The Hydrogenobyric Acid Structure Reveals the Corrin Ligand as an Entatic State Module Empowering B12 Cofactors for Catalysis

PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent

We introduce PyConSolv, a freely available Python package that automates the generation of conformers of metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal; only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of preparametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open source and free of charge.

A synthetic cell-free 36-enzyme reaction system for vitamin B12 production

Adenosylcobalamin (AdoCbl), a biologically active form of vitamin B12 (coenzyme B12), is one of the most complex metal-containing natural compounds and an essential vitamin for animals. However, AdoCbl can only be de novo synthesized by prokaryotes, and its industrial manufacturing to date was limited to bacterial fermentation. Here, we report a method for the synthesis of AdoCbl based on a cell-free reaction system performing a cascade of catalytic reactions from 5-aminolevulinic acid (5-ALA), an inexpensive compound. More than 30 biocatalytic reactions are integrated and optimized to achieve the complete cell-free synthesis of AdoCbl, after overcoming feedback inhibition, the complicated detection, instability of intermediate products, as well as imbalance and competition of cofactors. In the end, this cell-free system produces 417.41 μg/L and 5.78 mg/L of AdoCbl using 5-ALA and the purified intermediate product hydrogenobyrate as substrates, respectively. The strategies of coordinating synthetic modules of complex cell-free system describe here will be generally useful for developing cell-free platforms to produce complex natural compounds with long and complicated biosynthetic pathways.

The inorganic chemistry of the cobalt corrinoids - an update

The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B₁₂, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B₁₂-dependent enzymes is also given for the reader's convenience.

Biosynthesis of cobamides: Methods for the detection, analysis and production of cobamides and biosynthetic intermediates

Vitamin B₁₂, cobalamin, belongs to the broader cobamide family whose members are characterized by the presence of a cobalt-containing corrinoid ring. The ability to detect, isolate and characterize cobamides and their biosynthetic intermediates is an important prerequisite when attempting to study the synthesis of this remarkable group of compounds that play diverse roles across the three kingdoms of life. The synthesis of cobamides is restricted to only certain prokaryotes and their structural complexity entails an equally complex synthesis orchestrated through a multi-step biochemical pathway. In this chapter, we have outlined methods that we have found extremely helpful in the characterization of the biochemical pathway, including a plate microbiological assay, a corrinoid affinity extraction method, LCMS characterization and a multigene cloning strategy.

Vitamin B12 photoreceptors

Photoreceptor proteins enable living organisms to sense light and transduce this signal into biochemical outputs to elicit appropriate cellular responses. Their light sensing is typically mediated by covalently or noncovalently bound molecules called chromophores, which absorb light of specific wavelengths and modulate protein structure and biological activity. Known photoreceptors have been classified into about ten families based on the chromophore and its associated photosensory domain in the protein. One widespread photoreceptor family uses coenzyme B₁₂ or 5'-deoxyadenosylcobalamin, a biological form of vitamin B₁₂, to sense ultraviolet, blue, or green light, and its discovery revealed both a new type of photoreceptor and a novel functional facet of this vitamin, best known as an enzyme cofactor. Large strides have been made in our understanding of how these B₁₂-based photoreceptors function, high-resolution structural descriptions of their functional states are available, as are details of their unusual photochemistry. Additionally, they have inspired notable applications in optogenetics/optobiochemistry and synthetic biology. Here, we provide an overview of what is currently known about these B₁₂-based photoreceptors, their discovery, distribution, molecular mechanism of action, and the structural and photochemical basis of how they orchestrate signal transduction and gene regulation, and how they have been used to engineer optogenetic control of protein activities in living cells.

