Role of Arg100 in the Active Site of Adenosylcobalamin-Dependent Glutamate Mutase

Light Mediated Properties of a Thiolato-Derivative of Vitamin B12

Vitamin B₁₂ derivatives (Cbls = cobalamins) exhibit photolytic properties upon excitation with light. These properties can be modulated by several factors including the nature of the axial ligands. Upon excitation, homolytic cleavage of the organometallic bond to the upper axial ligand takes place in photolabile Cbls. The photosensitive nature of Cbls has made them potential candidates for light-activated drug delivery. The addition of a fluorophore to the nucleotide loop of thiolato Cbls has been shown to shift the region of photohomolysis to within the optical window of tissue (600-900 nm). With this possibility, there is a need to analyze photolytic properties of unique Cbls which contain a Co-S bond. Herein, the photodissociation of one such Cbl, namely, N-acetylcysteinylcobalamin (NACCbl), is analyzed based on density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. The S₀ and S₁ potential energy surfaces (PESs), as a function of axial bond lengths, were computed to determine the mechanism of photodissociation. Like other Cbls, the S₁ PES contains metal-to-ligand charge transfer (MLCT) and ligand field (LF) regions, but there are some unique differences. Interestingly, the S₁ PES of NACCbl contains three distinct minima regions opening several possibilities for the mechanism of radical pair (RP) formation. The mild photoresponsiveness, observed experimentally, can be attributed to the small gap in energy between the S₁ and S₀ PESs. Compared to other Cbls, the gap shown for NACCbl is neither exactly in line with the alkyl Cbls nor the nonalkyl Cbls.

Spectroscopic and computational studies of glutathionylcobalamin: nature of Co-S bonding and comparison to Co-C bonding in coenzyme B12

Glutathionylcobalamin (GSCbl) is a unique, biologically relevant cobalamin featuring an axial Co-S bond that distinguishes it from the enzymatically active forms of vitamin B(12), which possess axial Co-C bonds. GSCbl has been proposed to serve as an intermediate in cobalamin processing and, more recently, as a therapeutic for neurological disorders associated with oxidative stress. In this study, GSCbl and its close relative cysteinylcobalamin (CysCbl) were investigated using electronic absorption, circular dichroism, magnetic circular dichroism, and resonance Raman spectroscopies. The spectroscopic data were analyzed in the framework of density functional theory (DFT) and time-dependent DFT computations to generate experimentally validated electronic structure descriptions. Although the change in the upper axial ligand from an alkyl to a thiol group represents a major perturbation in terms of the size, basicity, and polarizability of the coordinating atom, our spectroscopic and computational results reveal striking similarities in electronic structure between methylcobalamin (MeCbl) and GSCbl, especially with regard to the σ donation from the alkyl/thiol ligand and the extent of mixing between the cobalt 3d and the ligand frontier orbitals. A detailed comparison of Co-C and Co-S bonding in MeCbl and GSCbl, respectively, is presented, and the implications of our results with respect to the proposed biological roles of GSCbl are discussed.

Hydrogen tunneling in adenosylcobalamin-dependent glutamate mutase: evidence from intrinsic kinetic isotope effects measured by intramolecular competition

Hydrogen atom transfer reactions between the substrate and coenzyme are key mechanistic features of all adenosylcobalamin-dependent enzymes. For one of these enzymes, glutamate mutase, we have investigated whether hydrogen tunneling makes a significant contribution to the mechanism by examining the temperature dependence of the deuterium kinetic isotope effect associated with the transfer of a hydrogen atom from methylaspartate to the coenzyme. To do this, we designed a novel intramolecular competition experiment that allowed us to measure the intrinsic kinetic isotope effect, even though hydrogen transfer may not be rate-determining. From the Arrhenius plot of the kinetic isotope effect, the ratio of the pre-exponential factors (A(H)/A(D)) was 0.17 +/- 0.04 and the isotope effect on the activation energy [DeltaE(a(D-H))] was 1.94 +/- 0.13 kcal/mol. The results imply that a significant degree of hydrogen tunneling occurs in glutamate mutase, even though the intrinsic kinetic isotope effects are well within the semiclassical limit and are much smaller than those measured for other AdoCbl enzymes and model reactions for which hydrogen tunneling has been implicated.

