevents AraC from interacting. This breaks the DNA loop. The two AraC arabinose complexes bind to the araI site which promotes transcription. When arabinose is present, AraC acts as an activator. class wikitable Metabolism of arabinose in E. coli Substrate Protein s Function Reversible Product small L small arabinose AraA isomerase yes small L small ribulose small L small ribulose AraB ribulokinase no small L small ribulose phosphate small L small ribulose phosphate AraD epimerase yes small D small xylulose phosphate If arabinose is present, it builds a complex AraC arabinose br This complex is needed for RNA ... more details
the conversion of glucose 6 phosphate into ribulose 5 phosphate . Image Ox Pentose phosphate pathway.svg ... lactone 2 , 6 phosphogluconate 3 , ribulose 5 phosphate 4 . The entire set of reactions ... NADP sup sup ribulose 5 phosphate NADPH CO sub 2 sub 6 phosphogluconate dehydrogenase Oxidative ... sub 2 sub , and ribulose 5 phosphate . The overall reaction for this process is Glucose 6 phosphate 2 NADP sup sup H sub 2 sub O &rarr ribulose 5 phosphate 2 NADPH 2 H sup sup CO sub 2 sub Non oxidative ... structure of ribose5P class wikitable Reactants Products Enzymes ribulose 5 phosphate ribose 5 phosphate Ribulose 5 Phosphate Isomerase ribulose 5 phosphate xylulose 5 phosphate Ribulose 5 Phosphate ... fructose 6 phosphate transketolase Net reaction 3 ribulose 5 phosphate 1 ribose 5 phosphate 2 ... more details
Methylotrophs are a diverse group of microorganism s that can use redox reduced one carbon compounds, such as methanol or methane , as the carbon source for their growth and multi carbon compounds that contain no carbon bonds, such as dimethyl ether and dimethylamine . This group of microorganisms also includes those capable of assimilating reduced one carbon compounds by way of carbon dioxide using the ribulose bisphosphate pathway. ref Anthony, C. The Biochemistry of Methylotrophs . Academic press, 1982, p. 2 3 ref These organisms should not be confused with Methanogen methanogens which on the contrary produce methane as a by product from various one carbon compounds such as carbon dioxide. Some methylotrophs can degrade the greenhouse gas methane , and in this case they are called methanotroph s. The methanotroph Methylococcus capsulatus is used to degrade methane and other pollutants. The abundance, purity, and low price of methanol compared to commonly used sugars make methylotrophs competent organisms for production of amino acid s, vitamins, recombinant proteins, single cell proteins , co enzyme s and cytochrome s. General Microbiology Methylotrophic organisms are able to grow at the expense of on or more of the compounds typically used by methophiles, but cannot use methane. Methylotrophs are a diverse group, including both Gram negative and Gram positive genera. None of them make resting structures like exospores and cyst and none of them have the complex intracellular membrane systems that characterize methanotrophs growing on methane There are two sub groups 1 obligate methylotrophs. 2 facultative methylotrophs. Obligate methylotrophs A single obligate methylotroph methylophilus is known. It is Gram negative, polarly flagelated rod capable of rapid growthy with methanol. Some strains can also utilize formaldehyde or methylamines. Carbon is assimilated via the ribulose mono phosphate pathway. Facultative methylotrophs It is relatively widely distributed tr ... more details
enzyme Name ribitol 2 dehydrogenase EC number 1.1.1.56 CAS number 9014 23 7 IUBMB EC number 1 1 1 56 GO code 0050255 image width caption In enzymology , a ribitol 2 dehydrogenase EC number 1.1.1.56 is an enzyme that catalysis catalyzes the chemical reaction ribitol NAD sup sup math rightleftharpoons math D ribulose NADH H sup sup Thus, the two substrate biochemistry substrates of this enzyme are ribitol and nicotinamide adenine dinucleotide NAD sup sup , whereas its 3 product chemistry products are D ribulose , nicotinamide adenine dinucleotide NADH , and hydrogen ion H sup sup . This enzyme belongs to the family of oxidoreductase s, specifically those acting on the CH OH group of donor with NAD or NADP as acceptor. The systematic name of this enzyme class is ribitol NAD 2 oxidoreductase . Other names in common use include adonitol dehydrogenase , ribitol dehydrogenase A wild type , ribitol dehydrogenase B mutant