The effect of acceptor modification upon the synthesis of dinucleoside phosphates catalyzed by non-specific ribonucleases of Penicillium claviforme

1979 ◽  
Vol 44 (2) ◽  
pp. 613-625 ◽  
Author(s):  
Valentina I. Gulyaeva ◽  
Antonín Holý
Keyword(s):  
Reaction Center ◽  
Hydroxy Group ◽  
Pyrimidine Ring ◽  
Phosphate Group ◽  
Mutual Orientation ◽  
Acceptor Molecule ◽  
Heterocyclic Base ◽  
Sugar Moiety ◽  
Cyclic Phosphate ◽  
Penicillium Claviforme

The present paper studies the effect of the modification of heterocyclic base, sugar moiety and the presence of phosphate group on the nucleoside acceptors in the synthesis of dinucleoside phosphates from adenosine 2',3'-cyclic phosphate as donor, catalyzed by nonspecific acidic extracellular and intracellular ribonucleases from Penicillium claviforme. The enzyme binds specifically the acceptor molecule, preferring cytosine nucleosides. It requires the presence of the whole sugar moiety, an exact mutual orientation of the heterocyclic base and the reaction center (5'-hydroxy group), and a suitable conformation of the acceptor molecule. The enzyme-acceptor bond is homochiral and the presence of the N3-H group in the pyrimidine ring is important. The reaction between the donor and the acceptor is bimolecular and is competitively inhibited by some purine nucleosides.

New pyrimidine (uridine) specific cyclizing 2'-ribonucleotidyltransferase and nonspecific decyclizing 2',3'-phosphodiesterase

1979 ◽  
Vol 44 (3) ◽  
pp. 957-975 ◽  
Author(s):  
Antonín Holý ◽  
Ivan Rosenberg
Keyword(s):  
Alkyl Esters ◽  
Native State ◽  
Heterocyclic Base ◽  
Pancreatic Ribonuclease ◽  
Sugar Moiety ◽  
High Preference ◽  
Alkyl Moiety ◽  
Cyclic Phosphate ◽  
Sepharose 4B ◽  
Cyclic Phosphates

Chromatography of an aqueous extract of rape seedlings on modified Cellex P, followed by chromatography on two types of modified Sepharose 4B, afforded two nucleolytic activities which split ribonucleoside 2',3'-cyclic phosphates. The first enzyme (C1) affording 2'-nucleotides on splitting, was characterized as a decyclizing 2',3'-phosphodiesterase, nonspecific towards the nature of the heterocyclic base. The second enzyme (D2) splits uridine 2',3'-cyclic phosphate and cytidine 2',3'-cyclic phosphate with high preference for the uridine derivative, its specificity towards the heterocyclic base and the sugar moiety resembling that of pancreatic ribonuclease. The products are in both cases 3'-ribonucleotides. The enzyme splits also alkyl esters of uridine 3'-phosphate with the intermediary formation of uridine 2',3'-cyclic phosphate. The splitting rate decreases with growing alkyl moiety. This enzyme is classified as a new pyrimidine specific cyclizing 2-ribonucleotidyltransferase (EC 2.7.7). Both enzymes were isolated free of other nucleolytic activities. In the native state they are stabilized by an acidic protein.

Preparation of analogues of cytosine and 2-pyrimidinone nucleosides and their effect on bacterial (Escherichia coli A 19) cytidine aminohydrolase

1985 ◽  
Vol 50 (2) ◽  
pp. 393-417 ◽  
Author(s):  
Antonín Holý ◽  
Anita Ludziša ◽  
Ivan Votruba ◽  
Kateřina Šedivá ◽  
Helmut Pischel
Keyword(s):  
Hydroxy Group ◽  
Necessary Conditions ◽  
Heterocyclic System ◽  
Similar Type ◽  
Open Chain ◽  
Heterocyclic Base ◽  
Basic Character ◽  
E Coli ◽  
Sugar Moiety ◽  
Derivatives Of

The set of compounds investigated as substrates and inhibitors of bacterial cytidine aminohydrolase (EC 3.5.4.5) consists of cytidine analogues modified in the heterocyclic base or the sugar moiety and analogues of the similar type derived from l-(β-D-ribofuranosyl)-2-pyrimidone (I) and its isomers. The latter group of compounds includes also open-chain derivatives of neutral and acidic character. These compounds were prepared by novel synthetic procedures. Minimum necessary conditions for the structure of an inhibitor of cytidine aminohydrolase from E. coli A 19 include: a heterocyclic system containing an Rf-N-CO-N(H) fragment of a basic character in which Rf denotes a β-D-aldopentafuranoside with a 3-hydroxy group of ribo-configuration; the 5-hydroxy group of the sugar moiety may bear a substituent, except a phosphomonoester function. The heterocyclic base may also bear substituents in positions other than α to the nucleoside bond which do not reduce substantially the basicity of the system and do not change the conformation of the nucleoside molecule.