Adenosyl radical: reagent and catalyst in enzyme reactions

Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans.

Critical role of arginine 160 of the EutB protein subunit for active site structure and radical catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase

The protein chemical, kinetic, and electron paramagnetic resonance (EPR) and electron spin-echo envelope modulation (ESEEM) spectroscopic properties of ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium with site-directed mutations in a conserved arginine residue (R160) of the active site containing EutB protein subunit have been characterized. R160 was predicted by a comparative model of EutB to play a critical role in protein structure and catalysis [Sun, L., and Warncke, K. (2006) Proteins: Struct., Funct., Bioinf. 64, 308-319]. R160I and R160E mutants fail to assemble into an EAL oligomer that can be isolated by the standard enzyme purification procedure. The R160K and R160A mutants assemble, but R160A EAL is catalytically inactive and reacts with substrates to form magnetically isolated Co(II) and unidentified radical species. R160A EAL activity is resurrected by externally added guanidinium to 2.3% of wild-type EAL. R160K EAL displays catalytic turnover of aminoethanol, with a 180-fold lower value of k(cat)/ K(M) relative to wild-type enzyme. R160K EAL also forms Co(II)-substrate radical pair intermediate states during turnover on aminoethanol and (S)-2-aminopropanol substrates. Simulations of the X-band EPR spectra show that the Co(II)-substrate radical pair separation distances are increased by 2.1 +/- 1.0 A in R160K EAL relative to wild-type EAL, which corresponds to the predicted 1.6 A change in arginine versus lysine side chain length. 14N ESEEM from a hyperfine-coupled protein nitrogen in wild type is absent in R160K EAL, which indicates that a guanidinium 14N of R160 interacts directly with the substrate radical through a hydrogen bond. ESEEM of the 2H-labeled substrate radical states in wild-type and R160K EAL shows that the native separation distances among the substrate C1 and C2, and coenzyme C5' reactant centers, are conserved in the mutant protein. The EPR and ESEEM measurements evince a protein-mediated force on the C5'-methyl center that is directed toward the reacting substrate species during the hydrogen atom transfer and radical rearrangement reactions. The results indicate that the positive charge at the residue 160 side chain terminus is required for proper folding of EutB, assembly of a stable EAL oligomer, and catalysis in the assembled oligomer.

Changes in the free energy profile of glutamate mutase imparted by the mutation of an active site arginine residue to lysine

Arginine 100 plays an important role in substrate recognition in adenosylcobalamin-dependent glutamate mutase. We have examined how the mutation of this residue to lysine affects the partitioning of tritium, incorporated at the exchangeable position of the coenzyme, between substrate and product. We find that partitioning of tritium back to the substrate predominates in the mutant enzyme, regardless of whether the reaction is run in the forward or reverse direction. This contrasts with the behavior of the wild-type enzyme in which tritium partitions equally between substrate and product, independent of the direction of the reaction. From this we conclude that the mutation significantly impairs the ability of the enzyme to catalyze the rearrangement of substrate radical to product radical. The results illustrate the importance of electrostatic interactions in stabilizing free radical intermediates in this class of enzymes.

Reaction of adenosylcobalamin-dependent glutamate mutase with 2-thiolglutarate

We have investigated the reaction of glutamate mutase with the glutamate analogue, 2-thiolglutarate. In the standard assay, 2-thiolglutarate behaves as a competitive inhibitor with a Ki of 0.05 mM. However, rather than simply binding inertly at the active site, 2-thiolglutarate elicits cobalt-carbon bond homolysis and the formation of 5'-deoxyadenosine. The enzyme exhibits a complicated EPR spectrum in the presence of 2-thiolglutarate that is markedly different from any previously observed with the enzyme. The spectrum was simulated well by assuming that it arises from electron-electron spin coupling between a thioglycolyl radical and low-spin Co2+ in cob(II)alamin. Analysis of the zero-field splitting parameters obtained from the simulations places the organic radical approximately 10 A from the cobalt and at a tilt angle of approximately 70 degrees to the normal of the corrin ring. This orientation is in good agreement with that expected from the crystal structure of glutamate mutase complexed with the substrate. 2-Thiolglutarate appears to react in a manner analogous to that of glutamate by first forming a thiolglutaryl radical at C-4 that then undergoes fragmentation to produce acrylate and the sulfur-stabilized thioglycolyl radical. The thioglycolyl radical accumulates on the enzyme, suggesting it is too stable to undergo further steps in the mechanism at a detectable rate.

Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a beta8alpha8, TIM-barrel fold and radical catalytic site structural features

The structure of the EutB protein from Salmonella typhimurium, which contains the active site of the coenzyme B12 (adenosylcobalamin)-dependent enzyme, ethanolamine ammonia-lyase, has been predicted by using structural proteomics techniques of comparative modelling. The 453-residue EutB protein displays no significant sequence identity with proteins of known structure. Therefore, secondary structure prediction and fold recognition algorithms were used to identify templates. Multiple three-dimensional template matching (threading) servers identified predominantly beta8alpha8, TIM-barrel proteins, and in particular, the large subunits of diol dehydratase (PDB: 1eex:A, 1dio:A) and glycerol dehydratase (PDB: 1mmf:A), as templates. Consistent with this identification, the dehydratases are, like ethanolamine ammonia-lyase, Class II coenzyme B12-dependent enzymes. Model building was performed by using MODELLER. Models were evaluated by using different programs, including PROCHECK and VERIFY3D. The results identify a beta8alpha8, TIM-barrel fold for EutB. The beta8alpha8, TIM-barrel fold is consistent with a central role of the alpha/beta-barrel structures in radical catalysis conducted by the coenzyme B12- and S-adenosylmethionine-dependent (radical SAM) enzyme superfamilies. The EutB model and multiple sequence alignment among ethanolamine ammonia-lyase, diol dehydratase, and glycerol dehydratase from different species reveal the following protein structural features: (1) a "cap" loop segment that closes the N-terminal region of the barrel, (2) a common cobalamin cofactor binding topography at the C-terminal region of the barrel, and (3) a beta-barrel-internal guanidinium group from EutB R160 that overlaps the position of the active-site potassium ion found in the dehydratases. R160 is proposed to have a role in substrate binding and radical catalysis.

Homocoenzyme B12and Bishomocoenzyme B12: Covalent Structural Mimics for Homolyzed, Enzyme-Bound Coenzyme B12

Efficient electrochemical syntheses of "homocoenzyme B(12)" (2, Co(beta)-(5'-deoxy-5'-adenosyl-methyl)-cob(III)alamin) and "bishomocoenzyme B(12)" (3, Co(beta)-[2-(5'-deoxy-5'-adenosyl)-ethyl]-cob(III)alamin) are reported here. These syntheses have provided crystalline samples of 2 and 3 in 94 and 77 % yield, respectively. In addition, in-depth investigations of the structures of 2 and 3 in solution were carried out and a high-resolution crystal structure of 2 was obtained. The two homologues of coenzyme B(12) (2 and 3) are suggested to function as covalent structural mimics of the hypothetical enzyme-bound "activated" (that is, "stretched" or even homolytically cleaved) states of the B(12) cofactor. From crude molecular models, the crucial distances from the corrin-bound cobalt center to the C5' atom of the (homo)adenosine moieties in 2 and 3 were estimated to be about 3.0 and 4.4 A, respectively. These values are roughly the same as those found in the two "activated" forms of coenzyme B(12) in the crystal structure of glutamate mutase. Indeed, in the crystal structure of 2, the cobalt center was observed to be at a distance of 2.99 A from the C5' atom of the homoadenosine moiety and the latter was found to be present in the unusual syn conformation. In solution, the organometallic moieties of 2 and 3 were shown to be rather flexible and to be considerably more dynamic than the equivalent group in coenzyme B(12). The homoadenosine moiety of 2 was indicated to occur in both the syn and the anti conformations.