Enzymatic activity of coenzyme B(12) derivatives with altered axial nucleotides: probing the mechanochemical triggering hypothesis in ribonucleotide reductase

First and second sphere interactions accelerate non-native N-alkylation catalysis by the thermostable, methanol-tolerant B12-dependent enzyme MtaC

The corrinoid protein MtaC, which is natively involved in methyl transferase catalysis, catalyzes N-alkylation of aniline using ethyl diazoacetate. Our results show how the native preference of B12 scaffolds for radical versus polar chemistry translates to non-native catalysis, which could guide selection of B12-dependent proteins for biocatalysis. MtaC also has high thermal stability and organic solvent tolerance, remaining folded even in pure methanol.

Structural basis for adenosylcobalamin activation in AdoCbl-dependent ribonucleotide reductases

Class II ribonucleotide reductases (RNR) catalyze the formation of an essential thiyl radical by homolytic cleavage of the Co-C bond in their adenosylcobalamin (AdoCbl) cofactor. Several mechanisms for the dramatic acceleration of Co-C bond cleavage in AdoCbl-dependent enzymes have been advanced, but no consensus yet exists. We present the structure of the class II RNR from Thermotoga maritima in three complexes: (i) with allosteric effector dTTP, substrate GDP, and AdoCbl; (ii) with dTTP and AdoCbl; (iii) with dTTP, GDP, and adenosine. Comparison of these structures gives the deepest structural insights so far into the mechanism of radical generation and transfer for AdoCbl-dependent RNR. AdoCbl binds to the active site pocket, shielding the substrate, transient 5'-deoxyadenosyl radical and nascent thiyl radical from solution. The e-propionamide side chain of AdoCbl forms hydrogen bonds directly to the α-phosphate group of the substrate. This interaction appears to cause a "locking-in" of the cofactor, and it is the first observation of a direct cofactor-substrate interaction in an AdoCbl-dependent enzyme. The structures support an ordered sequential reaction mechanism with release or relaxation of AdoCbl on each catalytic cycle. A conformational change of the AdoCbl adenosyl ribose is required to allow hydrogen transfer to the catalytic thiol group. Previously proposed mechanisms for radical transfer in B12-dependent enzymes cannot fully explain the transfer in class II RNR, suggesting that it may form a separate class that differs from the well-characterized eliminases and mutases.

Chemoselective deprotection of alpha-indole and imidazole ribonucleosides

A series of 2 ',3 '-isopropylidene and 5 '-trityl-protected alpha-indole and alpha/beta-benzimidazole and imidazole ribonucleosides were deprotected with different acids. Selectivity was achieved for 5 '-versus 2 ',3 '- deprotection by using formic acid in the alpha-indole ribonucleoside series. Treatment of alpha-indole ribonucleosides with a mixture of formic acid and ether at room temperature afforded 2 ',3 '-deprotected alpha-ribonucleosides, whereas treatment of the alpha-benzimidazole ribonucleosides with the same acid afforded the 5 '-deprotected ribonucleoside without any 2 ', 3 '-deprotected products. The structures of these ribonucleosides were elucidated with 2D (NOESY, COSY, and HMQC) NMR spectroscopy.

Synthesis, spectroscopic characterization, axial base coordination equilibrium and photolytic kinetics studies of a new coenzyme B12analogue-3′-deoxy-2′,3′-anhydrothymidylcobalamin

A new coenzyme B12 (AdoCbl) analogue, 3'-deoxy-2',3'-didehydrothymidylcobalamin (2',3'-anThyCbl) was prepared by the reaction of 5'-iodo-3'-deoxy-2',3'-dihydrothmidine with reduced B12a, and characterized by UV-Vis, CD, ESI-MS and NMR spectroscopies. Its axial base (dbzm) coordination equilibria with pH's and temperatures were investigated and showed similar features to those of coenzyme B12. Photolytic dynamics studies under homolytic and heterolytic conditions demonstrated that the Co-C bond of the analogue is slightly more photolabile relative to coenzyme B12.

Regio- and Stereoselective Glycosylation: Synthesis of 5-Haloimidazole α-Ribonucleosides

We describe the synthesis of novel 5-haloimidazole ribonucleosides as precursors of modified cobalamins. A regio- and stereoselective glycosylation of protected ribose with silylated 4(5)-haloimidazoles produces 5-haloimidazole ribonucleosides predominantly in the alpha-configuration (60-75%) without any 4-substituted imidazole ribonucleoside. The structure of the 5-fluoroimidazole ribonucleoside was confirmed by X-ray crystallography and 2D NMR spectroscopy.