Antivitamins B12: Synthesis and application as inhibitory ligand of the B12-tailoring enzyme CblC

Antivitamins B12 are non-natural corrinoids that have been designed to counteract the metabolic effects of vitamin B12 and related cobalamins (Cbls) in humans and other mammals. A basic structure- and reactivity-based concept typifies antivitamins B12 as close structural mimics of vitamin B12 that are not transformed by the cellular metabolism into organometallic B12-cofactors. Antivitamins B12 have the correct structure for efficient take-up and transport via the natural mammalian pathway for cobalamin assimilation. Thus they can be delivered to every cell in the body, where they are proposed to target and inhibit the Cbl tailoring enzyme CblC. Antivitamins B12 may be specifically inert Cbls or isostructural Cbl-analogues that carry a metal centre other than a cobalt-ion. The syntheses of two antivitamins B12 are detailed here, as are biochemical and crystallographic studies that provide insights into the crucial binding interactions of Cbl-based antivitamins B12 with the human B12-tailoring enzyme CblC. This key enzyme binds genuine antivitamins B12 as inert substrate mimics and enzyme inhibitors, effectively repressing the metabolic generation of the B12-cofactors. Hence, antivitamins B12 induce the diagnostic symptoms of (functional) B12-deficiency, as observed in healthy laboratory mice.

PorphyStruct: A Digital Tool for the Quantitative Assignment of Non-Planar Distortion Modes in Four-Membered Porphyrinoids

PorphyStruct, a new digital tool for the analysis of non‐planar distortion modes of different porphyrinoids, and its application to corrole structures is reported. The program makes use of the normal‐coordinate structure decomposition technique (NSD) and employs sets of normal modes equivalent to those established for porphyrins in order to describe the out‐of‐plane dislocation pattern of perimeter atoms from corroles, norcorroles, porphycenes and other porphyrinoids quantitatively and in analogy to the established terminology. A comparative study of 17 porphyrin structures shows very similar results to the original NSD analysis and no systematic error. Application to corroles is successful and reveals the necessity to implement an extended basis of normal modes for a large share of experimental structures. The results frequently show the concomitant occurence of several modes but remain interpretable. For group XI metal corroles the phenomenon of supersaddling was unravelled, allowing for more in‐depths discussions of structure‐function correlations.

Calculating metalation in cells reveals CobW acquires CoII for vitamin B12 biosynthesis while related proteins prefer ZnII

Protein metal-occupancy (metalation) in vivo has been elusive. To address this challenge, the available free energies of metals have recently been determined from the responses of metal sensors. Here, we use these free energy values to develop a metalation-calculator which accounts for inter-metal competition and changing metal-availabilities inside cells. We use the calculator to understand the function and mechanism of GTPase CobW, a predicted Co^II-chaperone for vitamin B₁₂. Upon binding nucleotide (GTP) and Mg^II, CobW assembles a high-affinity site that can obtain Co^II or Zn^II from the intracellular milieu. In idealised cells with sensors at the mid-points of their responses, competition within the cytosol enables Co^II to outcompete Zn^II for binding CobW. Thus, Co^II is the cognate metal. However, after growth in different [Co^II], Co^II-occupancy ranges from 10 to 97% which matches CobW-dependent B₁₂ synthesis. The calculator also reveals that related GTPases with comparable Zn^II affinities to CobW, preferentially acquire Zn^II due to their relatively weaker Co^II affinities. The calculator is made available here for use with other proteins.

The requirement for cobalt in vitamin B12: A paradigm for protein metalation

Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.

Synthesis, Spectral Characterization and Crystal Structure of Chlororhodibalamin: A Synthesis Platform for Rhodium Analogues of Vitamin B12 and for Rh-Based Antivitamins B12

Chlororhodibalamin (ClRhbl), a rhodium analogue of vitamin B12 (cyanocobalamin), was prepared in 84% yield by metalation of the metal-free B12 ligand hydrogenobalamin using the RhI-complex [Rh(CO)2Cl]2. ClRhbl was identified and characterized by UV/Vis, circular dichroism, high-resolution mass and heteronuclear NMR spectra. The RhIII-corrin ClRhbl features the ‘base-on’ architecture of vitamin B12. X-ray analysis of single crystals of ClRhbl have revealed its detailed 3D-geometry and close structural similarity to the CoIII-analogue chlorocobalamin (ClCbl). ClRhbl is a versatile starting material for the preparation of other rhodibalamins, among them the organometallic derivatives adenosylrhodibalamin and methylrhodibalamin, the Rh analogues of the important coenzyme and cofactor forms of B12, adenosylcobalamin and methylcobalamin.

