Genomes and Genes
Summary: Ribose substituted in the 1-, 3-, or 5-position by a phosphoric acid moiety.
- Claren J, Malisi C, Höcker B, Sterner R. Establishing wild-type levels of catalytic activity on natural and artificial (beta alpha)8-barrel protein scaffolds. Proc Natl Acad Sci U S A. 2009;106:3704-9 pubmed publisher..The results demonstrate that natural and inert artificial protein scaffolds can be converted into highly proficient enzymes in the laboratory, and provide insights into the mechanisms of enzyme evolution. ..
- Silva R, Pereira J, Canduri F, De Azevedo W, Basso L, Santos D. Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine. Arch Biochem Biophys. 2005;442:49-58 pubmed..Such knowledge may be helpful in designing new PNP inhibitors. ..
- Heine A, Luz J, Wong C, Wilson I. Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution. J Mol Biol. 2004;343:1019-34 pubmed
- Kochetov G, Sevostyanova I. Functional nonequivalence of transketolase active centers. IUBMB Life. 2010;62:797-802 pubmed publisher..In this article, we review experimental evidence of functional nonequivalence of the two active centers of TK, which are known to be identical by crystal X-ray structure analysis. ..
- Mao C, Cook W, Zhou M, Federov A, Almo S, Ealick S. Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues. Biochemistry. 1998;37:7135-46 pubmed..In contrast to human PNP, only one phosphate binding site was observed. Although binary complexes were observed for nucleoside, purine base, or phosphate, ribose 1-phosphate binding occurs only in the presence of purine base...
- Camici M, Tozzi M, Ipata P. Methods for the determination of intracellular levels of ribose phosphates. J Biochem Biophys Methods. 2006;68:145-54 pubmed..The comprehension of the role played by pentose phosphates may be greatly facilitated by the knowledge of their steady-state intracellular levels and of their changes in response to variations of intra- and extracellular signals. ..
- Valentini G, Stoppini M, Iadarola P, Malcovati M, Ferri G, Speranza M. Divergent binding sites in pyruvate kinases I and II from Escherichia coli. Biol Chem Hoppe Seyler. 1993;374:69-74 pubmed..Sequence comparison with E. coli type I, yeast and cat muscle pyruvate kinases shows that the binding regions of pyruvate kinase II are clearly divergent from those of pyruvate kinase I and of the eukaryotic enzymes. ..
- Yurshev V, Sevostyanova I, Solovjeva O, Zabrodskaya S, Kochetov G. Nonequivalence of transketolase active centers with respect to acceptor substrate binding. Biochem Biophys Res Commun. 2007;361:1044-7 pubmed..The phenomenon of nonequivalence becomes apparent when the substrate interacts with one of the two active centers. As a consequence of such interaction, the affinity of the second active center for ribose 5-phosphate decreases. ..
- Sengupta S, Sellers L, Matheson H, Fan T. Thymidine phosphorylase induces angiogenesis in vivo and in vitro: an evaluation of possible mechanisms. Br J Pharmacol. 2003;139:219-31 pubmed..Therefore, we postulate that 2-DDR could be mediating the angiogenic effects of TP possibly through an oxidative stress mechanism and additionally getting integrated in the endothelial metabolic machinery. ..
- d Muniz Pereira H, Oliva G, Garratt R. Purine nucleoside phosphorylase from Schistosoma mansoni in complex with ribose-1-phosphate. J Synchrotron Radiat. 2011;18:62-5 pubmed publisher..The ligand shows an intricate hydrogen-bonding network in the phosphate and ribose binding sites and adds a further chapter to our knowledge which could be of value in the future development of selective inhibitors. ..
