Phosphoryl transfer

FIGURE 10.26 Glucose transport in E. coli is mediated by the PEP-dependent phosphotransferase system. Enzyme I is phosphorylated in the first step by PEP. Successive phosphoryl transfers to HPr and Enzyme III in Steps 2 and 3 are followed by transport and phosphorylation of glucose. Enzyme II is the sugar transport channel. 

The subscripts illustrate an important point the phosphoryl transfer occurs entirely on the inside surface of the bacterial membrane. 

An example of a random, single-displacement mechanism is seen in the enzyme creatine kinase, a phosphoryl-transfer enzyme that uses ATP as a phosphoryl... 

FIGURE 19.22 The mntase that forms 2,3-BPG from 1,3-BPG requires 3-phosphoglyc-erate. The reaction is actually an intermolecular phosphoryl transfer from C-1 of 1,3-BPG to C-2 of 3-PG. 

FIGURE 19.25 The phosphoglycerate mutase of wheat germ catalyzes an intramolecn-lar phosphoryl transfer. 

FIGURE 19.28 The conversion of phosphoenolpyrnvate (PEP) to pyrnvate may be viewed as involving two steps phosphoryl transfer followed by an enol-keto tantomeriza-don. The tantomerizadon is spontaneons (AG -35-40 kJ/mol) and acconntsfor mnch of the free energy change for PEP hydrolysis. 

FIGURE 19.29 A mechanism for the pyruvate kinase reaction, based on NMR and EPR studies by Albert Mildvan and colleagues. Phosphoryl transfer from phosphoenolpyrnvate (PEP) to ADP occurs in four steps (a) a water on the Mg ion coordinated to ADP is replaced by the phosphoryl group of PEP (b) Mg dissociates from the -P of ADP (c) the phosphoryl group is transferred and (d) the enolate of pyruvate is protonated. (Adapted from Mildvan, A., 1979. Advances in Eiizymology 49 103-126.)... 

Synthetic nonhydrolyzable analogs of nucleoside triphosphates (Figure 33-13) allow investigators to distinguish the effects of nucleotides due to phosphoryl transfer from effects mediated by occupancy of allosteric nucleotide-binding sites on regulated enzymes. 

Figure 34-2 illustrates the intermediates and reactions for conversion of a-D-ribose 5-phosphate to inosine monophosphate (IMP). Separate branches then lead to AMP and GMP (Figure 34-3). Subsequent phosphoryl transfer from ATP converts AMP and GMP to ADP and GDP. Conversion of GDP to GTP involves a second phosphoryl transfer from ATP, whereas conversion of ADP to ATP is achieved primarily by oxidative phosphorylation (see Chapter 12).

Two phosphoribosyl transferases then convert adenine to AMP and hypoxanthine and guanine to IMP or GMP (Figure 34-4). A second salvage mechanism involves phosphoryl transfer from ATP to a purine ri-bonucleoside (PuR) ... 

Oxidation and amination of IMP forms AMP and GMP, and subsequent phosphoryl transfer from ATP forms ADP and GDP. Further phosphoryl transfer from ATP to GDP forms GTP. ADP is converted to ATP by oxidative phosphorylation. Reduction of NDPs forms dNDPs. 

For acyl transfer, phosphoryl transfer, and sulfonyl transfer, the primary kind of evidence in favor of concerted mechanisms for some reactions is a linear Bronsted plot of log k versus for a range of nucleophiles, spanning p/ir/ = - p r s = 0, coupled... 

In the quest for free metaphosphate, racemization has been observed for phosphoryl transfer from phenyl dihydrogen (R)-[ 0, " 0, 0]-phosphate to tert-butyl alcohol in MeCN. ... 

Compound (32) phosphorylates hindered alcohols in the presence of EtOH consistent with a dissociative mechanism involving a metaphosphate-like intermediate,since it proceeds with considerable racemization at phosphorus(Scheme 6). The extent of phosphoryl transfer which proceeds with retention of configuration is ca. 357, (i e. ca. 707. racemization) the excess of (S)p configuration would arise from transfer with configurational inversion, and might indicate a relatively free ... 

The involvement of monomeric metaphosphate in the phosphoryl transfer from phosphate monoesters, and of pentaco-ordinate intermediates from phosphotriesters represent two extremes in the mechanistics of the phosphoryl transfer process. Between the extremes are the (S 2)p processes involving transition states having various bond orders, but no true... 

Another group solved the crystal structure of the IGF-I RTK domain phosphorylated at two tyrosine residues within the activation loop and bound to an ATP analog. The ligand is not in a conformation compatible with phosphoryl transfer, and the activation loop is partially disordered. IGF-I RTK is trapped in a half-closed, previously unobserved conformation. This conformation may be intermediary between the open, inactive conformation and closed, active conformation of insulin and IGF-I RTKs. 

Keywords Semi-empirical MO, PM3, QM/MM. parameters, phosphoryl transfer, carbohydrate,... 

HYBRID POTENTIALS FOR THE SIMULATION OF PHOSPHORYL TRANSFER REACTIONS... 

The AMl/d-PhoT model [33] is a parameterization of a modified AMl/d Hamiltonian developed specifically to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined QM/MM simulations. The model is currently parametrized for H, O, and P atoms to reproduce... 

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74],... 

Case Study Comparison of DFT Functionals on Model Phosphoryl Transfer Reactions... 

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