The enzymatic activation of coenzyme B12

The enzymatic "activation" of coenzyme B12 (5'-deoxyadenosylcobalamin, AdoCbl), in which homolysis of the carbon-cobalt bond of the coenzyme is catalyzed by some 10(9)- to 10(14)-fold, remains one of the outstanding problems in bioinorganic chemistry. Mechanisms which feature the enzymatic manipulation of the axial Co-N bond length have been investigated by theoretical and experimental methods. Classical mechanochemical triggering, in which steric compression of the long axial Co-N bond leads to increased upward folding of the corrin ring and stretching of the Co-C bond is found to be feasible by molecular modeling, but the strain induced in the Co-C bond seems to be too small to account for the observed catalytic power. The modeling study shows that the effect is a steric one which depends on the size of the axial nucleotide base, as substitution of imidazole (Im) for the normal 5,6-dimethylbenzimidazole (Bzm) axial base decreases the Co-C bond labilization considerably. An experimental test was thus devised using the coenzyme analog with Im in place of Bzm (Ado(Im)Cbl). Studies of the enzymatic activation of this analog by the B12-dependent ribonucleoside triphosphate reductase from Lactobacillus leichmannii coupled with studies of the non-enzymatic homolytic lability of the Co-C bond of Ado(Im)Cbl show that the enzyme is only slightly less efficient (3.8-fold, 0.8 kcal mol(-1)) at activating Ado(Im)Cbl than at activating AdoCbl itself. This suggests, in agreement with the modeling study, that mechanochemical triggering can make only a small contribution to the enzymatic activation of AdoCbl. Another possibility, electronic stabilization of the Co(II) homolysis product by compression of the axial Co-N bond, requires that enzymatic activation be sensitive to the basicity of the axial nucleotide. Preliminary studies of the enzymatic activation of a coenzyme analog with a 5-fluoroimidazole axial nucleotide suggest that the catalysis of Co-C bond homolysis may indeed be significantly slowed by the decrease in basicity.

Regioselective glycosylation: synthesis of alpha-indoline nucleosides

Novel indoline ribonucleosides with the alpha-N-glycoside configuration are synthesized with very high regioselectivity in 90-96%yield, using TMS protected indolines and 2,3-O-(1-methylethylidene)-5-O-(triphenylmethyl)-alpha/beta-D-ribofuranose. The structures of these ribonucleosides were elucidated with X-ray crystallography as well as 2D (NOESY, COSY, and HMQC) NMR spectroscopy.

Kinetic and thermodynamic studies on ligand substitution reactions and base-on/base-off equilibria of cyanoimidazolylcobamide, a vitamin B12 analog with an imidazole axial nucleoside

Ligand substitution reactions of the vitamin B12 analog cyanoimidazolylcobamide, CN(Im)Cbl, with cyanide were studied. Cyanide substitutes imidazole (Im) in the alpha-position more slowly than it substitutes dimethylbenzimidazole in cyanocobalamin (vitamin B12). The kinetics of the displacement of Im by CN- showed saturation behaviour at high cyanide concentration; the limiting rate constant was found to be 0.0264 s(-1) at 25 degrees C and is characterized by the activation parameters: DeltaH(not =) = 111 +/- 2 kJ mol(-1), DeltaS(not =) = +97 +/- 6 J K(-1) mol(-1), and DeltaV(not =) = +9.3 +/- 0.3 cm3 mol(-1). These parameters are interpreted in terms of an I(d) mechanism. The equilibrium constant for the reaction of CN(Im)Cbl with CN- was found to be 861 +/- 75 M(-1), which is significantly less than that obtained for the reaction of cyanocobalamin with CN- (viz. 10(4) M(-1)). pKbase-off for the base-on/base-off equilibrium was determined spectrophotometrically and found to be 0.99 +/- 0.05, which is about 0.9 pH units higher than that obtained previously in the case of cyanocobalamin. In addition, the kinetics of the base-on/base-off reaction was studied using a pH-jump technique and the data obtained revealed evidence for an acid catalyzed reaction path. The results obtained in this study are discussed in reference to those reported previously for cyanocobalamin.