- Soderberg T. Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes. Archaea. 2005;1:347-52 pubmed
- Warlick B, Evans B, Erb T, Ramagopal U, Sriram J, Imker H, et al. 1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum. Biochemistry. 2012;51:8324-6 pubmed publisher..et al. (2012) Nat. Chem. Biol., in press]. Dethiomethylation, a novel route to DXP, is catalyzed by MTXu 5-P methylsulfurylase. An active site Cys displaces the enolate of DXP from MTXu 5-P, generating a methyl disulfide intermediate. ..
- Le Bras G, Garel J. Pyruvate kinase from Lactobacillus bulgaricus: possible regulation by competition between strong and weak effectors. Biochimie. 1993;75:797-802 pubmed
- Giorgelli F, Bottai C, Mascia L, Scolozzi C, Camici M, Ipata P. Recycling of alpha-D-ribose 1-phosphate for nucleoside interconversion. Biochim Biophys Acta. 1997;1335:6-22 pubmed
- Balestri F, Barsotti C, Lutzemberger L, Camici M, Ipata P. Key role of uridine kinase and uridine phosphorylase in the homeostatic regulation of purine and pyrimidine salvage in brain. Neurochem Int. 2007;51:517-23 pubmed..On the contrary, at relatively high UTP and CTP levels the inhibition of uridine kinase channels uridine towards phosphorolysis. The ribose-1-phosphate is then transformed into PRPP, which is used for purine salvage synthesis. ..
- Vara D, Campanella M, Canobbio I, Dunn W, Pizzorno G, Hirano M, et al. Autocrine amplification of integrin ?IIb?3 activation and platelet adhesive responses by deoxyribose-1-phosphate. Thromb Haemost. 2013;109:1108-19 pubmed publisher..Taken together, we present evidence that dRP is a novel autocrine amplifier of platelet activity, which acts on platelet redox levels and modulates integrin ?IIb?3. ..
- Maldonado M, Weerasinghe G, Ambroise F, Yamoah E, Londono M, Pelayo J, et al. The charged milieu: a major player in fertilization reactions. Acta Histochem. 2004;106:3-10 pubmed..The present study is a comprehensive survey of the effects of charge, pH and molecular structure on the fertilization activation continuum in a model system of sea urchins. ..
- Tran T, Christoffersen S, Allan P, Parker W, Piskur J, Serra I, et al. The crystal structure of Streptococcus pyogenes uridine phosphorylase reveals a distinct subfamily of nucleoside phosphorylases. Biochemistry. 2011;50:6549-58 pubmed publisher..This is in contrast to EcUP for which transition state stabilization occurs mostly at O4. ..
- Vimala A, Harinarayanan R. Transketolase activity modulates glycerol-3-phosphate levels in Escherichia coli. Mol Microbiol. 2016;100:263-77 pubmed publisher..This regulation could be prevalent in other organisms. ..
- Silva R, Schramm V. Uridine phosphorylase from Trypanosoma cruzi: kinetic and chemical mechanisms. Biochemistry. 2011;50:9158-66 pubmed publisher..Kinetic analysis as a function of pH indicates one protonated group essential for catalysis and for substrate binding. ..
- Fortpied J, Gemayel R, Vertommen D, van Schaftingen E. Identification of protein-ribulosamine-5-phosphatase as human low-molecular-mass protein tyrosine phosphatase-A. Biochem J. 2007;406:139-45 pubmed..Human recombinant LMWPTP-A displayed an RN5Pase activity that was higher than its tyrosine phosphatase activity, indicating that this phosphatase may participate in protein deglycation, a new form of protein repair. ..
- Sakuraba H, Yoneda K, Yoshihara K, Satoh K, Kawakami R, Uto Y, et al. Sequential aldol condensation catalyzed by hyperthermophilic 2-deoxy-d-ribose-5-phosphate aldolase. Appl Environ Microbiol. 2007;73:7427-34 pubmed..This promotes the formation of the unique dimeric structure and strengthens the hydrophobic intersubunit interactions. These structural features are considered responsible for the extremely high stability of the hyperthermophilic DERAs. ..