Handling methane: a Ni(i) F430-like cofactor derived from VB12 is active in methyl-coenzyme M reductase

An Ni(i) F₄₃₀-like cofactor derived from vitamin B₁₂ can catalyze methane formation in the active site of methyl-coenzyme M reductase.

Antivitamins B12 -Some Inaugural Milestones

The recently delineated structure- and reactivity-based concept of antivitamins B12 has begun to bear fruit by the generation, and study, of a range of such B12 -dummies, either vitamin B12 -derived, or transition metal analogues that also represent potential antivitamins B12 or specific B12 -antimetabolites. As reviewed here, this has opened up new research avenues in organometallic B12 -chemistry and bioinorganic coordination chemistry. Exploratory studies with antivitamins B12 have, furthermore, revealed some of their potential, as pharmacologically interesting compounds, for inducing B12 -deficiency in a range of organisms, from hospital resistant bacteria to laboratory mice. The derived capacity of antivitamins B12 to induce functional B12 -deficiency in mammalian cells and organs also suggest their valuable potential as growth inhibitors of cancerous human and animal cells.

Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis

Cobaltochelatase in aerobic cobalamin biosynthesis is a complex composed of three subunits. The large subunit CobN is a 140-kDa protein and is homologous to the ChlH subunit of magnesium chelatase. Previously we have reported the 2.5-Å structure of a cyanobacterial ChlH. Here we present the 1.8-Å structure of CobN from Mycobacterium tuberculosis. The overall structure of CobN and ChlH is similar, but significant difference occurs in the head domain. Structural comparison of domains between the two proteins unravels candidate regions for substrate binding and helps to locate a triad of residues that may be essential for metal ion binding.

Replacement of the Cobalt Center of Vitamin B12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal-Free B12 Ligands Hydrogenobalamin and Hydrogenobyric Acid

The (formal) replacement of Co in cobalamin (Cbl) by NiII generates nibalamin (Nibl), a new transition-metal analogue of vitamin B12 . Described here is Nibl, synthesized by incorporation of a NiII ion into the metal-free B12  ligand hydrogenobalamin (Hbl), itself prepared from hydrogenobyric acid (Hby). The related NiII  corrin nibyric acid (Niby) was similarly synthesized from Hby, the metal-free cobyric acid ligand. The solution structures of Hbl, and Niby and Nibl, were characterized by spectroscopic studies. Hbl features two inner protons bound at N2 and N4 of the corrin ligand, as discovered in Hby. X-ray analysis of Niby shows the structural adaptation of the corrin ligand to NiII ions and the coordination behavior of NiII . The diamagnetic Niby and Nibl, and corresponding isoelectronic CoI corrins, were deduced to be isostructural. Nibl is a structural mimic of four-coordinate base-off Cbls, as verified by its ability to act as a strong inhibitor of bacterial adenosyltransferase.

Biological concepts for catalysis and reactivity: empowering bioinspiration

Biological systems provide attractive reactivity blueprints for the design of challenging chemical transformations. Emulating the operating mode of natural systems may however not be so easy and direct translation of structural observations does not always afford the anticipated efficiency. Metalloenzymes rely on earth-abundant metals to perform an incredibly wide range of chemical transformations. To do so, enzymes in general have evolved tools and tricks to enable control of such reactivity. The underlying concepts related to these tools are usually well-known to enzymologists and bio(inorganic) chemists but may be a little less familiar to organometallic chemists. So far, the field of bioinspired catalysis has greatly focused on the coordination sphere and electronic effects for the design of functional enzyme models but might benefit from a paradigm shift related to recent findings in biological systems. The goal of this review is to bring these fields closer together as this could likely result in the development of a new generation of highly efficient bioinspired systems. This contribution covers the fields of redox-active ligands, entatic state reactivity, energy conservation through electron bifurcation, and quantum tunneling for C-H activation.