Solution Structure and Thermolysis of Coβ-5‘-Deoxyadenosylimidazolylcobamide, a Coenzyme B12 Analogue with an Imidazole Axial Nucleoside

The solution structure of Cobeta-5'-deoxyadenosylimidazolylcobamide, Ado(Im)Cbl, the coenzyme B(12) analogue in which the axial 5,6-dimethylbenzimidazole (Bzm) ligand is replaced by imidazole, has been determined by NMR-restrained molecular modeling. A two-state model, in which a conformation with the adenosyl moiety over the southern quadrant of the corrin and a conformation with the adenosyl ligand over the eastern quadrant of the corrin are both populated at room temperature, was required by the nOe data. A rotation profile and molecular dynamics simulations suggest that the eastern conformation is the more stable, in contrast to AdoCbl itself in which the southern conformation is preferred. Consensus structures of the two conformers show that the axial Co-N bond is slightly shorter and the corrin ring is less folded in Ado(Im)Cbl than in AdoCbl. A study of the thermolysis of Ado(Im)Cbl in aqueous solution (50-125 degrees C) revealed competing homolytic and heterolytic pathways as for AdoCbl but with heterolysis being 9-fold faster and homolysis being 3-fold slower at 100 degrees C than for AdoCbl. Determination of the pK(a)'s for the Ado(Im)Cbl base-on/base-off reaction and for the detached imidazole ribonucleoside as a function of temperature permitted correction of the homolysis and heterolysis rate constants for the temperature-dependent presence of the base-off species of Ado(Im)Cbl. Activation analysis of the resulting rate constants for the base-on species show that the entropy of activation for Ado(Im)Cbl homolysis (13.7 +/- 0.9 cal mol(-1) K(-1)) is identical with that of AdoCbl (13.5 +/- 0.7 cal mol(-1) K(-1)) but that the enthalpy of activation (34.8 kcal mol(-1)) is 1.0 +/- 0.4 kcal mol(-1) larger. The opposite effect is seen for heterolysis, where the enthalpies of activation are identical but the entropy of activation is 5 +/- 1 cal mol(-1) K(-1) less negative for Ado(Im)Cbl. Extrapolation to 37 degrees C provides a rate constant for Ado(Im)Cbl homolysis of 2.1 x 10(-9) s(-1), 4.3-fold smaller than for AdoCbl. Combined with earlier results for the enzyme-induced homolysis of Ado(Im)Cbl by the ribonucleoside triphosphate reductase from Lactobacillus leichmannii, the catalytic efficiency of the enzyme for homolysis of Ado(Im)Cbl at 37 degrees C can be calculated to be 4.0 x 10(8), 3.8-fold, or 0.8 kcal mol(-1), smaller than for AdoCbl. Thus, the bulky Bzm ligand makes at best a <1 kcal mol(-1) contribution to the enzymatic activation of coenzyme B(12).

Solution structure, enzymatic, and non-enzymatic reactivity of 3-isoadenosylcobalamin, a structural isomer of coenzyme B12 with surprising coenzymic activity

The coenzymic activity of eight analogs of coenzyme B(12) (5'-deoxyadenosyl-cobalamin, AdoCbl) with structural alterations in the Ado ligand has been investigated with the AdoCbl-dependent ribonucleoside triphosphate reductase (RTPR) from Lactobacillus leichmannii. Six of the analogs were partially active coenzymes, and one, 3-iso-5'-deoxyadenosylcobalamin (3-IsoAdoCbl) was nearly as active as AdoCbl itself. NMR-restrained molecular modeling of 3-IsoAdoCbl revealed a highly conformationally mobile structure which required a four state model to be consistent with the NMR data. Thus, two conformations, one with the IsoAdo ligand over the eastern quadrant of the corrin, and one with the IsoAdo ligand over the northern quadrant, each undergo a facile syn/anti conformational equilibrium in the IsoAdo ligand. Spectrophotometric measurement of the kinetics of RTPR-induced cleavage of the carbon-cobalt bond of 3-IsoAdoCbl showed that it binds to the enzyme with the same affinity as AdoCbl, but its homolysis is only 20% as rapid. Investigation of the non-enzymatic thermolysis of 3-IsoAdoCbl showed that like AdoCbl, 3-IsoAdoCbl decomposes by competing homolytic and heterolytic pathways. A complete temperature-dependent kinetic and product analysis, followed by correction for the base-off species permitted deconvolution of the specific rate constant for both pathways. Eyring plots for the homolysis and heterolysis rate constant cross at 93 degrees C, so that homolysis is the predominant pathway at high temperature, but heterolysis is the predominant pathway at low temperature. At 37 degrees C, the homolysis of 3-IsoAdoCbl is 5.5-fold faster than that of AdoCbl, and the enzyme catalyzes carbon-cobalt bond homolysis in 3-IsoAdoCbl by a factor of 5.9 x 10(7), only 3.9% of the catalytic efficiency with AdoCbl itself. It seems likely that the conformational flexibility of 3-IsoAdoCbl allows it to adopt a coformation in which the hydrogen bonding patterns of the adenine moiety are similar to those of AdoCbl itself, and that this is responsible for the high enzymatic activity of this analog.