- Iverson T, Panosian T, Birmingham W, Nannemann D, Bachmann B. Molecular differences between a mutase and a phosphatase: investigations of the activation step in Bacillus cereus phosphopentomutase. Biochemistry. 2012;51:1964-75 pubmed publisher..These results permit a proposal for activation of PPM and explain some of the essential features that distinguish between the catalytic cycles of PPM and alkaline phosphatase. ..
- ..Ribozymes (catalytic RNAs) were the center of a presumed RNA world in the early origin of life. In this issue, Lau and Unrau show evidence that an RNA world could have used a similar evolutionary pathway as most proteins do. ..
- Liu D, Caperelli C. Carbocyclic substrates for de novo purine biosynthesis. J Biol Chem. 1991;266:16699-702 pubmed..This study has afforded carbocyclic substrate analogues, in particular for the chemically labile phosphoribosyl amine, for the initial steps of de novo purine biosynthesis. ..
- Wielgus Kutrowska B, Bzowska A, Tebbe J, Koellner G, Shugar D. Purine nucleoside phosphorylase from Cellulomonas sp.: physicochemical properties and binding of substrates determined by ligand-dependent enhancement of enzyme intrinsic fluorescence, and by protective effects of ligands on thermal inactivation of t. Biochim Biophys Acta. 2002;1597:320-34 pubmed
- Soderberg T, Alver R. Transaldolase of Methanocaldococcus jannaschii. Archaea. 2004;1:255-62 pubmed..A readily available source of thermophilic pentose phosphate pathway enzymes including transaldolase may have direct application in enzymatic biohydrogen production. ..
- Solov eva O, Bykova I, Meshalkina L, Kovina M, Kochetov G. Cleaving of ketosubstrates by transketolase and the nature of the products formed. Biochemistry (Mosc). 2001;66:932-6 pubmed..However, the glycolaldehyde cannot be found the free state because it condenses with another glycolaldehyde residue formed in the course of the cleavage of another ketosubstrate molecule yielding erythrulose...
- Budworth H, Dianov G. Mode of inhibition of short-patch base excision repair by thymine glycol within clustered DNA lesions. J Biol Chem. 2003;278:9378-81 pubmed
- Moccand C, Kaufmann M, Fitzpatrick T. It takes two to tango: defining an essential second active site in pyridoxal 5'-phosphate synthase. PLoS ONE. 2011;6:e16042 pubmed publisher..Finally, we provide evidence that a single arginine residue of the C terminus of Pdx1 is responsible for coordinating co-operativity in this elaborate protein machinery. ..
- Bozdagi O, Wang X, Martinelli G, Prell G, Friedrich V, Huntley G, et al. Imidazoleacetic acid-ribotide induces depression of synaptic responses in hippocampus through activation of imidazoline receptors. J Neurophysiol. 2011;105:1266-75 pubmed publisher..KU-14R, an I(3)-R antagonist, partially attenuated responses to IAA-RP. Taken together, these data support a role for IAA-RP in modulating synaptic transmission in the hippocampus through activation of I-Rs. ..
- Panosian T, Nannemann D, Watkins G, Phelan V, McDonald W, Wadzinski B, et al. Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point into the catalytic cycle. J Biol Chem. 2011;286:8043-54 pubmed publisher..However, the two mechanisms may be reconciled if substrate encounters the enzyme at a different point in the catalytic cycle. ..
- Sevostyanova I, Selivanov V, Yurshev V, Solovjeva O, Zabrodskaya S, Kochetov G. Cooperative binding of substrates to transketolase from Saccharomyces cerevisiae. Biochemistry (Mosc). 2009;74:789-92 pubmed..In the presence of Mg2+, nonequivalence of the active sites is not observed. ..
- Meshalkina L, Solovjeva O, Khodak Y, Drutsa V, Kochetov G. Isolation and properties of human transketolase. Biochemistry (Mosc). 2010;75:873-80 pubmed..The values of the Michaelis constant were determined for ThDP and a pair of physiological substrates of the enzyme (xylulose 5-phosphate and ribose 5-phosphate). ..