Ultrafast Excited State Dynamics and Fluorescence from Vitamin B12 and Organometallic [Co]-C≡C-R Cobalamins

Cobalamins are cobalt-centered cyclic tetrapyrrole ring-based molecules that provide cofactors for exceptional biological processes and possess unique and synthetically tunable photochemistry. Typical cobalamins are characterized by a visible absorption spectrum consisting of peaks labeled α, β, and sh. The physical basis of these peaks as having electronic origin or as a vibronic progression is ambiguous despite much investigation. Here, for the first time, cobalamin fluorescence is identified in several derivatives. The fluorescence lifetime is ca. 100–200 fs with quantum yields on the order of 10^–6–10^–5 because of rapid population of “dark” excited states. The results are compared with the fluorescent analogue with zinc replacing the cobalt in the corrin ring. Analysis of the breadth of the emission spectrum provides evidence that a vibrational progression in a single excited electronic state makes the dominant contribution to the visible absorption band.

Biosynthesis of the modified tetrapyrroles-the pigments of life

Modified tetrapyrroles are large macrocyclic compounds, consisting of diverse conjugation and metal chelation systems and imparting an array of colors to the biological structures that contain them. Tetrapyrroles represent some of the most complex small molecules synthesized by cells and are involved in many essential processes that are fundamental to life on Earth, including photosynthesis, respiration, and catalysis. These molecules are all derived from a common template through a series of enzyme-mediated transformations that alter the oxidation state of the macrocycle and also modify its size, its side-chain composition, and the nature of the centrally chelated metal ion. The different modified tetrapyrroles include chlorophylls, hemes, siroheme, corrins (including vitamin B12), coenzyme F430, heme d1, and bilins. After nearly a century of study, almost all of the more than 90 different enzymes that synthesize this family of compounds are now known, and expression of reconstructed operons in heterologous hosts has confirmed that most pathways are complete. Aside from the highly diverse nature of the chemical reactions catalyzed, an interesting aspect of comparative biochemistry is to see how different enzymes and even entire pathways have evolved to perform alternative chemical reactions to produce the same end products in the presence and absence of oxygen. Although there is still much to learn, our current understanding of tetrapyrrole biogenesis represents a remarkable biochemical milestone that is summarized in this review.

Zinc Substitution of Cobalt in Vitamin B12 : Zincobyric acid and Zincobalamin as Luminescent Structural B12 -Mimics

Replacing the central cobalt ion of vitamin B12 by other metals has been a long-held aspiration within the B12 -field. Herein, we describe the synthesis from hydrogenobyric acid of zincobyric acid (Znby) and zincobalamin (Znbl), the Zn-analogues of the natural cobalt-corrins cobyric acid and vitamin B12 , respectively. The solution structures of Znby and Znbl were studied by NMR-spectroscopy. Single crystals of Znby were produced, providing the first X-ray crystallographic structure of a zinc corrin. The structures of Znby and of computationally generated Znbl were found to resemble the corresponding CoII -corrins, making such Zn-corrins potentially useful for investigations of B12 -dependent processes. The singlet excited state of Znby had a short life-time, limited by rapid intersystem crossing to the triplet state. Znby allowed the unprecedented observation of a corrin triplet (ET =190 kJ mol-1 ) and was found to be an excellent photo-sensitizer for 1 O2 (ΦΔ =0.70).

The Hydrogenobyric Acid Structure Reveals the Corrin Ligand as an Entatic State Module Empowering B12 Cofactors for Catalysis

The B₁₂ cofactors instill a natural curiosity regarding the primordial selection and evolution of their corrin ligand. Surprisingly, this important natural macrocycle has evaded molecular scrutiny, and its specific role in predisposing the incarcerated cobalt ion for organometallic catalysis has remained obscure. Herein, we report the biosynthesis of the cobalt-free B₁₂ corrin moiety, hydrogenobyric acid (Hby), a compound crafted through pathway redesign. Detailed insights from single-crystal X-ray and solution structures of Hby have revealed a distorted helical cavity, redefining the pattern for binding cobalt ions. Consequently, the corrin ligand coordinates cobalt ions in desymmetrized "entatic" states, thereby promoting the activation of B₁₂ -cofactors for their challenging chemical transitions. The availability of Hby also provides a route to the synthesis of transition metal analogues of B₁₂ .