Nucleotidyl transfer reaction

The role of divalent cations in the mechanism of enzyme catalysed phosphoryl and nucleotidyl transfer reactions. A. S. Mildvan and C. M. Grisham, Struct. Bonding (Berlin), 1974,20,1-21 (88),... 

Catalyzed Phosphoryl and Nucleotidyl Transfer Reactions. - H. P. C. Hogenkamp,... 

The mechanisms of nucleotide oligomer synthesis catalyzed by proteinoids have not reported. A tentative mechanism rests on the supposition that the proteinoid nucleotide complex is an intermediate of an enzyme-like nucleotidyl transfer reaction. 

Contents A. S. Mildvan, C. M. Grisham The Role of Divalent Cations in the Mechanism of Enzyme Catalyzed Phosphoryl and Nucleotidyl Transfer Reactions. - H.P.C.Hogenkamp, G.N.Sando The Enzymatic Reduction of Ribonucleotides. - W. T. Oosterhuis The Electronic State of Iron in Some Natural Iron Compounds. Determination by Mossbauer and ESR Spectroscopy. - A. Trautwein Mossbauer Spectroscopy on Heme Proteins. 

S. Shuman, Y. Liu, and B. Schwer. 1994. Covalent catalysis in nucleotidyl transfer reactions Essential motifs in Saccharomyces cerevisiae RNA capping enzyme are conserved in Schizosaccharomyces pombe and viral capping enzymes and among polynucleotide ligases Proc. Natl. Acad. Sci. U. S. A. 91 12046-12050. (PubMed) (Full Text in PMC)... 

Phosphoryl and nucleotidyl transfer reactions are nucleophilic displacements on phosphorus 3—6), and like analogous displacements on carbon (7) or on metal ions (5), have been found to take place by mechanisms varying between two extreme or limiting cases 1. In the dissociative or SnI mechanism the initial departure of the leaving nucleophile, yields the planar triply coordinate metaphosphate anion as a reactive chemical intermediate (3, 8), which then combines with the entering ligand on either face of the metaphosphate plane 2. In the associative... 

Bojin, M.D. and Schlick, T. (2007) A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase B. J. Phvs. Chem. B, 111, 11244-11252. 

The inference from stereochemical studies is that pseudorotation is not involved in enzymic phosphoryl and nucleotidyl transfer reactions. However, the involvement of pseudorotation has been postulated in several biological reactions involving six-membered-ring phosphorus species. These are discussed in Section 4. 

Pre-steady-state studies of Y-family polymerases indicate that for nucleotidyl transfer reaction to occur, the polymerases have to undergo... 

The basic enzymatic function of RNAP is the transfer of the nucleotidyl motif firom the rNTP substrates to the hydroxyl at the 3 -end of the nascent RNA transcript. The nucleotidyl transfer reaction can be simplified as... 

The catalytic center of RNAP includes the binding site for the 3 -end of RNA and the insertion site for the incoming rNTP. In the nucleotidyl transfer reaction, the 3 -OH group in the sugar ring of the RNA primer reacts with the a-phosphorous atom of a ribonucleoside triphosphate by nucleophilic attack, then the Pa-Oap bond is broken and pyrophosphate (PPj) is released. Thus, a nucleotidyl addition to the RNA primer is achieved. Structural and biochemical data have shown that the active centers of all polymerases share certain common features a pair of metal ions (normally divalent magnesium ions Mg " and three universally conserved carboxylates. The two-metal-ion mechanism for the nucleotidyl transfer reaction... 

Fig. 4 The proposed nucleotidyl transfer reaction mechanism. Step 1 The proton of the 3 OH of RNA primer transfers to a solvait water and a proton on water transfers to 02a of a-phosphate simultaneously Step 2 the proton of the 02a atom rotates to the side of P-phosphate Step 3 the 3 0 atom performs a nucleophilic attack at the a-phosphorus atom of the a-phosphate Step 4 the Pa-03p bond of the intermediate cleaves to form a phosphodiester bond and the proton on 02a migrates to 03 P...

We proposed the following detailed nucleotidyl transfer reaction mechanism for yeast RNA polymerase II, shown in Fig. 4. The proton of the 3 OH first transfers to the 02a of a-phosphate via a solvent water molecule, then one of the water molecule s protons transfers to the bridging phosphate 03p atom. Note that the water molecule is located by our CHARMM molecular dynamics (MD) simulations. 

Zhang Y, Zhu R, Zhang R, de la Lande A, Salahub D (2012) On the mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase n (Unpublished)... 

A very few stable nucleoside monophosphate coenzymes are formed through nucleotidyl transfer reactions. 

The anhydride bonds formed in nucleotidyl transfer reactions are usually equal to or greater in free enei of hydrolysis than the anhydride bond of ATP which was broken however, these reactions are driven to completion by the cleavage of pyrophosphate by pyrophosphatase. The latter is a reaction of high free energy, and this makes the synthetic process virtually irreversible. 

ATP is the primary source of utilizable energy for biosynthetic reactions, but other purine and pyrimidine nucleoside triphosphates (GTP, UTP, CTP) occur in cells and are formed by phosphoryl transfer from ATP, as described in detail in Chapter 4. These are also high-energy compounds, and their hydrolysis can be coupled to energetically unfavorable reactions. This most commonly takes place through nucleotidyl transfer reactions leading to group-transfer coenzymes (Section II, B, 3). 

Cytidine nucleotides apparently are the only nucleotides involved in the activation and transfer of alcohols. Like many other group-transfer coenzymes, they are formed by an ordinary nucleotidyl transfer reaction ... 

The bulk of the cellular nucleotides are in the form of the polymers RNA and DNA. In each case the polymerization process is simply a nucleotidyl transfer reaction of nucleoside triphosphates to form a chain of nucleoside monophosphates in 3, 5 -phosphodiester linkage, with consequent release of pyrophosphate. 

Mildvan and Grisham have reviewed the role of bivalent cations in the mechanism of enzyme-catalysed phosphoryl and nucleotidyl transfer reactions. 

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