- Sevostyanova I, Solovjeva O, Kochetov G. Two methods for determination of transketolase activity. Biochemistry (Mosc). 2006;71:560-2 pubmed..It is not needed in the second method. The range of transketolase concentration in the activity assay is 0.036-0.144 U/ml for the first method and 1.8-6.8 U/ml for the second one...
- Goenrich M, Thauer R, Yurimoto H, Kato N. Formaldehyde activating enzyme (Fae) and hexulose-6-phosphate synthase (Hps) in Methanosarcina barkeri: a possible function in ribose-5-phosphate biosynthesis. Arch Microbiol. 2005;184:41-8 pubmed..6 U/mg) and hexulose-6-phosphate synthase (Hps) activity (4.4 U/mg). The results support the recent proposal that in methanogenic archaea Fae and Hps could have a function in ribose phosphate synthesis. ..
- Esposito S, Massaro G, Vona V, Di Martino Rigano V, Carfagna S. Glutamate synthesis in barley roots: the role of the plastidic glucose-6-phosphate dehydrogenase. Planta. 2003;216:639-47 pubmed
- Sakuraba H, Tsuge H, Shimoya I, Kawakami R, Goda S, Kawarabayasi Y, et al. The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix. J Biol Chem. 2003;278:10799-806 pubmed..These structural features are considered to be responsible for the extremely high stability of the A. pernix enzyme. This is the first description of the structure of hyperthermophilic DERA and of aldolase from the Archaea domain. ..
- Zeng X, Saxild H. Identification and characterization of a DeoR-specific operator sequence essential for induction of dra-nupC-pdp operon expression in Bacillus subtilis. J Bacteriol. 1999;181:1719-27 pubmed..Binding of DeoR protein to the operator DNA was confirmed by a gel electrophoresis mobility shift assay. Moreover, deoxyribose-5-phosphate was shown to be a likely candidate for the true inducer of the dra-nupC-pdp expression. ..
- Apel T, Scherer A, Adachi T, Auch D, Ayane M, Reth M. The ribose 5-phosphate isomerase-encoding gene is located immediately downstream from that encoding murine immunoglobulin kappa. Gene. 1995;156:191-7 pubmed..We thus show that two genes with very different expression patterns, a housekeeping gene and a gene expressed in a tissue-specific manner, can be located on a chromosome in close proximity to each other. ..
- Guerrero Mendiola C, García Trejo J, Encalada R, Saavedra E, Ramirez Silva L. The contribution of two isozymes to the pyruvate kinase activity of Vibrio cholerae: One K+-dependent constitutively active and another K+-independent with essential allosteric activation. PLoS ONE. 2017;12:e0178673 pubmed publisher..In addition, Western blot analysis indicated that both enzymes were co-expressed. Therefore, it is concluded that VcIPK and VcIIPK contribute to the activity of pyruvate kinase in this ?-proteobacterium. ..
- Rodriguez Y, Howard M, Cuneo M, Prasad R, Wilson S. Unencumbered Pol ? lyase activity in nucleosome core particles. Nucleic Acids Res. 2017;45:8901-8915 pubmed publisher..These results indicate 5'-dRP gap trimming proceeds unperturbed within the NCP; whereas, gap filling is strongly limited. In the absence of additional factors, base excision repair in NCPs will stall at the gap-filling step. ..
- Alderwick L, Lloyd G, Lloyd A, Lovering A, Eggeling L, Besra G. Biochemical characterization of the Mycobacterium tuberculosis phosphoribosyl-1-pyrophosphate synthetase. Glycobiology. 2011;21:410-25 pubmed publisher..Here, we report a detailed biochemical and biophysical study of Mt-PrsA, which exhibits the most rapid enzyme kinetics reported for a pRpp synthetase. ..