The first 3′:5′-cyclic nucleotide–amino acid complex:L-His–cIMP

2012 ◽  
Vol 68 (8) ◽  
pp. o311-o316 ◽  
Author(s):  
Katarzyna Ślepokura
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Cyclic Nucleotide ◽  
Phosphate Group ◽  
Specific Amino Acid ◽  
Π Stacking ◽  
Cyclic Phosphate ◽  
Nucleotide Recognition ◽  
Group Play ◽  
Phosphate Groups

In the crystal structure of the L-His–cIMP complex,i.e.L-histidinium inosine 3′:5′-cyclic phosphate [systematic name: 5-(2-amino-2-carboxyethyl)-1H-imidazol-3-ium 7-hydroxy-2-oxo-6-(6-oxo-6,9-dihydro-1H-purin-9-yl)-4a,6,7,7a-tetrahydro-4H-1,3,5,2λ5-furo[3,2-d][1,3,2λ5]dioxaphosphinin-2-olate], C6H10N3O2+·C10H10N4O7P−, the Hoogsteen edge of the hypoxanthine (Hyp) base of cIMP and the Hyp face are engaged in specific amino acid–nucleotide (His...cIMP) recognition,i.e.by abutting edge-to-edge and by π–π stacking, respectively. The Watson–Crick edge of Hyp and the cIMP phosphate group play a role in nonspecific His...cIMP contacts. The interactions between the cIMP anions (anti/C3′–endo/trans–gauche/chair conformers) are realized mainly between riboses and phosphate groups. The results for this L-His–cIMP complex, compared with those for the previously reported solvated L-His–IMP crystal structure, indicate a different nature of amino acid–nucleotide recognition and interactions upon the 3′:5′-cyclization of the nucleotide phosphate group.

The SO4·̄induced Oxidation of 2′-Deoxyuridine-5′-phosphate, Uridine-5′-phosphate and Thymidine-5′-phosphate. An ESR Study in Aqueous Solution

1990 ◽  
Vol 45 (1-2) ◽  
pp. 47-58 ◽  
Author(s):  
Knut Hildenbrand
Keyword(s):  
Aqueous Solution ◽  
Radical Cation ◽  
Esr Spectroscopy ◽  
Radical Cations ◽  
Phosphate Group ◽  
Anoxic Conditions ◽  
Radical Site ◽  
Sugar Moiety ◽  
Type Radical ◽  
Phosphate Addition

Abstract Reactions of photolytically generated SO4·̄ with 2′-deoxyuridine-5′-phosphate (5′-dUMP), uridine-5′-phosphate (5′-UMP) and thymidine-5′-phosphate (5′-dTMP) were studied by ESR spectroscopy in aqueous solution under anoxic conditions. From 5′-dUMP and 5′-UMP the 5′,5-cyclicphosphate-6-yl radicals 10 and 11 were generated (pH 2 -11) whereas from 5′-dTMP at pH 3 -8 the 5,6-dihydro-6-hydroxy-5-yl radical 14 and at pH 7 -1 1 the 5-methylene-2′-deoxyuridine-5′-phosphate radical 15 was produced. In the experiments with 5′-UMP in addition to radical 11 the signals of sugar radicals 12 and 13 were detected. It is assumed that the base radical cations act as intermediates in the SO4·̄-induced radical reac­tions. The 5′-phosphate group adds intramolecularly to the C(5)−C(6) bond of the uraclilyl radical cation whereas the thymidyl radical cation of 5′-dTMP reacts with H2O at pH < 8 to yield the 6-OH-5yl adduct 14 deprotonates at pH > 7 thus forming the allyl-type radical 15. In 5′-UMP transfer of the radical site from the base to the sugar moiety competes with intramolecular phosphate addition.

TheN1-(2′-deoxyribofuranoside) of 3-iodo-5-nitroindole: a universal nucleoside forming nitro–iodo interactions

2009 ◽  
Vol 65 (3) ◽  
pp. o100-o102 ◽  
Author(s):  
Simone Budow ◽  
Peter Leonard ◽  
Henning Eickmeier ◽  
Hans Reuter ◽  
Frank Seela
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Nitro Group ◽  
Hydroxy Group ◽  
Torsion Angle ◽  
Title Compound ◽  
Stacking Interactions ◽  
Sugar Moiety ◽  
Determining Factors

The title compound [systematic name: 1-(2-deoxy-β-D-erythro-pentofuranosyl)-3-iodo-5-nitro-1H-indole], C13H13IN2O5, exhibits anantiglycosylic bond conformation with a χ torsion angle of −114.9 (3)°. The furanose moiety shows a twisted C2′-endosugar pucker (S-type), withP= 141.3° and τm = 40.3°. The orientation of the exocyclic C4′—C5′ bond is +ap(gauche,trans), with a γ torsion angle of 177.4 (2)°. The extended crystal structure is stabilized by hydrogen bonding and I...O contacts, as well as by stacking interactions. The O atoms of the nitro group act as acceptors, forming bifurcated hydrogen bonds within theacplane. Additionally, the iodo substituent forms an interplanar contact with an O atom of the nitro group, and another contact with the O atom of the 5′-hydroxy group of the sugar moiety within theacplane is observed. These contacts can be considered as the structure-determining factors for the molecular packing in the crystal structure.