enzyme with different properties , and ribitol dehydrogenase D mutant enzyme with different properties . This enzyme participates in pentose and glucuronate interconversions . References reflist 1 cite journal author HOLLMANN S, TOUSTER O date 1957 title The L xylulose xylitol enzyme and other polyol dehydrogenases of guinea pig liver mitochondria journal J. Biol. Chem. volume 225 pages 87&ndash 102 pmid 13416220 issue 1 cite journal author Nordlie RC and Fromm HJ date 1959 title Ribitol dehydrogenase. II. Studies on the reaction mechanism journal J. Biol. Chem. volume 234 pages 2523&ndash 2531 pmid 14427582 cite journal author Wood WA, McDonough MJ and Jacobs LB date 1961 title Ribitol and D arabitol utilization by Aerobacter aerogenes journal J. Biol. Chem. volume 236 pages 2190&ndash 2195 1.1.1 enzyme stub Category EC 1.1.1 Category NADH dependent enzymes Category Enzymes of unknown structure it Ribitolo 2 deidrogenasi ja 2 ... more details
enzyme Name ribitol 5 phosphate 2 dehydrogenase EC number 1.1.1.137 CAS number 37250 67 2 IUBMB EC number 1 1 1 137 GO code 0050256 image width caption In enzymology , a ribitol 5 phosphate 2 dehydrogenase EC number 1.1.1.137 is an enzyme that catalysis catalyzes the chemical reaction D ribitol 5 phosphate NAD P math rightleftharpoons math D ribulose 5 phosphate NAD P H H sup sup The 3 substrate biochemistry substrates of this enzyme are D ribitol 5 phosphate , nicotinamide adenine dinucleotide NAD sup sup , and nicotinamide adenine dinucleotide phosphate NADP sup sup , whereas its 4 product chemistry products are D ribulose 5 phosphate , nicotinamide adenine dinucleotide NADH , nicotinamide adenine dinucleotide phosphate NADPH , and hydrogen ion H sup sup . This enzyme belongs to the family of oxidoreductase s, specifically those acting on the CH OH group of donor with NAD or NADP as acceptor. The systematic name of this enzyme class is D ribitol 5 phosphate NAD P 2 oxidoreductase . This enzyme is also called dehydrogenase, ribitol 5 phosphate . This enzyme participates in pentose and glucuronate interconversions . References reflist 1 cite journal author GLASER L date 1963 title Ribitol 5 phosphate dehydrogenase from Lactobacillus plantarum journal Biochim. Biophys. Acta. volume 67 pages 525 30 pmid 13948358 doi 10.1016 0006 3002 63 91863 8 1.1.1 enzyme stub Category EC 1.1.1 Category NADPH dependent enzymes Category NADH dependent enzymes Category Enzymes of unknown structure it Ribitolo 5 fosfato 2 deidrogenasi ja 5 2 ... more details
Orphan date September 2011 Infobox protein family Symbol DHBP synthase Name DHBP synthase image PDB 1g58 EBI.jpg width caption crystal structure of 3,4 dihydroxy 2 butanone 4 phosphate synthase gold derivative Pfam PF00926 Pfam clan InterPro IPR000422 SMART PROSITE MEROPS SCOP 1iez TCDB OPM family OPM protein CAZy CDD In molecular biology, 3,4 dihydroxy 2 butanone 4 phosphate synthase DHBP synthase RibB EC number 4.1.99.12 is an enzyme which catalysis catalyses the conversion of ribulose 5 phosphate D ribulose 5 phosphate to formate and 3,4 dihydroxy 2 butanone 4 phosphate , the latter serving as the biosynthetic precursor for the xylene ring of riboflavin . ref name pmid9211332 cite journal author Richter G, Krieger C, Volk R, Kis K, Ritz H, Gotze E, Bacher A title Biosynthesis of riboflavin 3,4 dihydroxy 2 butanone 4 phosphate synthase journal Meth. Enzymol. volume 280 issue pages 374 82 year 1997 pmid 9211332 doi 10.1016 S0076 6879 97 80128 0 url ref In Photobacterium leiognathi , the riboflavin synthesis genes ribB DHBP synthase , ribE riboflavin synthase , ribH lumazone synthase and ribA GTP cyclohydrolase II all reside in the lux operon . ref name pmid11396941 cite journal author Lin JW, Chao YF, Weng SF title Riboflavin synthesis genes ribE, ribB, ribH, ribA reside in the lux operon of Photobacterium leiognathi journal Biochem. Biophys. Res. Commun. volume 284 issue 3 pages 587 95 year 2001 month June pmid 11396941 doi 10.1006 bbrc.2001.5013 url ref RibB is sometimes found as a bifunctional enzyme with GTP cyclohydrolase II that catalyses the first committed step in the biosynthesis of riboflavin. No sequence biology sequence s with significant homology to DHBP synthase are found in the metazoa . References reflist InterPro content IPR000422 Category Protein families ... more details
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