- Roos A, Mariano S, Kowalinski E, Salmon L, Mowbray S. D-ribose-5-phosphate isomerase B from Escherichia coli is also a functional D-allose-6-phosphate isomerase, while the Mycobacterium tuberculosis enzyme is not. J Mol Biol. 2008;382:667-79 pubmed publisher..coli RpiB in which histidine 99 was changed to asparagine and that of wild-type M. tuberculosis enzyme, both co-crystallized with the substrate ribose-5-phosphate, shed additional light on the reaction mechanism of RpiBs generally...
- Horinouchi N, Ogawa J, Kawano T, Sakai T, Saito K, Matsumoto S, et al. One-pot microbial synthesis of 2'-deoxyribonucleoside from glucose, acetaldehyde, and a nucleobase. Biotechnol Lett. 2006;28:877-81 pubmed..About 33 mM 2'-deoxyinosine was produced from 600 mM glucose, 333 mM acetaldehyde and 100 mM adenine in 24 h. 2'-Deoxyinosine was produced from adenine due to the adenosine deaminase activity of E. coli transformants. ..
- Horinouchi N, Ogawa J, Kawano T, Sakai T, Saito K, Matsumoto S, et al. Biochemical retrosynthesis of 2'-deoxyribonucleosides from glucose, acetaldehyde, and a nucleobase. Appl Microbiol Biotechnol. 2006;71:615-21 pubmed..2'-Deoxyinosine (9.9 mM) was produced from glucose, acetaldehyde, and adenine through three-step reactions via fructose 1,6-diphosphate and then 2-deoxyribose 5-phosphate, the molar yield as to glucose being 17.8%. ..
- Hommel U, Eberhard M, Kirschner K. Phosphoribosyl anthranilate isomerase catalyzes a reversible amadori reaction. Biochemistry. 1995;34:5429-39 pubmed
- Stura E, Ghosh S, Garcia Junceda E, Chen L, Wong C, Wilson I. Crystallization and preliminary crystallographic data for class I deoxyribose-5-phosphate aldolase from Escherichia coli: an application of reverse screening. Proteins. 1995;22:67-72 pubmed..6 A. A new method, reverse screening, designed to minimize protein utilization during the screening process was used to determine supersaturation and crystallization conditions. ..
- Stoffel S, Alibu V, Hubert J, Ebikeme C, Portais J, Bringaud F, et al. Transketolase in Trypanosoma brucei. Mol Biochem Parasitol. 2011;179:1-7 pubmed publisher..Metabolite profiling to compare wild type and TKT null mutants revealed substantial increases in transketolase substrate metabolites coupled to loss of sedoheptulose 7-phosphate, a principal product of the transketolase reaction. ..
- de Bruin M, van Capel T, Smid K, van der Born K, Fukushima M, Hoekman K, et al. Role of platelet derived endothelial cell growth factor/thymidine phosphorylase in fluoropyrimidine sensitivity and potential role of deoxyribose-1-phosphate. Nucleosides Nucleotides Nucleic Acids. 2004;23:1485-90 pubmed..In order to provide an explanation for this difference in activation of 5'DFUR and 5FU, we studied the role of the 5FU co-substrate, dR-1-P, needed for its activation. ..
- Rashid N, Kanai T, Atomi H, Imanaka T. Among multiple phosphomannomutase gene orthologues, only one gene encodes a protein with phosphoglucomutase and phosphomannomutase activities in Thermococcus kodakaraensis. J Bacteriol. 2004;186:6070-6 pubmed publisher..Our results clearly indicate that, among the four PMM gene orthologues in T. kodakaraensis, only one gene, TK1108, actually encodes a protein with PGM and PMM activities...
- Mottram D, Nobrega I. Formation of sulfur aroma compounds in reaction mixtures containing cysteine and three different forms of ribose. J Agric Food Chem. 2002;50:4080-6 pubmed