Method for the Selective 2′-O-Substitution of Nucleosides

1980 ◽  
Vol 35 (1-2) ◽  
pp. 163-167 ◽  
Author(s):  
C. Sauer ◽  
U. Schwabe
Keyword(s):  
Cyclic Amp ◽  
Phosphate Group ◽  
New Method ◽  
Protecting Groups ◽  
Step Procedure ◽  
One Step ◽  
Cyclic Phosphate ◽  
Neutral Conditions

Abstract This paper presents a new method for selective reactions of predetermined sugar hydroxyls of nucleosides. Suc-cinylated nucleosides were investigated as examples for the use of the cyclic phosphate group for protecting purposes. Starting from cyclic AMP the 2′-O-group was selectively succinylated yielding 93% 2′-O-succinyl cyclic AMP. The cyclic phosphate was enzymatically dephosphorylated in a one step procedure under neutral conditions and 2′-O -succinyl adenosine containing a small amount of the 3′-O-isomer was produced in 91% yield. When establishment of equilibrium of the 2′-O-and 3′-O-isomers was allowed, 54% yield of crystallized 3′-O-succinyl adenosine was prod­ uced. The results suggest that the easily accessible cyclic monophosphates are good protecting groups for the pro­ duction of nucleoside derivatives, especially at the 2′-O-position under neutral conditions.

Cytochemical Localization of Polysaccharides in Diplodia Maydis With Thiosemicarbazide : Evaluation of Three Fixatives For Pa:Tsc:Os Reaction

1976 ◽  
Vol 34 ◽  
pp. 48-49 ◽  
Author(s):  
Judith A. Murphy ◽  
Mary R. Thompson ◽  
A.J. Pappelis
Keyword(s):  
Reaction Center ◽  
Osmium Tetroxide ◽  
Periodic Acid ◽  
Cytochemical Localization ◽  
Thin Sections ◽  
Selective Reaction ◽  
Amorphous Character

In an attempt to identify polysaccharide components in thin sections of D. maydis, procedures were employed such that a PAS localization could be carried out. Three different fixatives were evaluated ie. glutaraldehyde, formaldehyde and paraformaldehyde. These were used in conjunction with periodic acid (PA), thiosemicarbazide(TSC), and osmium tetroxide(Os) to localize polysaccharides in V. maydis using a pre-embedded reaction procedure. Polysaccharide localization is based on the oxidation of vic-glycol groups by PA, and the binding of TSC as a selective reaction center for the formation of osmium black. The reaction product is sufficiently electron opaque, insoluble in lipids, not altered when tissue is embedded, and has a fine amorphous character.

Role of the Small (40S) Subunits in the Structure of the Interface of Eukaryotic Ribosomes

1980 ◽  
Vol 38 ◽  
pp. 548-549
Author(s):  
M. Boublik ◽  
N. Robakis ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Structural Similarity ◽  
High Resolution Electron Microscopy ◽  
Peptide Bond ◽  
Uranyl Acetate ◽  
Mutual Orientation ◽  
Mutual Position ◽  
Peptide Bond Formation ◽  
Resolution Electron ◽  
Direct Technique ◽  
Structural Details

Ribosomes are ribonucleoprotein particles which process the genetic information coded in mRNA into protein synthesis. The analogy in function and composition of ribosomes from various sources, both prokaryotic and eukaryo-tic, imply a structural similarity. At present, high resolution electron microscopy is the most direct technique with a potential to resolve the extent of the structural homology of ribosomal particles at a macromolecular level. The structure of ribosomes is highly complex as a result of the large number of their constituents. In general, 80S eukaryotic monosomes consist of two uneven subunits - large (60S) and small (40S) - accomodating four different RNAs and approximately 80 different proteins. Mutual orientation of both subunits on the monosome is of particular interest because it determines the interface, the supposed site of interactions of ribosomes with other macro-molecules involved in peptide bond formation. Since entrapping of the contrasting solution (0.5% aqueous uranyl acetate) obscures all structural details in the interface, information on its architecture is limited to an indirect reconstruction based on the established 3-D structure of both sub-units and their mutual position after association.

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